Amine GHOZLANE (5a60a2f6) at 24 Mar 13:53
Add reminding message
Amine GHOZLANE (4277ab6b) at 11 Mar 17:35
Add fastq.gz submission
Amine GHOZLANE (aec062c0) at 01 Mar 13:38
Update of Alientrimmer
The workflow failed during progression for the key 1f9285a1aea7b. tool_id:toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/cat2/1.0.0 error: Traceback (most recent call last): File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/9418d6ba89d0/concatenate_datacollection/catWrapper.py", line 32, in main() File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/9418d6ba89d0/concatenate_datacollection/catWrapper.py", line 15, in main infile = sys.argv[2] IndexError: list index out of range
This is the result of the submission of files with a weird extension. The modification must be performed in shaman...
The workflow failed during progression for the key 4a94702383b7. tool_id:toolshed.pasteur.fr/repos/aghozlane/extract_fasta/extract_fasta/1.0 error: Error no element detected in the file : /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/004/270/dataset_4270379.dat
The workflow failed during progression for the key 1ac0530c8e36a.
tool_id:toolshed.pasteur.fr/repos/aghozlane/extract_result/extract_result/1.0 error: Sample not identified : .fastq Sample not identified : .fastq Traceback (most recent call last): File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 616, in main() File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 584, in main args.split_pattern) File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 333, in parse_otu_table sample_read[header_name[i].replace(split_pattern, "")].update({"mapped":header[i]}) KeyError: '.fastq'
The error message is now: The suffix: {0} did not allow to associate the fastq filenames and sample names in the OTU table. We recommend to specify a unique suffix like _R1 to identify paired fastq files.
The workflow failed during progression for the key 1ac0530c8e36a.
tool_id:toolshed.pasteur.fr/repos/aghozlane/extract_result/extract_result/1.0 error: Sample not identified : .fastq Sample not identified : .fastq Traceback (most recent call last): File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 616, in main() File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 584, in main args.split_pattern) File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/aghozlane/extract_result/c7a4fef90a51/extract_result/extract_result.py", line 333, in parse_otu_table sample_read[header_name[i].replace(split_pattern, "")].update({"mapped":header[i]}) KeyError: '.fastq'
The workflow failed during progression for the key 4e81304f4076. tool_id:toolshed.pasteur.fr/repos/fmareuil/shaman_tools/alienTrimmer_shaman/0.4.2_shaman_1 error: Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 159 at java.base/java.lang.StringLatin1.charAt(StringLatin1.java:47) at java.base/java.lang.String.charAt(String.java:693) at AlienTrimmer.main(AlienTrimmer.java:1075)
The workflow failed during progression for the key 1f13e56ef1d9f. tool_id:toolshed.pasteur.fr/repos/fmareuil/pear/iuc_pear/0.9.10.1 error: Fatal error: Exit code 1 () [ERROR] - Cannot determine the file type of /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/003/707/dataset_3707715.dat. Ensure it is a BZIP2/GZIP compressed FASTQ file or plain FASTQ. [ERROR] - Cannot determine the file type of /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/003/707/dataset_3707716.dat. Ensure it is a BZIP2/GZIP compressed FASTQ file or plain FASTQ.
tool_id:toolshed.pasteur.fr/repos/fmareuil/pear/iuc_pear/0.9.10.1 error: Fatal error: Exit code 1 () [ERROR] - Cannot determine the file type of /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/003/707/dataset_3707711.dat. Ensure it is a BZIP2/GZIP compressed FASTQ file or plain FASTQ. [ERROR] - Cannot determine the file type of /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/003/707/dataset_3707712.dat. Ensure it is a BZIP2/GZIP compressed FASTQ file or plain FASTQ.
The workflow failed during progression for the key 1aaab62fca4dd. tool_id:upload1 error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/tools/data_source/upload.py", line 276, in main() File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/tools/data_source/upload.py", line 269, in main metadata.append(add_file(dataset, registry, output_path)) File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/tools/data_source/upload.py", line 127, in add_file convert_spaces_to_tabs=dataset.space_to_tab, File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/lib/galaxy/datatypes/upload_util.py", line 55, in handle_upload convert_spaces_to_tabs=convert_spaces_to_tabs, File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 736, in handle_uploaded_dataset_file_internal auto_decompress=auto_decompress, File "/pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 694, in handle_compressed_file raise IOError('Problem uncompressing %s data, please try retrieving the data uncompressed: %s' % (compressed_type, e)) IOError: Problem uncompressing gz data, please try retrieving the data uncompressed: CRC check failed 0x0 != 0xab612a4bL
Shaman failed to submit data for the history 4a946636d4a0
The workflow failed during progression for the key 4a94702383b7. tool_id:toolshed.pasteur.fr/repos/aghozlane/extract_fasta/extract_fasta/1.0 error: Error no element detected in the file : /pasteur/zeus/projets/p00/galaxy-prod/galaxy-dist/database/files/004/270/dataset_4270379.dat
The workflow failed during progression for the key 1f9285a1aea7b. tool_id:toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/cat2/1.0.0 error: Traceback (most recent call last): File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/9418d6ba89d0/concatenate_datacollection/catWrapper.py", line 32, in main() File "/pasteur/zeus/projets/p00/galaxy-prod/shed_tools/toolshed.pasteur.fr/repos/fmareuil/concatenate_datacollection/9418d6ba89d0/concatenate_datacollection/catWrapper.py", line 15, in main infile = sys.argv[2] IndexError: list index out of range
Amine GHOZLANE (336c0a6d) at 09 Jul 15:59
Solve split pattern extract_result
Amine GHOZLANE (b3ae8b50) at 04 May 14:48
update to last version of bioblend
Amine GHOZLANE (25f1621c) at 22 Apr 17:56
Update test program