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