RNA-star error (contact adminstrator) at UseGalaxy.org -- Resolved

usegalaxy.org support
#1

I’m trying to run STAR-fusion by using data from previous RNA STAR aligment and a plug’n play reference.

These were the settings:

STAR-Fusion

Dataset Information

Number: 484
Name: STAR-Fusion on data 477, data 90, and others: fusion_candidates.final
Created: Sun Dec 20 00:02:25 2020 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: tabular

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3+galaxy1
Galaxy Tool Version: 0.5.4-3+galaxy1
Tool Version: None
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: None
History Content API ID: bbd44e69cb8906b575af0a8b89f94c6f
Job API ID: bbd44e69cb8906b514b6ba106ce1ce07
History API ID: a7538c218afd56b8
UUID: de7435f9-f145-49e2-86e5-48c266dc7584

Tool Parameters

Input Parameter Value
Use output from earlier STAR run or let STAR Fusion control running STAR use_chimeric
Chimeric junction file from STAR (with STAR-Fusion settings) * 426: RNA STAR on data 398, data 395, and others: chimeric junctions
Source for sequence to search history
Select the reference genome (FASTA file) * 91: GRCh38.p13.genome.fa uncompressed
Gene model (gff3,gtf) file for splice junctions and fusion gene detection * 90: gencode.v35.annotation.gtf.gz
Result of BLAST±blastn of the reference fasta sequence with itself * 477: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz
Settings to use default
Job Resource Parameters no

Inheritance Chain

STAR-Fusion on data 477, data 90, and others: fusion_candidates.final

After 3 weeks waiting for the job to run, I got the following error:

Dataset Error Report

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3+galaxy1 .

Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.

1 Like
#2

Update

Issues with RNA-star have been corrected. Please rerun any previously failed jobs.

Hello @GACG1

Thanks for reporting the problem. We are correcting the configuration right now and will write back when it is OK to rerun.

cc @nate

#3

Hello @jennaj !

I tried again, this time with a different error, I’m not sure if it is related to the previous bug:

Dataset Error Report

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3+galaxy1 .

Details

Tool generated the following standard error:

  • Running CMD: ln -s /pylon5/mc48nsp/xcgalaxy/main/staging//32889758/inputs/dataset_47405235.dat /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/tmp_star_fusion_genome_dir/ref_genome.fa * Running CMD: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/tmp_star_fusion_genome_dir/ref_genome.fa.star.idx --genomeFastaFiles /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/tmp_star_fusion_genome_dir/ref_genome.fa --limitGenomeGenerateRAM 40419136213 --sjdbGTFfile /pylon5/mc48nsp/xcgalaxy/main/staging//32889758/inputs/dataset_47405030.dat --sjdbOverhang 100 * Running CMD: ln -sf /pylon5/mc48nsp/xcgalaxy/main/staging//32889758/inputs/dataset_47405030.dat /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/tmp_star_fusion_genome_dir/ref_annot.gtf * Running CMD: /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/blast_pairs.gz /pylon5/mc48nsp/xcgalaxy/main/staging/32889758/working/tmp_star_fusion_genome_dir/blast_pairs.idx Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 1. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 1. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 5. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 7. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 7. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 16. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 16. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 18. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 18. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 19. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 19. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 19. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 19. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 19. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 19. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 24. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 25. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 25. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 29. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 29. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 29. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 29. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 29. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 29. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 30. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 30. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 30. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 30. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 30. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 30. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 32. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 32. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 33. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 33. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 34. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 34. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 36. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 36. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 36. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 36. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 36. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 36. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 38. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 38. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 38. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 38. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 38. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 38. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 41. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 41. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 41. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 41. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 41. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 41. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 43. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 44. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 44. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 46. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 46. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 46. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 46. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 46. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 46. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 47. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 48. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 48. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 48. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 48. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 48. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 48. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 49. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 49. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 49. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 49. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 49. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/in … s.pl line 26, <$fh> line 27297. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27297. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27298. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27302. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27305. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27306. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27306. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27306. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27306. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27306. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27306. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27307. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27307. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27308. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27310. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27310. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27311. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27314. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27315. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27315. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27315. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27315. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27315. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27315. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27316. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27318. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27318. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27318. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27318. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27318. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27318. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27319. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27319. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27319. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27319. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27319. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27319. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27320. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27320. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27323. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27323. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27323. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27323. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27323. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27323. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27326. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27326. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27329. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27332. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27332. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27333. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27333. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27336. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27338. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27338. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27338. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27338. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27338. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27338. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27339. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27339. Use of uninitialized value $per_id in concatenation (.) or string at
1 Like
#4

part 2 of the error:

/pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27340. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27340. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27341. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27341. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27342. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27342. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27346. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27346. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27346. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27346. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 28, <$fh> line 27346. Use of uninitialized value $geneB in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 29, <$fh> line 27346. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27347. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27347. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27351. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27351. Use of uninitialized value $Evalue in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26, <$fh> line 27353. Use of uninitialized value $geneA in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27355. Use of uninitialized value $geneB in string eq at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 24, <$fh> line 27355. Use of uninitialized value $per_id in concatenation (.) or string at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/util/index_blast_pairs.pl line 26,

#5

Hi @GACG1

The job seems to be aborted due to running out of resources (memory). This could be due to problematic inputs or the data really is too large to process.

My guess is that the human custom genome is the issue – is there a reason why you are not using the natively indexed human genome? This tool will never work with a really large custom genome at usegalaxy.org (and other public Galaxy servers).

Thanks!

#6

I see! I will try to use the built-in indexed human genome then
I used the one found in ensembl because I can download it and then compare with results I created offline. I thought it wouldn’t differ so much from the one indexed in galaxy in terms of size.

1 Like
#7

It doesn’t, but when a custom genome is used and a tool requires an index, that indexing step is part of the pre-processing before the tool is actually executed. Very handy for small genomes that are unlikely to be natively indexed, but that can create two large jobs instead of just one for larger genomes, plus indexing takes a bit more resource than the mapping. Most mammal genomes will exceed resources and even some plants.

If you need or want to manipulate the chromosome identifiers at some point in tabular data, this is a good tool and a mapping file between the Ensembl build of the genome version (what you loaded) and the UCSC build of that same genome version (what is natively indexed) already exists: **Replace column** by values which are defined in a convert file.

Since you are changing genome builds (but not versions), you’ll need to also update your reference annotation. That same tool would work well on a GTF dataset, or you can find a different source with UCSC based identifiers. Gencode, etc. But if you are comparing data run with the original GTF created in and out of Galaxy, stick with the original annotation for all analysis – just convert the chromosome identifiers so they all match up during processing. You can convert the IDs to all match up in either format once the analysis is reduced to tabular results, for those comparisons.

FAQs: https://galaxyproject.org/support

#8

Hello @jennaj !

As per your instructions, I tried running STAR fusion again with the built-in genome. The sequencing failed so I tried running STAR fusion with the option “let star fusion control star”.
Still, I’m getting an error when trying to align my human RNA-seq experiment.

I can do RNA star, but STAR fusion does not work. I got this error now:

STAR-Fusion

Dataset Information

Number: 516
Name: STAR-Fusion on data 477, data 90, and others: fusion_candidates.final
Created: Mon Jan 25 23:41:49 2021 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: tabular

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3+galaxy1
Galaxy Tool Version: 0.5.4-3+galaxy1
Tool Version: None
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: None
History Content API ID: bbd44e69cb8906b5b1052187eb096033
Job API ID: bbd44e69cb8906b52fd209a6b7210e2d
History API ID: a7538c218afd56b8
UUID: 3d934161-c044-4f6e-813d-bd9986a454c5

Tool Parameters

Input Parameter Value
Use output from earlier STAR run or let STAR Fusion control running STAR use_fastq
left.fq file * 500: Cutadapt on data 354 and data 353: Read 1 Output
right.fq file (actually optional, but highly recommended) * 501: Cutadapt on data 354 and data 353: Read 2 Output
Source for sequence to search cached
Genome to search /cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38.fa
Gene model (gff3,gtf) file for splice junctions and fusion gene detection * 90: gencode.v35.annotation.gtf.gz
Result of BLAST±blastn of the reference fasta sequence with itself * 477: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play.tar.gz
Settings to use default
Job Resource Parameters no

Inheritance Chain

STAR-Fusion on data 477, data 90, and others: fusion_candidates.final

ERROR:
Remote job server indicated a problem running or monitoring this job.

