/projects/Splicing_Analysis/
Downloading nextflow dependencies. It may require a few seconds, please wait .. 
Downloading nextflow dependencies. It may require a few seconds, please wait .. 

      N E X T F L O W
      version 24.04.4 build 5917
      created 01-08-2024 07:05 UTC (03:05 EDT)
      cite doi:10.1038/nbt.3820
      http://nextflow.io


Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /projects/Splicing_Analysis/
- you may complete the installation by moving it to a directory in your $PATH

N E X T F L O W  ~  version 20.04.1
Launching `/projects/Splicing_Analysis/splicing-pipelines-nf/main.nf` [stoic_bell] - revision: 74d36bf465
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Splicing-pipelines - N F  ~  version 0.1
=====================================
Run name                    : 23pal003004_Splicing
Date                        : 10-21-24
Final prefix                : 23pal003004_Splicing_10-21-24
Assembly name               : GRCh38
WARN: Access to undefined parameter `singularity_cache` -- Initialise it to a default value eg. `params.singularity_cache = some_value`
Singularity Cache Folder    : null
Reads                       : /projects/Splicing_Analysis/reads.csv
Bams                        : false
Single-end                  : false
GTF                         : /projects/gencode.v47.primary_assembly.annotation.gtf
STAR index                  : /projects/star_indexes/star_overhangs_2.7.9a/star_150/
Stranded                    : second-strand
strType                     : 1
Soft_clipping               : true
Save unmapped               : false
rMATS pairs file            : /projects/Splicing_Analysis/rmats_pairs.txt
Adapter                     : /projects/Splicing_Analysis/splicing-pipelines-nf/adapters/TruSeq3-PE.fa
Read Length                 : 150
Overhang                    : 149
Minimum length              : 20
Sliding window              : true
rMATS variable read length  : true
rMATS statoff               : false
rMATS paired stats          : true
rMATS novel splice sites    : false
rMATS Minimum Intron Length : 50
rMATS Maximum Exon Length   : 500
Mismatch                    : 5
filterScore                 : 0.66
sjdbOverhangMin             : 3
STAR memory                 : Not provided, Using STAR task max memory
stringtie merge memory      : 30 GB
Test                        : false
Download from               : FASTQs directly provided
Key file                    : Not provided
Outdir                      : /projects/Splicing_Analysis/
Max Retries                 : 5
Max CPUs                    : 72
Max memory                  : 760 GB
Max time                    : 3d
Mega time                   : 20h
Google Cloud disk-space     : false
Debug                       : false
WARN: The access of `config` object is deprecated
Error strategy              : finish
Workdir cleanup             : false


executor >  slurm (27)
[0e/6f8e66] process > fastqc (DD98_progenitors)      [100%] 4 of 4 ✔
[d5/e032e1] process > trimmomatic (DD39_progenitors) [100%] 4 of 4 ✔
[69/30ebd1] process > fastqc_trimmed (DD39_progen... [100%] 4 of 4 ✔
[1d/a691cb] process > star (DD39_progenitors)        [100%] 4 of 4 ✔
[a3/225374] process > stringtie (DD39_progenitors)   [100%] 4 of 4 ✔
[3e/10acb0] process > prep_de                        [100%] 1 of 1 ✔
[82/876689] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[22/6a90ca] process > rmats (P_Old_vs_P_Young gen... [  0%] 0 of 2
[d5/754b9f] process > multiqc (1)                    [100%] 1 of 1 ✔
[6b/12b14f] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[46/761f27] process > collect_tool_versions_env2     [100%] 1 of 1 ✔

