Issue with single contig

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Issue with single contig

Zoe Clarke-2
Hello!

Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.

I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:

ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.

I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:

0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section

I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:

Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089

I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?

Thanks so much!
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
Personal website: https://zoe-clarke.weebly.com/

_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Issue with single contig

Carson Holt-2
Your datacenter may have implemented the temporary storage (“/tmp” by default) to be in memory storage. As a result, every file you store is really being stored in RAM behind the scenes.  Or you have specified TMP= in the control files to point to in memory storage.  The result is that, at some point there was not enough memory left.  You may want to ask about this and ensure that you can point to a real node based disk storage like traditional /tmp space.

—Carson



On Oct 9, 2020, at 5:39 AM, Zoe Clarke <[hidden email]> wrote:

Hello!

Sorry to bother you again. I am having a very specific problem with one of my contigs, and I was hoping you could help.

I can cancelled my last Maker run because one of my contigs failed around 56,000 times according to the output_rnd1_master_datastore_index.log file. It was just perpetually failing during the run with the following message:

ERROR: Chunk failed at level:0, tier_type:0open3: fork failed: Cannot allocate memory at dir/File/NFSLock.pm line 1037.

I am running Maker over multiple nodes, so I figured there might be an issue with a log file getting truncated or malformed. Looking at the files stored in the void for this contig, there are also a ton of files which I think might be causing an issue:

