Dear Prof. Jennifer Hillman-Jackson.
Thank you for your earlier suggestion, and my apologies for a very delayed follow-up.
I tried recreating the collection in Galaxy and deliberately left the “remove file extension” option unchecked. Unfortunately, the job still failed.
I then followed your alternative suggestion using the Extract Element Identifiers and Relabel Identifiers tools to restore the file extensions. Unfortunately, this did not resolve the issue either.
The generated symlinks are now created with the .gff3 suffix, for example: input_directory/SRR38521030_Staphylococcus*aureus_ST8_CC8.gff3
However, the wrapper still invokes Panaroo with: -i input_directory/*.gff
Since all generated files end with .gff3, the wildcard appears not to match any files and Panaroo receives the literal string input_directory/*.gff, leading to: FileNotFoundError: input_directory/*.gff
From the generated command line it looks like the wrapper may currently create .gff3 links while still expecting .gff inputs.
I have included the full Galaxy command line and error message below in case the additional details are helpful for debugging.
Thank you again for your time and assistance.
Best regards,
Le Tuan Loc
Run 1: not using Relabel Identifiers
CLI: mkdir outdir && mkdir input_directory && ln -fs ‘/data/dnb13/galaxy_db/files/b/7/5/dataset_b754a17d-3319-444d-88d1-912474ce52e1.dat’ ‘input_directory/AP017922.1_Staphylococcus_aureus_ST398_CC398_ISU926.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/b/a/0/dataset_ba0dd125-511e-431a-882b-ce2d13f17f57.dat’ ‘input_directory/AP017922.1_Staphylococcus_aureus_ST6272_CC72_JP080.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/8/3/f/dataset_83f6d967-07b2-4872-a04f-c8fb3c7ef3e9.dat’ ‘input_directory/ERR107794_Staphylococcus_aureus_ST36_CC30.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/6/e/dataset_a6e9cdca-174a-4fae-9bc9-99e67e5628c4.dat’ ‘input_directory/ERR107822_Staphylococcus_aureus_ST22_CC22.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/d/1/c/dataset_d1c435c6-a785-4a15-81ff-38597c91e088.dat’ ‘input_directory/ERR10900234_Staphylococcus_aureus_ST121_CC121.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/9/4/c/dataset_94c4a8fd-1792-494b-af7b-595d7eabff6d.dat’ ‘input_directory/ERR10900246_Staphylococcus_aureus_ST121_CC121.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/3/7/c/dataset_37c5e3d0-2e5a-4a4e-9a31-2f589435bbd8.dat’ ‘input_directory/ERS1179830_Sraphylococcus_aureus_ST36_CC30_NRS740_TN-82.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/e/2/c/dataset_e2c0dca6-e97a-436b-8fed-9a076aa591b1.dat’ ‘input_directory/GCF_000695215.1_Staphylococcus_aureus_ST22_CC22.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/9/8/7/dataset_9871073f-9be5-4d4b-a7dd-c763fc1d646a.dat’ ‘input_directory/GCF_000695875.1_Staphylococcus_aureus_ST8_CC8.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/d/2/b/dataset_d2b1e361-cbef-40ec-8e65-c49bebec048b.dat’ ‘input_directory/GCF_001887075.1_Staphylococcus_aureus_ST398_CC398_E154.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/1/4/4/dataset_144edb93-f972-4657-8fa9-adbcf74fede7.dat’ ‘input_directory/GCF_003031485.1_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/0/4/2/dataset_0425a6f0-5a7b-4913-9450-15401500ba94.dat’ ‘input_directory/GCF_009811395.1_Staphylococcus_aureus_ST8_CC8.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/1/1/dataset_a11e4b51-788e-422e-9d6a-88ca56f78c02.dat’ ‘input_directory/GCF_030342405.2_Staphylococcus_aureus_ST45_CC45_BSN01_Closure_genomic.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/5/8/1/dataset_5810ba99-0879-4e83-900c-7105d704773f.dat’ ‘input_directory/GCF_041356355.1_Staphylococcus_aureus_ST5_CC5_MRSA-16.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/8/f/3/dataset_8f395a45-d303-49bb-9bbb-607f4d7a52de.dat’ ‘input_directory/GCF_053749775.1_Staphylococcus_aureus_ST45_CC_45_SAIE_GP_04.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/2/0/0/dataset_200b6581-969d-4055-b3b7-228ed3b16da9.dat’ ‘input_directory/SRR1159867_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/4/0/dataset_a4015227-7905-43f9-b9b5-6113deb8c1b5.dat’ ‘input_directory/SRR13194715_Staphylococcus_aureus_ST30_CC_30_144KP_subject_1135.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/b/7/e/dataset_b7ea8b8c-2b42-4870-8921-3db7fbd8d4d1.dat’ ‘input_directory/SRR27644380_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/c/b/7/dataset_cb7a1890-be3c-4e0a-951a-0d7ae68e894d.dat’ ‘input_directory/SRR38521030_Staphylococcus_aureus_ST8_CC8.gff3’ && panaroo --clean-mode ‘strict’ --codon-table ‘11’ --remove-invalid-genes --threshold ‘0.98’ --family_threshold ‘0.7’ --len_dif_percent ‘0.98’ --family_len_dif_percent ‘0.0’ --search_radius ‘5000’ --refind_prop_match ‘0.2’ --refind-mode ‘default’ --min_trailing_support ‘2’ --trailing_recursive ‘1’ --edge_support_threshold ‘1.0’ --remove_by_consensus ‘False’ --high_var_flag ‘5’ --min_edge_support_sv ‘2’ --alignment ‘core’ --aligner ‘mafft’ --core_entropy_filter 0.1 -i input_directory/*.gff -o outdir -t ${GALAXY_SLOTS:-8} && mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab && mv outdir/combined_protein_cdhit_out.txt outdir/combined_protein_cdhit_out.fa