executor >  slurm (27)
[0e/6f8e66] process > fastqc (DD98_progenitors)      [100%] 4 of 4 ✔
[d5/e032e1] process > trimmomatic (DD39_progenitors) [100%] 4 of 4 ✔
[69/30ebd1] process > fastqc_trimmed (DD39_progen... [100%] 4 of 4 ✔
[1d/a691cb] process > star (DD39_progenitors)        [100%] 4 of 4 ✔
[a3/225374] process > stringtie (DD39_progenitors)   [100%] 4 of 4 ✔
[3e/10acb0] process > prep_de                        [100%] 1 of 1 ✔
[82/876689] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[22/6a90ca] process > rmats (P_Old_vs_P_Young gen... [  0%] 0 of 2
[d5/754b9f] process > multiqc (1)                    [100%] 1 of 1 ✔
[6b/12b14f] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[46/761f27] process > collect_tool_versions_env2     [100%] 1 of 1 ✔
Error executing process > 'rmats (P_Old_vs_P_Young gencode)'

Caused by:
  Process `rmats (P_Old_vs_P_Young gencode)` terminated with an error exit status (1)

Command executed:

  echo DD98_progenitors.Aligned.sortedByCoord.out.bam,DD21_progenitors.Aligned.sortedByCoord.out.bam > b1.txt
  echo DD48_progenitors.Aligned.sortedByCoord.out.bam,DD39_progenitors.Aligned.sortedByCoord.out.bam > b2.txt
  rmats.py         --b1 b1.txt --b2 b2.txt         --gtf gencode.v47.primary_assembly.annotation.gtf         --od ./         --tmp tmp         --libType fr-secondstrand         -t paired         --nthread 30         --readLength 150         --mil 50         --mel 500 --variable-read-length  --paired-stats  --allow-clipping
  rmats_config="config_for_rmats_and_postprocessing.txt"
  echo b1 b1.txt > $rmats_config
  echo b2 b2.txt >> $rmats_config
  echo rmats_gtf       gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo ref_gtf         gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo fasta           GRCh38 >> $rmats_config
  echo reads           paired >> $rmats_config
  echo readlen         150 >> $rmats_config
  echo rmats_id        P_Old_vs_P_Young >> $rmats_config
  
  LU_postprocessing.R
  
  # save .command.* logs
  task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash

Command exit status:
  1

Command output:
  Average number of transcripts per gene is 4.914914
  Average number of exons per transcript is 5.579182
  Average number of exons per transcript excluding one-exon tx is 5.948980
  Average number of gene per geneGroup is 10.417184
  statistic: 0.04871249198913574
  
  read outcome totals across all BAMs
  USED: 182296943
  NOT_PAIRED: 5149055
  NOT_NH_1: 256246142
  NOT_EXPECTED_CIGAR: 21947137
  NOT_EXPECTED_READ_LENGTH: 0
  NOT_EXPECTED_STRAND: 0
  EXON_NOT_MATCHED_TO_ANNOTATION: 688568009
  JUNCTION_NOT_MATCHED_TO_ANNOTATION: 592092171
  CLIPPED: 0
  total: 1746299457
  outcomes by BAM written to: tmp/2024-10-21-23_30_12_919476_read_outcomes_by_bam.txt
  
  novel: 2237.2689270973206
  The splicing graph and candidate read have been saved into tmp/2024-10-21-23_30_12_919476_*.rmats
  save: 1.3625683784484863
  loadsg: 0.024065732955932617
  
  ==========
  Done processing each gene from dictionary to compile AS events
  Found 99126 exon skipping events
  Found 9496 exon MX events
  Found 35250 alt SS events
  There are 21118 alt 3 SS events and 14132 alt 5 SS events.
  Found 13244 RI events
  ==========
  
  ase: 3.2730495929718018
  count: 2.6802449226379395
  Processing count files.
  Done processing count files.
  [1] "/projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5"
  [1] "2024-10-22 00:08:16 EDT"
  [1] "2024-10-22"
  [1] "Loading human genome, hg38"
  [1] "CA loaded"
  [1] "RI loaded"
  [1] "A3SS loaded"
  [1] "A5SS loaded"
  [1] "MXE loaded"
  [1] "Processing CA...."
  [1] "Table of number of events per chromosome"
  < table of extent 0 >
  [1] "NOTE: We removes caffolds, assembly patches and alternate loci (haplotypes). These were needed for mapping purposes."