0                         run.log.child.112                                     WCK01_AAF20200214_F8-ctg57.118-119.raw.section       WCK01_AAF20200214_F8-ctg57.55-56.raw.section
1                         run.log.child.113                                     WCK01_AAF20200214_F8-ctg57.118.pred.raw.section      WCK01_AAF20200214_F8-ctg57.55.pred.raw.section
10                        run.log.child.114                                     WCK01_AAF20200214_F8-ctg57.118.raw.section           WCK01_AAF20200214_F8-ctg57.55.raw.section
11                        run.log.child.115                                     WCK01_AAF20200214_F8-ctg57.119-120.raw.section       WCK01_AAF20200214_F8-ctg57.56-57.raw.section
12                        run.log.child.116                                     WCK01_AAF20200214_F8-ctg57.119.pred.raw.section      WCK01_AAF20200214_F8-ctg57.56.pred.raw.section
2                         run.log.child.117                                     WCK01_AAF20200214_F8-ctg57.119.raw.section           WCK01_AAF20200214_F8-ctg57.5-6.raw.section
3                         run.log.child.118                                     WCK01_AAF20200214_F8-ctg57.11.pred.raw.section       WCK01_AAF20200214_F8-ctg57.56.raw.section
4                         run.log.child.119                                     WCK01_AAF20200214_F8-ctg57.11.raw.section            WCK01_AAF20200214_F8-ctg57.57-58.raw.section
5                         run.log.child.12                                      WCK01_AAF20200214_F8-ctg57.120-121.raw.section       WCK01_AAF20200214_F8-ctg57.57.pred.raw.section
6                         run.log.child.120                                     WCK01_AAF20200214_F8-ctg57.120.pred.raw.section      WCK01_AAF20200214_F8-ctg57.57.raw.section
7                         run.log.child.121                                     WCK01_AAF20200214_F8-ctg57.120.raw.section           WCK01_AAF20200214_F8-ctg57.58-59.raw.section
8                         run.log.child.122                                     WCK01_AAF20200214_F8-ctg57.121-122.raw.section       WCK01_AAF20200214_F8-ctg57.58.pred.raw.section
9                         run.log.child.123                                     WCK01_AAF20200214_F8-ctg57.12-13.raw.section         WCK01_AAF20200214_F8-ctg57.58.raw.section
evidence_0.gff            run.log.child.124                                     WCK01_AAF20200214_F8-ctg57.121.end.blastn.holdover   WCK01_AAF20200214_F8-ctg57.59-60.raw.section
evidence_100.gff          run.log.child.125                                     WCK01_AAF20200214_F8-ctg57.121.end.blastx.holdover   WCK01_AAF20200214_F8-ctg57.59.pred.raw.section
evidence_101.gff          run.log.child.13                                      WCK01_AAF20200214_F8-ctg57.121.pred.raw.section      WCK01_AAF20200214_F8-ctg57.59.raw.section
evidence_102.gff          run.log.child.14                                      WCK01_AAF20200214_F8-ctg57.121.raw.section           WCK01_AAF20200214_F8-ctg57.5.pred.raw.section
evidence_103.gff          run.log.child.15                                      WCK01_AAF20200214_F8-ctg57.122-123.raw.section       WCK01_AAF20200214_F8-ctg57.5.raw.section
evidence_104.gff          run.log.child.16                                      WCK01_AAF20200214_F8-ctg57.122.pred.raw.section      WCK01_AAF20200214_F8-ctg57.60-61.raw.section
evidence_105.gff          run.log.child.17                                      WCK01_AAF20200214_F8-ctg57.122.raw.section           WCK01_AAF20200214_F8-ctg57.60.pred.raw.section
evidence_106.gff          run.log.child.18                                      WCK01_AAF20200214_F8-ctg57.123-124.raw.section       WCK01_AAF20200214_F8-ctg57.60.raw.section
evidence_107.gff          run.log.child.19                                      WCK01_AAF20200214_F8-ctg57.123.pred.raw.section      WCK01_AAF20200214_F8-ctg57.61-62.raw.section
evidence_108.gff          run.log.child.2                                       WCK01_AAF20200214_F8-ctg57.123.raw.section           WCK01_AAF20200214_F8-ctg57.61.pred.raw.section
evidence_109.gff          run.log.child.20                                      WCK01_AAF20200214_F8-ctg57.124-125.raw.section       WCK01_AAF20200214_F8-ctg57.61.raw.section
evidence_10.gff           run.log.child.21                                      WCK01_AAF20200214_F8-ctg57.124.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62-63.raw.section
evidence_110.gff          run.log.child.22                                      WCK01_AAF20200214_F8-ctg57.124.raw.section           WCK01_AAF20200214_F8-ctg57.62.pred.raw.section
