fabiolauria
commented
1 year ago Hi Beata, thank you for using riboWaltz. As you correctly reported, the message about the stop_codon is just a warning and can be ignored. About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best Fabio
scholtzb
laillern
Hi Fabio,
I am trying to run riboWaltz on galaxy.eu. The transcriptome-mapped.bam file was generated by RNA STAR, using the built-in index and hg38 on the Galaxy server, and gencode.v43.basic.annotation.gtf.gz, which I uploaded into Galaxy directly from the database. I used the same gtf for riboWaltz. RiboWaltz failed to run, with the following error message:
Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning message: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Error in (function (x) : attempt to apply non-function
If I understand correctly from your feedback on previous issues, the "The "phase" metadata column contains non-NA values for features of type stop_codon." is just a warning, and should not cause the failure. But I cannot figure out what the last line, "Error in (function (x) : attempt to apply non-function" may refer to, although I suppose it indicates the error causing the failure.
Your help would be greatly appreciated,
Thank you very much,
Beata
I am copying here the command line from Galaxy:
ln -s /data/dnb08/galaxy_db/files/2/9/8/dataset_2989d96b-5e2d-4547-8700-b4e45121c568.dat ls180_1'.bam' && Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/ribowaltz_process/6d4c94373bba/ribowaltz_process/ribowaltz.R' -b . -g '/data/dnb08/galaxy_db/files/e/1/0/dataset_e10dfbb5-19e4-49cf-a8eb-29ea41fa2295.dat' --refseq_sep '' --params_duplicate_filterting '[{"extremity": "both", "keep": "shortest"}]' --params_peridiocity_filterting '[{"periodicity_threshold": 50}]' --params_psite_additional '[{"flanking": 6, "use_start": true, "psite_extrimity": "auto", "cl": 99}]' --params_coverage_additional '[{"psites_per_region": true, "min_overlap": 1, "start_nts": 0, "stop_nts": 0}]' --psite_info_rdata '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_e1178f2c-57e6-4162-b986-bea0a3ca3aaa.dat' --codon_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_32b21edf-1c05-4f7e-82e1-a1b5e8f81f6d.dat' --cds_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_a6016f82-a5e0-45d6-be7d-587c497ef070.dat' && cd plots && for i in /.pdf; do mv $i ${i/\//-}; done;