Command error:
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
      colnames, colSums, dirname, do.call, duplicated, eval, evalq,
      Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
      lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
      pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
      rowSums, sapply, setdiff, sort, table, tapply, union, unique,
      unsplit, which, which.max, which.min
  
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: rtracklayer
  Error in `$<-.data.frame`(`*tmp*`, "Event_type", value = "CA") : 
    replacement has 1 row, data has 0
  Calls: get_postprocessing_table -> $<- -> $<-.data.frame
  Execution halted

Work dir:
  /projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

executor >  slurm (27)
[0e/6f8e66] process > fastqc (DD98_progenitors)      [100%] 4 of 4 ✔
[d5/e032e1] process > trimmomatic (DD39_progenitors) [100%] 4 of 4 ✔
[69/30ebd1] process > fastqc_trimmed (DD39_progen... [100%] 4 of 4 ✔
[1d/a691cb] process > star (DD39_progenitors)        [100%] 4 of 4 ✔
[a3/225374] process > stringtie (DD39_progenitors)   [100%] 4 of 4 ✔
[3e/10acb0] process > prep_de                        [100%] 1 of 1 ✔
[82/876689] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[22/6a90ca] process > rmats (P_Old_vs_P_Young gen... [ 50%] 1 of 2, failed: 1
[d5/754b9f] process > multiqc (1)                    [100%] 1 of 1 ✔
[6b/12b14f] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[46/761f27] process > collect_tool_versions_env2     [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'rmats (P_Old_vs_P_Young gencode)'

Caused by:
  Process `rmats (P_Old_vs_P_Young gencode)` terminated with an error exit status (1)

Command executed:

  echo DD98_progenitors.Aligned.sortedByCoord.out.bam,DD21_progenitors.Aligned.sortedByCoord.out.bam > b1.txt
  echo DD48_progenitors.Aligned.sortedByCoord.out.bam,DD39_progenitors.Aligned.sortedByCoord.out.bam > b2.txt
  rmats.py         --b1 b1.txt --b2 b2.txt         --gtf gencode.v47.primary_assembly.annotation.gtf         --od ./         --tmp tmp         --libType fr-secondstrand         -t paired         --nthread 30         --readLength 150         --mil 50         --mel 500 --variable-read-length  --paired-stats  --allow-clipping
  rmats_config="config_for_rmats_and_postprocessing.txt"
  echo b1 b1.txt > $rmats_config
  echo b2 b2.txt >> $rmats_config
  echo rmats_gtf       gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo ref_gtf         gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo fasta           GRCh38 >> $rmats_config
  echo reads           paired >> $rmats_config
  echo readlen         150 >> $rmats_config
  echo rmats_id        P_Old_vs_P_Young >> $rmats_config
  
  LU_postprocessing.R
  
  # save .command.* logs
  task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash

Command exit status:
  1

Command output:
  Average number of transcripts per gene is 4.914914
  Average number of exons per transcript is 5.579182
  Average number of exons per transcript excluding one-exon tx is 5.948980
  Average number of gene per geneGroup is 10.417184
  statistic: 0.04871249198913574
  
  read outcome totals across all BAMs
  USED: 182296943
  NOT_PAIRED: 5149055
  NOT_NH_1: 256246142
  NOT_EXPECTED_CIGAR: 21947137
  NOT_EXPECTED_READ_LENGTH: 0
  NOT_EXPECTED_STRAND: 0
  EXON_NOT_MATCHED_TO_ANNOTATION: 688568009
  JUNCTION_NOT_MATCHED_TO_ANNOTATION: 592092171
  CLIPPED: 0
  total: 1746299457
  outcomes by BAM written to: tmp/2024-10-21-23_30_12_919476_read_outcomes_by_bam.txt
  
  novel: 2237.2689270973206
  The splicing graph and candidate read have been saved into tmp/2024-10-21-23_30_12_919476_*.rmats
  save: 1.3625683784484863
  loadsg: 0.024065732955932617
  