evidence_111.gff          run.log.child.23                                      WCK01_AAF20200214_F8-ctg57.125.pred.raw.section      WCK01_AAF20200214_F8-ctg57.62.raw.section
evidence_112.gff          run.log.child.24                                      WCK01_AAF20200214_F8-ctg57.125.raw.section           WCK01_AAF20200214_F8-ctg57.63-64.raw.section
evidence_113.gff          run.log.child.25                                      WCK01_AAF20200214_F8-ctg57.12.pred.raw.section       WCK01_AAF20200214_F8-ctg57.63.pred.raw.section
evidence_114.gff          run.log.child.26                                      WCK01_AAF20200214_F8-ctg57.1-2.raw.section           WCK01_AAF20200214_F8-ctg57.63.raw.section
evidence_115.gff          run.log.child.27                                      WCK01_AAF20200214_F8-ctg57.12.raw.section            WCK01_AAF20200214_F8-ctg57.64-65.raw.section
evidence_116.gff          run.log.child.28                                      WCK01_AAF20200214_F8-ctg57.13-14.raw.section         WCK01_AAF20200214_F8-ctg57.64.pred.raw.section
evidence_116.gff.ann      run.log.child.29                                      WCK01_AAF20200214_F8-ctg57.13.pred.raw.section       WCK01_AAF20200214_F8-ctg57.64.raw.section
evidence_116.gff.def      run.log.child.3                                       WCK01_AAF20200214_F8-ctg57.13.raw.section            WCK01_AAF20200214_F8-ctg57.65-66.raw.section
evidence_116.gff.seq      run.log.child.30                                      WCK01_AAF20200214_F8-ctg57.14-15.raw.section         WCK01_AAF20200214_F8-ctg57.65.pred.raw.section
evidence_117.gff          run.log.child.31                                      WCK01_AAF20200214_F8-ctg57.14.pred.raw.section       WCK01_AAF20200214_F8-ctg57.65.raw.section
evidence_118.gff          run.log.child.32                                      WCK01_AAF20200214_F8-ctg57.14.raw.section            WCK01_AAF20200214_F8-ctg57.66-67.raw.section
evidence_119.gff          run.log.child.33                                      WCK01_AAF20200214_F8-ctg57.15-16.raw.section         WCK01_AAF20200214_F8-ctg57.66.pred.raw.section
evidence_11.gff           run.log.child.34                                      WCK01_AAF20200214_F8-ctg57.15.pred.raw.section       WCK01_AAF20200214_F8-ctg57.66.raw.section
evidence_120.gff          run.log.child.35                                      WCK01_AAF20200214_F8-ctg57.15.raw.section            WCK01_AAF20200214_F8-ctg57.67-68.raw.section
evidence_121.gff          run.log.child.36                                      WCK01_AAF20200214_F8-ctg57.16-17.raw.section         WCK01_AAF20200214_F8-ctg57.67.pred.raw.section
evidence_122.gff          run.log.child.37                                      WCK01_AAF20200214_F8-ctg57.16.pred.raw.section       WCK01_AAF20200214_F8-ctg57.6-7.raw.section
evidence_123.gff          run.log.child.38                                      WCK01_AAF20200214_F8-ctg57.16.raw.section            WCK01_AAF20200214_F8-ctg57.67.raw.section
evidence_124.gff          run.log.child.39                                      WCK01_AAF20200214_F8-ctg57.17-18.raw.section         WCK01_AAF20200214_F8-ctg57.68-69.raw.section
evidence_125.gff          run.log.child.4                                       WCK01_AAF20200214_F8-ctg57.17.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.pred.raw.section
evidence_12.gff           run.log.child.40                                      WCK01_AAF20200214_F8-ctg57.17.raw.section            WCK01_AAF20200214_F8-ctg57.68.raw.section
evidence_13.gff           run.log.child.41                                      WCK01_AAF20200214_F8-ctg57.18-19.raw.section         WCK01_AAF20200214_F8-ctg57.68.start.blastn.holdover
evidence_14.gff           run.log.child.42                                      WCK01_AAF20200214_F8-ctg57.18.pred.raw.section       WCK01_AAF20200214_F8-ctg57.68.start.blastx.holdover
evidence_15.gff           run.log.child.43                                      WCK01_AAF20200214_F8-ctg57.18.raw.section            WCK01_AAF20200214_F8-ctg57.69-70.raw.section
evidence_16.gff           run.log.child.44                                      WCK01_AAF20200214_F8-ctg57.19-20.raw.section         WCK01_AAF20200214_F8-ctg57.69.end.blastn.holdover
evidence_17.gff           run.log.child.45                                      WCK01_AAF20200214_F8-ctg57.19.pred.raw.section       WCK01_AAF20200214_F8-ctg57.69.pred.raw.section
evidence_18.gff           run.log.child.46                                      WCK01_AAF20200214_F8-ctg57.19.raw.section            WCK01_AAF20200214_F8-ctg57.69.raw.section
evidence_19.gff           run.log.child.47                                      WCK01_AAF20200214_F8-ctg57.1.pred.raw.section        WCK01_AAF20200214_F8-ctg57.6.pred.raw.section
