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,
Christopher
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:
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0
Galaxy Tool Version: 0.20.0
Tool Version:
Tool Standard Output: stdout
<
http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout>
Tool Standard Error: stderr
<
http://dkfzgalaxy/datasets/971c2f882eb14ac3/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.
<
http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params>
additional_reports
Submit the corresponding Bismark deduplication report 197: Bismark
Deduplicate on data 133: deduplication report
<
http://dkfzgalaxy/datasets/622377f5e70addd2/show_params>
Submit the corresponding Bismark splitting report 189: Bismark Meth.
Extractor on data 60 and data 133: Splitting Report
<
http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params>
Submit the corresponding Bismark M-bias report 190: Bismark Meth.
Extractor on data 60 and data 133: Mbias Report
<
http://dkfzgalaxy/datasets/47db6b20871008b9/show_params>
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/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py'
--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
core
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)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.previti(a)dkfz.de <
http://www.dkfz.de/>
www.dkfz.de <
http://www.dkfz.de/>
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537
Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.