  ==========
  Done processing each gene from dictionary to compile AS events
  Found 99126 exon skipping events
  Found 9496 exon MX events
  Found 35250 alt SS events
  There are 21118 alt 3 SS events and 14132 alt 5 SS events.
  Found 13244 RI events
  ==========
  
  ase: 3.2730495929718018
  count: 2.6802449226379395
  Processing count files.
  Done processing count files.
  [1] "/projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5"
  [1] "2024-10-22 00:08:16 EDT"
  [1] "2024-10-22"
  [1] "Loading human genome, hg38"
  [1] "CA loaded"
  [1] "RI loaded"
  [1] "A3SS loaded"
  [1] "A5SS loaded"
  [1] "MXE loaded"
  [1] "Processing CA...."
  [1] "Table of number of events per chromosome"
  < table of extent 0 >
  [1] "NOTE: We removes caffolds, assembly patches and alternate loci (haplotypes). These were needed for mapping purposes."

Command error:
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
      colnames, colSums, dirname, do.call, duplicated, eval, evalq,
      Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
      lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
      pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
      rowSums, sapply, setdiff, sort, table, tapply, union, unique,
      unsplit, which, which.max, which.min
  
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: rtracklayer
  Error in `$<-.data.frame`(`*tmp*`, "Event_type", value = "CA") : 
    replacement has 1 row, data has 0
  Calls: get_postprocessing_table -> $<- -> $<-.data.frame
  Execution halted

Work dir:
  /projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

executor >  slurm (27)
[0e/6f8e66] process > fastqc (DD98_progenitors)      [100%] 4 of 4 ✔
[d5/e032e1] process > trimmomatic (DD39_progenitors) [100%] 4 of 4 ✔
[69/30ebd1] process > fastqc_trimmed (DD39_progen... [100%] 4 of 4 ✔
[1d/a691cb] process > star (DD39_progenitors)        [100%] 4 of 4 ✔
[a3/225374] process > stringtie (DD39_progenitors)   [100%] 4 of 4 ✔
[3e/10acb0] process > prep_de                        [100%] 1 of 1 ✔
[82/876689] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[ae/2eea78] process > rmats (P_Old_vs_P_Young gff... [100%] 2 of 2, failed: 2 ✘
[d5/754b9f] process > multiqc (1)                    [100%] 1 of 1 ✔
[6b/12b14f] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[46/761f27] process > collect_tool_versions_env2     [100%] 1 of 1 ✔
-[splicing-pipelines-nf] Pipeline completed with errors-

Error executing process > 'rmats (P_Old_vs_P_Young gencode)'

Caused by:
  Process `rmats (P_Old_vs_P_Young gencode)` terminated with an error exit status (1)

Command executed:

  echo DD98_progenitors.Aligned.sortedByCoord.out.bam,DD21_progenitors.Aligned.sortedByCoord.out.bam > b1.txt
  echo DD48_progenitors.Aligned.sortedByCoord.out.bam,DD39_progenitors.Aligned.sortedByCoord.out.bam > b2.txt
  rmats.py         --b1 b1.txt --b2 b2.txt         --gtf gencode.v47.primary_assembly.annotation.gtf         --od ./         --tmp tmp         --libType fr-secondstrand         -t paired         --nthread 30         --readLength 150         --mil 50         --mel 500 --variable-read-length  --paired-stats  --allow-clipping
  rmats_config="config_for_rmats_and_postprocessing.txt"
  echo b1 b1.txt > $rmats_config
  echo b2 b2.txt >> $rmats_config
  echo rmats_gtf       gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo ref_gtf         gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo fasta           GRCh38 >> $rmats_config
  echo reads           paired >> $rmats_config
  echo readlen         150 >> $rmats_config
  echo rmats_id        P_Old_vs_P_Young >> $rmats_config
  