evidence_1.gff            run.log.child.48                                      WCK01_AAF20200214_F8-ctg57.1.raw.section             WCK01_AAF20200214_F8-ctg57.6.raw.section
evidence_20.gff           run.log.child.49                                      WCK01_AAF20200214_F8-ctg57.20-21.raw.section         WCK01_AAF20200214_F8-ctg57.70-71.raw.section
evidence_21.gff           run.log.child.5                                       WCK01_AAF20200214_F8-ctg57.20.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.end.blastn.holdover
evidence_22.gff           run.log.child.50                                      WCK01_AAF20200214_F8-ctg57.20.raw.section            WCK01_AAF20200214_F8-ctg57.70.end.blastx.holdover
evidence_23.gff           run.log.child.51                                      WCK01_AAF20200214_F8-ctg57.21-22.raw.section         WCK01_AAF20200214_F8-ctg57.70.pred.raw.section
evidence_24.gff           run.log.child.52                                      WCK01_AAF20200214_F8-ctg57.21.pred.raw.section       WCK01_AAF20200214_F8-ctg57.70.raw.section
evidence_25.gff           run.log.child.53                                      WCK01_AAF20200214_F8-ctg57.21.raw.section            WCK01_AAF20200214_F8-ctg57.71-72.raw.section
evidence_25.gff.ann       run.log.child.54                                      WCK01_AAF20200214_F8-ctg57.22-23.raw.section         WCK01_AAF20200214_F8-ctg57.71.pred.raw.section
evidence_25.gff.def       run.log.child.55                                      WCK01_AAF20200214_F8-ctg57.22.pred.raw.section       WCK01_AAF20200214_F8-ctg57.71.raw.section
evidence_25.gff.seq       run.log.child.56                                      WCK01_AAF20200214_F8-ctg57.22.raw.section            WCK01_AAF20200214_F8-ctg57.72-73.raw.section
evidence_26.gff           run.log.child.57                                      WCK01_AAF20200214_F8-ctg57.23-24.raw.section         WCK01_AAF20200214_F8-ctg57.72.pred.raw.section
evidence_27.gff           run.log.child.58                                      WCK01_AAF20200214_F8-ctg57.23.pred.raw.section       WCK01_AAF20200214_F8-ctg57.72.raw.section
evidence_28.gff           run.log.child.59                                      WCK01_AAF20200214_F8-ctg57.2-3.raw.section           WCK01_AAF20200214_F8-ctg57.73-74.raw.section
evidence_29.gff           run.log.child.6                                       WCK01_AAF20200214_F8-ctg57.23.raw.section            WCK01_AAF20200214_F8-ctg57.73.pred.raw.section
evidence_2.gff            run.log.child.60                                      WCK01_AAF20200214_F8-ctg57.23.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.73.raw.section
evidence_30.gff           run.log.child.61                                      WCK01_AAF20200214_F8-ctg57.23.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.73.start.blastn.holdover
evidence_31.gff           run.log.child.62                                      WCK01_AAF20200214_F8-ctg57.24-25.raw.section         WCK01_AAF20200214_F8-ctg57.73.start.blastx.holdover
evidence_32.gff           run.log.child.63                                      WCK01_AAF20200214_F8-ctg57.24.pred.raw.section       WCK01_AAF20200214_F8-ctg57.74-75.raw.section
evidence_33.gff           run.log.child.64                                      WCK01_AAF20200214_F8-ctg57.24.raw.section            WCK01_AAF20200214_F8-ctg57.74.pred.raw.section
evidence_34.gff           run.log.child.65                                      WCK01_AAF20200214_F8-ctg57.25-26.raw.section         WCK01_AAF20200214_F8-ctg57.74.raw.section
evidence_35.gff           run.log.child.66                                      WCK01_AAF20200214_F8-ctg57.25.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.75-76.raw.section
evidence_36.gff           run.log.child.67                                      WCK01_AAF20200214_F8-ctg57.25.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.end.blastn.holdover
evidence_37.gff           run.log.child.68                                      WCK01_AAF20200214_F8-ctg57.25.raw.section            WCK01_AAF20200214_F8-ctg57.75.end.blastx.holdover
evidence_38.gff           run.log.child.69                                      WCK01_AAF20200214_F8-ctg57.26-27.raw.section         WCK01_AAF20200214_F8-ctg57.75.pred.raw.section
evidence_39.gff           run.log.child.7                                       WCK01_AAF20200214_F8-ctg57.26.pred.raw.section       WCK01_AAF20200214_F8-ctg57.75.raw.section
evidence_3.gff            run.log.child.70                                      WCK01_AAF20200214_F8-ctg57.26.raw.section            WCK01_AAF20200214_F8-ctg57.76-77.raw.section
