Bismark - Bug in Bismark Pretty Report ?

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Bismark - Bug in Bismark Pretty Report ?

Dear Galaxy Community,

I just recently started testing the Bismark methylation tools, everything works fine until I try to make a "pretty report".
Some information is not included in the report, instead you see placeholders
I attached the output I  get and shown below are the job parameters.
Does anybody know where to fix this?

Best regards,

Bismark Pretty Report

Dataset Information

Number: 198
Name: Bismark Pretty Report on data 190, data 189, and others: Download pretty html report
Created: Thu 07 Mar 2019 03:24:40 PM (UTC)
Filesize: 2.7 MB
Dbkey: ?
Format: html

Job Information

Galaxy Tool ID:
Galaxy Tool Version: 0.20.0
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 0
History Content API ID: 971c2f882eb14ac3 (41433)
Job API ID: 58816697357e736f (22051)
History API ID: 5fccce9c1b3793da (807)
UUID: 45bedd12-6ce5-4d63-a1e2-e05883b0c356
Full Path: /opt/galaxy/galaxy/database/files/038/dataset_38737.dat

Tool Parameters

Input Parameter Value Note for rerun
Submit a Bismark mapping report 191: Bismark Meth. Extractor on data 60 and data 133: Genome-wide methylation report.
Submit the corresponding Bismark deduplication report 197: Bismark Deduplicate on data 133: deduplication report
Submit the corresponding Bismark splitting report 189: Bismark Meth. Extractor on data 60 and data 133: Splitting Report
Submit the corresponding Bismark M-bias report 190: Bismark Meth. Extractor on data 60 and data 133: Mbias Report
Submit the corresponding Bismark nucleotide report

Create a separate logfile, otherwise logs are added to the dataset info. False

Inheritance Chain

Bismark Pretty Report on data 190, data 189, and others: Download pretty html report

Command Line

python '/opt/galaxy/shed_tools/'  --alignment_report '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat'  --dedup_report '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat' --splitting_report '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat' --mbias_report '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat'  --output_html_report '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat'

Job Metrics


Cores Allocated 8
Job End Time 2019-03-07 16:49:58
Job Runtime (Wall Clock) 25 minutes
Job Start Time 2019-03-07 16:24:43
Memory Allocated (MB) 510000

Job Dependencies

Dependency Dependency Type Version
bismark conda 0.20.0

Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661


Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Bismark_Pretty_Report_on_data_190,_data_189,_and_others__Download_pretty_html_report_html.html (3M) Download Attachment