  LU_postprocessing.R
  
  # save .command.* logs
  task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash

Command exit status:
  1

Command output:
  Average number of transcripts per gene is 4.914914
  Average number of exons per transcript is 5.579182
  Average number of exons per transcript excluding one-exon tx is 5.948980
  Average number of gene per geneGroup is 10.417184
  statistic: 0.04871249198913574
  
  read outcome totals across all BAMs
  USED: 182296943
  NOT_PAIRED: 5149055
  NOT_NH_1: 256246142
  NOT_EXPECTED_CIGAR: 21947137
  NOT_EXPECTED_READ_LENGTH: 0
  NOT_EXPECTED_STRAND: 0
  EXON_NOT_MATCHED_TO_ANNOTATION: 688568009
  JUNCTION_NOT_MATCHED_TO_ANNOTATION: 592092171
  CLIPPED: 0
  total: 1746299457
  outcomes by BAM written to: tmp/2024-10-21-23_30_12_919476_read_outcomes_by_bam.txt
  
  novel: 2237.2689270973206
  The splicing graph and candidate read have been saved into tmp/2024-10-21-23_30_12_919476_*.rmats
  save: 1.3625683784484863
  loadsg: 0.024065732955932617
  
  ==========
  Done processing each gene from dictionary to compile AS events
  Found 99126 exon skipping events
  Found 9496 exon MX events
  Found 35250 alt SS events
  There are 21118 alt 3 SS events and 14132 alt 5 SS events.
  Found 13244 RI events
  ==========
  
  ase: 3.2730495929718018
  count: 2.6802449226379395
  Processing count files.
  Done processing count files.
  [1] "/projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5"
  [1] "2024-10-22 00:08:16 EDT"
  [1] "2024-10-22"
  [1] "Loading human genome, hg38"
  [1] "CA loaded"
  [1] "RI loaded"
  [1] "A3SS loaded"
  [1] "A5SS loaded"
  [1] "MXE loaded"
  [1] "Processing CA...."
  [1] "Table of number of events per chromosome"
  < table of extent 0 >
  [1] "NOTE: We removes caffolds, assembly patches and alternate loci (haplotypes). These were needed for mapping purposes."

Command error:
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
      colnames, colSums, dirname, do.call, duplicated, eval, evalq,
      Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
      lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
      pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
      rowSums, sapply, setdiff, sort, table, tapply, union, unique,
      unsplit, which, which.max, which.min
  
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: rtracklayer
  Error in `$<-.data.frame`(`*tmp*`, "Event_type", value = "CA") : 
    replacement has 1 row, data has 0
  Calls: get_postprocessing_table -> $<- -> $<-.data.frame
  Execution halted

Work dir:
  /projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

executor >  slurm (27)
[0e/6f8e66] process > fastqc (DD98_progenitors)      [100%] 4 of 4 ✔
[d5/e032e1] process > trimmomatic (DD39_progenitors) [100%] 4 of 4 ✔
[69/30ebd1] process > fastqc_trimmed (DD39_progen... [100%] 4 of 4 ✔
[1d/a691cb] process > star (DD39_progenitors)        [100%] 4 of 4 ✔
[a3/225374] process > stringtie (DD39_progenitors)   [100%] 4 of 4 ✔
[3e/10acb0] process > prep_de                        [100%] 1 of 1 ✔
[82/876689] process > stringtie_merge (1)            [100%] 1 of 1 ✔
[ae/2eea78] process > rmats (P_Old_vs_P_Young gff... [100%] 2 of 2, failed: 2 ✘
[d5/754b9f] process > multiqc (1)                    [100%] 1 of 1 ✔
[6b/12b14f] process > collect_tool_versions_env1     [100%] 1 of 1 ✔
[46/761f27] process > collect_tool_versions_env2     [100%] 1 of 1 ✔
-[splicing-pipelines-nf] Pipeline completed with errors-
Error executing process > 'rmats (P_Old_vs_P_Young gencode)'