evidence_40.gff           run.log.child.71                                      WCK01_AAF20200214_F8-ctg57.27-28.raw.section         WCK01_AAF20200214_F8-ctg57.76.pred.raw.section
evidence_41.gff           run.log.child.72                                      WCK01_AAF20200214_F8-ctg57.27.pred.raw.section       WCK01_AAF20200214_F8-ctg57.76.raw.section
evidence_42.gff           run.log.child.73                                      WCK01_AAF20200214_F8-ctg57.27.raw.section            WCK01_AAF20200214_F8-ctg57.77-78.raw.section
evidence_43.gff           run.log.child.74                                      WCK01_AAF20200214_F8-ctg57.28-29.raw.section         WCK01_AAF20200214_F8-ctg57.77.pred.raw.section
evidence_44.gff           run.log.child.75                                      WCK01_AAF20200214_F8-ctg57.28.pred.raw.section       WCK01_AAF20200214_F8-ctg57.77.raw.section
evidence_45.gff           run.log.child.76                                      WCK01_AAF20200214_F8-ctg57.28.raw.section            WCK01_AAF20200214_F8-ctg57.78-79.raw.section
evidence_46.gff           run.log.child.77                                      WCK01_AAF20200214_F8-ctg57.29-30.raw.section         WCK01_AAF20200214_F8-ctg57.78.pred.raw.section
evidence_47.gff           run.log.child.78                                      WCK01_AAF20200214_F8-ctg57.29.pred.raw.section       WCK01_AAF20200214_F8-ctg57.7-8.raw.section
evidence_48.gff           run.log.child.79                                      WCK01_AAF20200214_F8-ctg57.29.raw.section            WCK01_AAF20200214_F8-ctg57.78.raw.section
evidence_49.gff           run.log.child.8                                       WCK01_AAF20200214_F8-ctg57.2.pred.raw.section        WCK01_AAF20200214_F8-ctg57.79-80.raw.section
evidence_4.gff            run.log.child.80                                      WCK01_AAF20200214_F8-ctg57.2.raw.section             WCK01_AAF20200214_F8-ctg57.79.pred.raw.section
evidence_50.gff           run.log.child.81                                      WCK01_AAF20200214_F8-ctg57.2.start.blastn.holdover   WCK01_AAF20200214_F8-ctg57.79.raw.section
evidence_51.gff           run.log.child.82                                      WCK01_AAF20200214_F8-ctg57.2.start.blastx.holdover   WCK01_AAF20200214_F8-ctg57.7.pred.raw.section
evidence_52.gff           run.log.child.83                                      WCK01_AAF20200214_F8-ctg57.30-31.raw.section         WCK01_AAF20200214_F8-ctg57.7.raw.section
evidence_53.gff           run.log.child.84                                      WCK01_AAF20200214_F8-ctg57.30.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80-81.raw.section
evidence_54.gff           run.log.child.85                                      WCK01_AAF20200214_F8-ctg57.30.raw.section            WCK01_AAF20200214_F8-ctg57.80.pred.raw.section
evidence_55.gff           run.log.child.86                                      WCK01_AAF20200214_F8-ctg57.31-32.raw.section         WCK01_AAF20200214_F8-ctg57.80.raw.section
evidence_56.gff           run.log.child.87                                      WCK01_AAF20200214_F8-ctg57.31.pred.raw.section       WCK01_AAF20200214_F8-ctg57.80.start.blastn.holdover
evidence_57.gff           run.log.child.88                                      WCK01_AAF20200214_F8-ctg57.31.raw.section            WCK01_AAF20200214_F8-ctg57.80.start.blastx.holdover
evidence_58.gff           run.log.child.89                                      WCK01_AAF20200214_F8-ctg57.32-33.raw.section         WCK01_AAF20200214_F8-ctg57.81-82.raw.section
evidence_59.gff           run.log.child.9                                       WCK01_AAF20200214_F8-ctg57.32.pred.raw.section       WCK01_AAF20200214_F8-ctg57.81.pred.raw.section
evidence_5.gff            run.log.child.90                                      WCK01_AAF20200214_F8-ctg57.32.raw.section            WCK01_AAF20200214_F8-ctg57.81.raw.section
evidence_60.gff           run.log.child.91                                      WCK01_AAF20200214_F8-ctg57.33-34.raw.section         WCK01_AAF20200214_F8-ctg57.82-83.raw.section
evidence_61.gff           run.log.child.92                                      WCK01_AAF20200214_F8-ctg57.33.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.end.blastn.holdover
evidence_62.gff           run.log.child.93                                      WCK01_AAF20200214_F8-ctg57.33.raw.section            WCK01_AAF20200214_F8-ctg57.82.end.blastx.holdover
evidence_63.gff           run.log.child.94                                      WCK01_AAF20200214_F8-ctg57.34-35.raw.section         WCK01_AAF20200214_F8-ctg57.82.pred.raw.section