  • Running CMD: ln -s /cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38.fa /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa
  • Running CMD: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa.star.idx --genomeFastaFiles /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa --limitGenomeGenerateRAM 40419136213 --sjdbGTFfile /pylon5/mc48nsp/xcgalaxy/main/staging//33077213/inputs/dataset_47405030.dat --sjdbOverhang 100

EXITING because of INPUT ERROR: could not open genomeFastaFile: /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa

Jan 26 06:15:03 … FATAL ERROR, exiting
Error, cmd: STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa.star.idx --genomeFastaFiles /pylon5/mc48nsp/xcgalaxy/main/staging/33077213/working/tmp_star_fusion_genome_dir/ref_genome.fa --limitGenomeGenerateRAM 40419136213 --sjdbGTFfile /pylon5/mc48nsp/xcgalaxy/main/staging//33077213/inputs/dataset_47405030.dat --sjdbOverhang 100 died with ret 26624 at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/lib/Pipeliner.pm line 116.
Pipeliner::run(Pipeliner=HASH(0x1df2528)) called at /pylon5/mc48nsp/xcgalaxy/conda/envs/__star-fusion@0.5.4/lib/STAR-Fusion/FusionFilter/prep_genome_lib.pl line 208

1 Like
#9

@GACG1

What I notice first is that the reference GTF still has header lines.

Remove those and confirm that the chromosome identifiers between all inputs are an exact match.

Until those are done, we cannot determine if the data is actually too large or if the input format/content is contributing to the failure. Tools fail with all sorts of odd errors when the inputs are problematic – so the error you are getting is not necessary what is actually going wrong.

Review the FAQs I sent before. This one may also help provide some context:

In short, if inputs are problematic, those need to be fixed by you before more (reliable/specific) troubleshooting advice can be offered.

#10

Just to be sure, maybe I’m missing something or the tool does not specify it enough.
I downloaded the GTF directly from gencode, without any modification. RNA-star, bowtie and HTseq all accepted this GTF file and worked well with my samples by using the indexed bult-in genome.
For STAR fusion, I used a simple fastq file (paired-end), the recommended trinity plug’n’play file, this same GTF downloaded from gencode and the built-in fasta reference file.

I got worried that it was another type of internal error because it is spitting an error when getting the ref.genome.fa obtained directly from cvmfs

#11

@jennaj after a lot of tinkering, I discovered that the main problem is that star-fusion on galaxy have many bugs that were corrected on newer versions. For example, GTF files with genes without trancrispt ID should be filtered off in versions before 0.7, but on newer versions this is not needed. Is there any possibility of updating the version of star in galaxy? It is on version 1.9.1 but the Galaxy version is 0.5.4 (3).
Maybe I could create an ansible playbook for installation of a newer version, how can I share this with galaxy admins?

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#12

Hi @GACG1

There are a few choices:

  1. For immediate use, filter the GTF of unwanted data lines and do remove the header lines. Those don’t always cause problems during mapping but will often cause problems with later analysis steps.

  2. To request that the tool wrapper is upgraded, or to contribute to that yourself, open an issue ticket at the tool’s repository (load the tool in Galaxy, use the Options menu > See in ToolShed, and the location of the tool’s repo will be linked). If you plan to contribute, this is how: Tools in Galaxy. The IUC also has a Gitter chat if you want to get some feedback first, or while working on this: galaxy-iuc/iuc - Gitter

Note: The version of the tool wrapper is distinct from the underlying tool version. The version of the underlying tool is reported on the “Job Details” page within Galaxy (after execution), and in the tool’s development repository. The conda version is what is used in Galaxy for most tools. Often updated underlying tools require that the wrapper is also adjusted, or at least the dependencies.

Once the updated tool is incorporated into the ToolShed, all usegalaxy.* servers will pick up and install the new wrapper version (and underlying tool version if upgraded). And if you want to add that to your own Galaxy, it can be installed directly.

Thanks for taking the time to do the detective work and reporting that back here!!

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#13

2 posts were split to a new topic: GTF data in Galaxy