Error: Traceback (most recent call last):
File “/usr/local/bin/panaroo”, line 10, in
sys.exit(main())
^^^^^^
File “/usr/local/lib/python3.11/site-packages/panaroo/_main_.py”, line 318, in main
with open(args.input_files[0], “r”) as file:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: ‘input_directory/*.gff’
Run 02: using Relabel identifier
CLI: mkdir outdir && mkdir input_directory && ln -fs ‘/data/dnb13/galaxy_db/files/b/7/5/dataset_b754a17d-3319-444d-88d1-912474ce52e1.dat’ ‘input_directory/AP017922.1_Staphylococcus_aureus_ST398_CC398_ISU926.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/b/a/0/dataset_ba0dd125-511e-431a-882b-ce2d13f17f57.dat’ ‘input_directory/AP017922.1_Staphylococcus_aureus_ST6272_CC72_JP080.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/8/3/f/dataset_83f6d967-07b2-4872-a04f-c8fb3c7ef3e9.dat’ ‘input_directory/ERR107794_Staphylococcus_aureus_ST36_CC30.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/6/e/dataset_a6e9cdca-174a-4fae-9bc9-99e67e5628c4.dat’ ‘input_directory/ERR107822_Staphylococcus_aureus_ST22_CC22.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/d/1/c/dataset_d1c435c6-a785-4a15-81ff-38597c91e088.dat’ ‘input_directory/ERR10900234_Staphylococcus_aureus_ST121_CC121.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/9/4/c/dataset_94c4a8fd-1792-494b-af7b-595d7eabff6d.dat’ ‘input_directory/ERR10900246_Staphylococcus_aureus_ST121_CC121.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/3/7/c/dataset_37c5e3d0-2e5a-4a4e-9a31-2f589435bbd8.dat’ ‘input_directory/ERS1179830_Sraphylococcus_aureus_ST36_CC30_NRS740_TN-82.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/e/2/c/dataset_e2c0dca6-e97a-436b-8fed-9a076aa591b1.dat’ ‘input_directory/GCF_000695215.1_Staphylococcus_aureus_ST22_CC22.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/9/8/7/dataset_9871073f-9be5-4d4b-a7dd-c763fc1d646a.dat’ ‘input_directory/GCF_000695875.1_Staphylococcus_aureus_ST8_CC8.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/d/2/b/dataset_d2b1e361-cbef-40ec-8e65-c49bebec048b.dat’ ‘input_directory/GCF_001887075.1_Staphylococcus_aureus_ST398_CC398_E154.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/1/4/4/dataset_144edb93-f972-4657-8fa9-adbcf74fede7.dat’ ‘input_directory/GCF_003031485.1_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/0/4/2/dataset_0425a6f0-5a7b-4913-9450-15401500ba94.dat’ ‘input_directory/GCF_009811395.1_Staphylococcus_aureus_ST8_CC8.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/1/1/dataset_a11e4b51-788e-422e-9d6a-88ca56f78c02.dat’ ‘input_directory/GCF_030342405.2_Staphylococcus_aureus_ST45_CC45_BSN01_Closure_genomic.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/5/8/1/dataset_5810ba99-0879-4e83-900c-7105d704773f.dat’ ‘input_directory/GCF_041356355.1_Staphylococcus_aureus_ST5_CC5_MRSA-16.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/8/f/3/dataset_8f395a45-d303-49bb-9bbb-607f4d7a52de.dat’ ‘input_directory/GCF_053749775.1_Staphylococcus_aureus_ST45_CC_45_SAIE_GP_04.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/2/0/0/dataset_200b6581-969d-4055-b3b7-228ed3b16da9.dat’ ‘input_directory/SRR1159867_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/a/4/0/dataset_a4015227-7905-43f9-b9b5-6113deb8c1b5.dat’ ‘input_directory/SRR13194715_Staphylococcus_aureus_ST30_CC_30_144KP_subject_1135.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/b/7/e/dataset_b7ea8b8c-2b42-4870-8921-3db7fbd8d4d1.dat’ ‘input_directory/SRR27644380_Staphylococcus_aureus_ST5_CC5.gff3’ && ln -fs ‘/data/dnb13/galaxy_db/files/c/b/7/dataset_cb7a1890-be3c-4e0a-951a-0d7ae68e894d.dat’ ‘input_directory/SRR38521030_Staphylococcus_aureus_ST8_CC8.gff3’ && panaroo --clean-mode ‘strict’ --codon-table ‘11’ --remove-invalid-genes --threshold ‘0.98’ --family_threshold ‘0.7’ --len_dif_percent ‘0.98’ --family_len_dif_percent ‘0.0’ --search_radius ‘5000’ --refind_prop_match ‘0.2’ --refind-mode ‘default’ --min_trailing_support ‘2’ --trailing_recursive ‘1’ --edge_support_threshold ‘1.0’ --remove_by_consensus ‘False’ --high_var_flag ‘5’ --min_edge_support_sv ‘2’ --alignment ‘core’ --aligner ‘mafft’ --core_entropy_filter 0.1 -i input_directory/*.gff -o outdir -t ${GALAXY_SLOTS:-8} && mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab && mv outdir/combined_protein_cdhit_out.txt outdir/combined_protein_cdhit_out.fa
Error: Traceback (most recent call last):
File “/usr/local/bin/panaroo”, line 10, in
sys.exit(main())
^^^^^^
File “/usr/local/lib/python3.11/site-packages/panaroo/_main_.py”, line 318, in main
with open(args.input_files[0], “r”) as file:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: ‘input_directory/*.gff’