evidence_64.gff           run.log.child.95                                      WCK01_AAF20200214_F8-ctg57.34.pred.raw.section       WCK01_AAF20200214_F8-ctg57.82.raw.section
evidence_65.gff           run.log.child.96                                      WCK01_AAF20200214_F8-ctg57.3-4.raw.section           WCK01_AAF20200214_F8-ctg57.83-84.raw.section
evidence_66.gff           run.log.child.97                                      WCK01_AAF20200214_F8-ctg57.34.raw.section            WCK01_AAF20200214_F8-ctg57.83.pred.raw.section
evidence_67.gff           run.log.child.98                                      WCK01_AAF20200214_F8-ctg57.35-36.raw.section         WCK01_AAF20200214_F8-ctg57.83.raw.section
evidence_68.gff           run.log.child.99                                      WCK01_AAF20200214_F8-ctg57.35.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84-85.raw.section
evidence_69.gff           WCK01_AAF20200214_F8-ctg57.0-1.raw.section            WCK01_AAF20200214_F8-ctg57.35.raw.section            WCK01_AAF20200214_F8-ctg57.84.pred.raw.section
evidence_6.gff            WCK01_AAF20200214_F8-ctg57.0.pred.raw.section         WCK01_AAF20200214_F8-ctg57.36-37.raw.section         WCK01_AAF20200214_F8-ctg57.84.raw.section
evidence_70.gff           WCK01_AAF20200214_F8-ctg57.0.raw.section              WCK01_AAF20200214_F8-ctg57.36.pred.raw.section       WCK01_AAF20200214_F8-ctg57.84.start.blastn.holdover
evidence_70.gff.ann       WCK01_AAF20200214_F8-ctg57.100-101.raw.section        WCK01_AAF20200214_F8-ctg57.36.raw.section            WCK01_AAF20200214_F8-ctg57.84.start.blastx.holdover
evidence_70.gff.def       WCK01_AAF20200214_F8-ctg57.100.pred.raw.section       WCK01_AAF20200214_F8-ctg57.37-38.raw.section         WCK01_AAF20200214_F8-ctg57.85-86.raw.section
evidence_70.gff.seq       WCK01_AAF20200214_F8-ctg57.100.raw.section            WCK01_AAF20200214_F8-ctg57.37.pred.raw.section       WCK01_AAF20200214_F8-ctg57.85.pred.raw.section
evidence_71.gff           WCK01_AAF20200214_F8-ctg57.101-102.raw.section        WCK01_AAF20200214_F8-ctg57.37.raw.section            WCK01_AAF20200214_F8-ctg57.85.raw.section
evidence_72.gff           WCK01_AAF20200214_F8-ctg57.10-11.raw.section          WCK01_AAF20200214_F8-ctg57.38-39.raw.section         WCK01_AAF20200214_F8-ctg57.86-87.raw.section
evidence_73.gff           WCK01_AAF20200214_F8-ctg57.101.pred.raw.section       WCK01_AAF20200214_F8-ctg57.38.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.end.blastn.holdover
evidence_74.gff           WCK01_AAF20200214_F8-ctg57.101.raw.section            WCK01_AAF20200214_F8-ctg57.38.raw.section            WCK01_AAF20200214_F8-ctg57.86.end.blastx.holdover
evidence_75.gff           WCK01_AAF20200214_F8-ctg57.102-103.raw.section        WCK01_AAF20200214_F8-ctg57.39-40.raw.section         WCK01_AAF20200214_F8-ctg57.86.pred.raw.section
evidence_76.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.39.pred.raw.section       WCK01_AAF20200214_F8-ctg57.86.raw.section
evidence_77.gff           WCK01_AAF20200214_F8-ctg57.102.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.39.raw.section            WCK01_AAF20200214_F8-ctg57.87-88.raw.section
evidence_78.gff           WCK01_AAF20200214_F8-ctg57.102.pred.raw.section       WCK01_AAF20200214_F8-ctg57.3.pred.raw.section        WCK01_AAF20200214_F8-ctg57.87.pred.raw.section
evidence_79.gff           WCK01_AAF20200214_F8-ctg57.102.raw.section            WCK01_AAF20200214_F8-ctg57.3.raw.section             WCK01_AAF20200214_F8-ctg57.87.raw.section
evidence_7.gff            WCK01_AAF20200214_F8-ctg57.103-104.raw.section        WCK01_AAF20200214_F8-ctg57.40-41.raw.section         WCK01_AAF20200214_F8-ctg57.88-89.raw.section
evidence_80.gff           WCK01_AAF20200214_F8-ctg57.103.pred.raw.section       WCK01_AAF20200214_F8-ctg57.40.pred.raw.section       WCK01_AAF20200214_F8-ctg57.88.pred.raw.section
evidence_81.gff           WCK01_AAF20200214_F8-ctg57.103.raw.section            WCK01_AAF20200214_F8-ctg57.40.raw.section            WCK01_AAF20200214_F8-ctg57.88.raw.section
evidence_82.gff           WCK01_AAF20200214_F8-ctg57.104-105.raw.section        WCK01_AAF20200214_F8-ctg57.41-42.raw.section         WCK01_AAF20200214_F8-ctg57.89-90.raw.section
evidence_83.gff           WCK01_AAF20200214_F8-ctg57.104.pred.raw.section       WCK01_AAF20200214_F8-ctg57.41.pred.raw.section       WCK01_AAF20200214_F8-ctg57.89.pred.raw.section
evidence_84.gff           WCK01_AAF20200214_F8-ctg57.104.raw.section            WCK01_AAF20200214_F8-ctg57.41.raw.section            WCK01_AAF20200214_F8-ctg57.8-9.raw.section
evidence_85.gff           WCK01_AAF20200214_F8-ctg57.105-106.raw.section        WCK01_AAF20200214_F8-ctg57.42-43.raw.section         WCK01_AAF20200214_F8-ctg57.89.raw.section
evidence_86.gff           WCK01_AAF20200214_F8-ctg57.105.pred.raw.section       WCK01_AAF20200214_F8-ctg57.42.pred.raw.section       WCK01_AAF20200214_F8-ctg57.8.pred.raw.section
evidence_87.gff           WCK01_AAF20200214_F8-ctg57.105.raw.section            WCK01_AAF20200214_F8-ctg57.42.raw.section            WCK01_AAF20200214_F8-ctg57.8.raw.section
evidence_88.gff           WCK01_AAF20200214_F8-ctg57.106-107.raw.section        WCK01_AAF20200214_F8-ctg57.43-44.raw.section         WCK01_AAF20200214_F8-ctg57.90-91.raw.section
evidence_89.gff           WCK01_AAF20200214_F8-ctg57.106.pred.raw.section       WCK01_AAF20200214_F8-ctg57.43.pred.raw.section       WCK01_AAF20200214_F8-ctg57.90.pred.raw.section
evidence_8.gff            WCK01_AAF20200214_F8-ctg57.106.raw.section            WCK01_AAF20200214_F8-ctg57.43.raw.section            WCK01_AAF20200214_F8-ctg57.90.raw.section
evidence_90.gff           WCK01_AAF20200214_F8-ctg57.107-108.raw.section        WCK01_AAF20200214_F8-ctg57.44-45.raw.section         WCK01_AAF20200214_F8-ctg57.9-10.raw.section
evidence_91.gff           WCK01_AAF20200214_F8-ctg57.107.pred.raw.section       WCK01_AAF20200214_F8-ctg57.44.pred.raw.section       WCK01_AAF20200214_F8-ctg57.91-92.raw.section
evidence_92.gff           WCK01_AAF20200214_F8-ctg57.107.raw.section            WCK01_AAF20200214_F8-ctg57.44.raw.section            WCK01_AAF20200214_F8-ctg57.91.pred.raw.section
evidence_93.gff           WCK01_AAF20200214_F8-ctg57.108-109.raw.section        WCK01_AAF20200214_F8-ctg57.45-46.raw.section         WCK01_AAF20200214_F8-ctg57.91.raw.section
evidence_94.gff           WCK01_AAF20200214_F8-ctg57.108.pred.raw.section       WCK01_AAF20200214_F8-ctg57.45.pred.raw.section       WCK01_AAF20200214_F8-ctg57.92-93.raw.section
evidence_95.gff           WCK01_AAF20200214_F8-ctg57.108.raw.section            WCK01_AAF20200214_F8-ctg57.4-5.raw.section           WCK01_AAF20200214_F8-ctg57.92.pred.raw.section
evidence_96.gff           WCK01_AAF20200214_F8-ctg57.109-110.raw.section        WCK01_AAF20200214_F8-ctg57.45.raw.section            WCK01_AAF20200214_F8-ctg57.92.raw.section
evidence_96.gff.ann       WCK01_AAF20200214_F8-ctg57.109.pred.raw.section       WCK01_AAF20200214_F8-ctg57.46-47.raw.section         WCK01_AAF20200214_F8-ctg57.93-94.raw.section
evidence_96.gff.def       WCK01_AAF20200214_F8-ctg57.109.raw.section            WCK01_AAF20200214_F8-ctg57.46.pred.raw.section       WCK01_AAF20200214_F8-ctg57.93.pred.raw.section
evidence_96.gff.seq       WCK01_AAF20200214_F8-ctg57.10.pred.raw.section        WCK01_AAF20200214_F8-ctg57.46.raw.section            WCK01_AAF20200214_F8-ctg57.93.raw.section
evidence_97.gff.ann       WCK01_AAF20200214_F8-ctg57.10.raw.section             WCK01_AAF20200214_F8-ctg57.47-48.raw.section         WCK01_AAF20200214_F8-ctg57.94-95.raw.section
evidence_97.gff.def       WCK01_AAF20200214_F8-ctg57.110-111.raw.section        WCK01_AAF20200214_F8-ctg57.47.pred.raw.section       WCK01_AAF20200214_F8-ctg57.94.pred.raw.section
evidence_97.gff.seq       WCK01_AAF20200214_F8-ctg57.110.pred.raw.section       WCK01_AAF20200214_F8-ctg57.47.raw.section            WCK01_AAF20200214_F8-ctg57.94.raw.section
evidence_98.gff.ann       WCK01_AAF20200214_F8-ctg57.110.raw.section            WCK01_AAF20200214_F8-ctg57.48-49.raw.section         WCK01_AAF20200214_F8-ctg57.95-96.raw.section
evidence_98.gff.def       WCK01_AAF20200214_F8-ctg57.111-112.raw.section        WCK01_AAF20200214_F8-ctg57.48.pred.raw.section       WCK01_AAF20200214_F8-ctg57.95.pred.raw.section
evidence_98.gff.seq       WCK01_AAF20200214_F8-ctg57.11-12.raw.section          WCK01_AAF20200214_F8-ctg57.48.raw.section            WCK01_AAF20200214_F8-ctg57.95.raw.section
evidence_99.gff           WCK01_AAF20200214_F8-ctg57.111.pred.raw.section       WCK01_AAF20200214_F8-ctg57.48.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastn.holdover
evidence_99.gff.ann       WCK01_AAF20200214_F8-ctg57.111.raw.section            WCK01_AAF20200214_F8-ctg57.48.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.96.end.blastx.holdover
evidence_99.gff.def       WCK01_AAF20200214_F8-ctg57.112-113.raw.section        WCK01_AAF20200214_F8-ctg57.49-50.raw.section         WCK01_AAF20200214_F8-ctg57.96.end.section.holdover
evidence_99.gff.seq       WCK01_AAF20200214_F8-ctg57.112.pred.raw.section       WCK01_AAF20200214_F8-ctg57.49.pred.raw.section       WCK01_AAF20200214_F8-ctg57.96.pred.raw.section
evidence_9.gff            WCK01_AAF20200214_F8-ctg57.112.raw.section            WCK01_AAF20200214_F8-ctg57.49.raw.section            WCK01_AAF20200214_F8-ctg57.96.raw.section
query.fasta               WCK01_AAF20200214_F8-ctg57.113-114.raw.section        WCK01_AAF20200214_F8-ctg57.4.pred.raw.section        WCK01_AAF20200214_F8-ctg57.96.start.blastn.holdover
query.masked.fasta        WCK01_AAF20200214_F8-ctg57.113.pred.raw.section       WCK01_AAF20200214_F8-ctg57.4.raw.section             WCK01_AAF20200214_F8-ctg57.96.start.blastx.holdover
query.masked.fasta.index  WCK01_AAF20200214_F8-ctg57.113.raw.section            WCK01_AAF20200214_F8-ctg57.50-51.raw.section         WCK01_AAF20200214_F8-ctg57.97.pred.raw.section
query.masked.gff          WCK01_AAF20200214_F8-ctg57.114-115.raw.section        WCK01_AAF20200214_F8-ctg57.50.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.98.pred.raw.section
run.log.child.0           WCK01_AAF20200214_F8-ctg57.114.pred.raw.section       WCK01_AAF20200214_F8-ctg57.50.end.blastx.holdover    WCK01_AAF20200214_F8-ctg57.98.start.blastn.holdover
run.log.child.1           WCK01_AAF20200214_F8-ctg57.114.raw.section            WCK01_AAF20200214_F8-ctg57.50.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99-100.raw.section
run.log.child.10          WCK01_AAF20200214_F8-ctg57.114.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.50.raw.section            WCK01_AAF20200214_F8-ctg57.99.end.blastn.holdover
run.log.child.100         WCK01_AAF20200214_F8-ctg57.114.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.50.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.99.end.blastx.holdover
run.log.child.101         WCK01_AAF20200214_F8-ctg57.115-116.raw.section        WCK01_AAF20200214_F8-ctg57.51-52.raw.section         WCK01_AAF20200214_F8-ctg57.99.pred.raw.section
run.log.child.102         WCK01_AAF20200214_F8-ctg57.115.end.blastn.holdover    WCK01_AAF20200214_F8-ctg57.51.pred.raw.section       WCK01_AAF20200214_F8-ctg57.99.raw.section
run.log.child.103         WCK01_AAF20200214_F8-ctg57.115.pred.raw.section       WCK01_AAF20200214_F8-ctg57.51.raw.section            WCK01_AAF20200214_F8-ctg57.99.start.blastx.holdover
run.log.child.104         WCK01_AAF20200214_F8-ctg57.115.raw.section            WCK01_AAF20200214_F8-ctg57.52-53.raw.section         WCK01_AAF20200214_F8-ctg57.99.start.section.holdover
run.log.child.105         WCK01_AAF20200214_F8-ctg57.116-117.raw.section        WCK01_AAF20200214_F8-ctg57.52.pred.raw.section       WCK01_AAF20200214_F8-ctg57.9.pred.raw.section
run.log.child.106         WCK01_AAF20200214_F8-ctg57.116.pred.raw.section       WCK01_AAF20200214_F8-ctg57.52.raw.section            WCK01_AAF20200214_F8-ctg57.9.raw.section
run.log.child.107         WCK01_AAF20200214_F8-ctg57.116.raw.section            WCK01_AAF20200214_F8-ctg57.53-54.raw.section         WCK01_AAF20200214_F8-ctg57.gff.ann
run.log.child.108         WCK01_AAF20200214_F8-ctg57.117-118.raw.section        WCK01_AAF20200214_F8-ctg57.53.pred.raw.section       WCK01_AAF20200214_F8-ctg57.gff.def
run.log.child.109         WCK01_AAF20200214_F8-ctg57.117.pred.raw.section       WCK01_AAF20200214_F8-ctg57.53.raw.section            WCK01_AAF20200214_F8-ctg57.gff.seq
run.log.child.11          WCK01_AAF20200214_F8-ctg57.117.raw.section            WCK01_AAF20200214_F8-ctg57.54-55.raw.section
run.log.child.110         WCK01_AAF20200214_F8-ctg57.117.start.blastn.holdover  WCK01_AAF20200214_F8-ctg57.54.pred.raw.section
run.log.child.111         WCK01_AAF20200214_F8-ctg57.117.start.blastx.holdover  WCK01_AAF20200214_F8-ctg57.54.raw.section

I set clean_try=1 and am trying to fix this contig (it's only this one contig which is causing trouble), but I'm wondering if it's also okay to completely delete the void directory to force it to start this contig from scratch. I have already tried rerunning maker with clean_try=1 two times and now I'm getting an mpich2 error:

Fatal error in MPI_Send: Invalid count, error stack:
MPI_Send(173): MPI_Send(buf=0x2aec3d6a3010, count=-1279995089, MPI_CHAR, dest=15, tag=9999, MPI_COMM_WORLD) failed
MPI_Send(97).: Negative count, value is -1279995089

I am currently trying again with fewer MPI jobs requested, worrying that there might be a memory issue on the computer cluster I am using. My temporary directory still has lots of space, but I have ~200G RAM per node and sometimes the jobs use a ton of RAM. I don't have too many more contigs left of this run, so I just really don't want to mess anything up. Do you have any advice?

Thanks so much!
Zoe

______________________________________
Zoe Clarke
PhD candidate in Computational Biology at U of T
_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

smime.p7s (1K) Download Attachment