Caused by:
  Process `rmats (P_Old_vs_P_Young gencode)` terminated with an error exit status (1)

Command executed:

  echo DD98_progenitors.Aligned.sortedByCoord.out.bam,DD21_progenitors.Aligned.sortedByCoord.out.bam > b1.txt
  echo DD48_progenitors.Aligned.sortedByCoord.out.bam,DD39_progenitors.Aligned.sortedByCoord.out.bam > b2.txt
  rmats.py         --b1 b1.txt --b2 b2.txt         --gtf gencode.v47.primary_assembly.annotation.gtf         --od ./         --tmp tmp         --libType fr-secondstrand         -t paired         --nthread 30         --readLength 150         --mil 50         --mel 500 --variable-read-length  --paired-stats  --allow-clipping
  rmats_config="config_for_rmats_and_postprocessing.txt"
  echo b1 b1.txt > $rmats_config
  echo b2 b2.txt >> $rmats_config
  echo rmats_gtf       gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo ref_gtf         gencode.v47.primary_assembly.annotation.gtf >> $rmats_config
  echo fasta           GRCh38 >> $rmats_config
  echo reads           paired >> $rmats_config
  echo readlen         150 >> $rmats_config
  echo rmats_id        P_Old_vs_P_Young >> $rmats_config
  
  LU_postprocessing.R
  
  # save .command.* logs
  task_hash=`basename ${PWD} | cut -c1-6`; mkdir command-logs-$task_hash ; cp .command.*{err,log,sh} command-logs-$task_hash

Command exit status:
  1

Command output:
  Average number of transcripts per gene is 4.914914
  Average number of exons per transcript is 5.579182
  Average number of exons per transcript excluding one-exon tx is 5.948980
  Average number of gene per geneGroup is 10.417184
  statistic: 0.04871249198913574
  
  read outcome totals across all BAMs
  USED: 182296943
  NOT_PAIRED: 5149055
  NOT_NH_1: 256246142
  NOT_EXPECTED_CIGAR: 21947137
  NOT_EXPECTED_READ_LENGTH: 0
  NOT_EXPECTED_STRAND: 0
  EXON_NOT_MATCHED_TO_ANNOTATION: 688568009
  JUNCTION_NOT_MATCHED_TO_ANNOTATION: 592092171
  CLIPPED: 0
  total: 1746299457
  outcomes by BAM written to: tmp/2024-10-21-23_30_12_919476_read_outcomes_by_bam.txt
  
  novel: 2237.2689270973206
  The splicing graph and candidate read have been saved into tmp/2024-10-21-23_30_12_919476_*.rmats
  save: 1.3625683784484863
  loadsg: 0.024065732955932617
  
  ==========
  Done processing each gene from dictionary to compile AS events
  Found 99126 exon skipping events
  Found 9496 exon MX events
  Found 35250 alt SS events
  There are 21118 alt 3 SS events and 14132 alt 5 SS events.
  Found 13244 RI events
  ==========
  
  ase: 3.2730495929718018
  count: 2.6802449226379395
  Processing count files.
  Done processing count files.
  [1] "/projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5"
  [1] "2024-10-22 00:08:16 EDT"
  [1] "2024-10-22"
  [1] "Loading human genome, hg38"
  [1] "CA loaded"
  [1] "RI loaded"
  [1] "A3SS loaded"
  [1] "A5SS loaded"
  [1] "MXE loaded"
  [1] "Processing CA...."
  [1] "Table of number of events per chromosome"
  < table of extent 0 >
  [1] "NOTE: We removes caffolds, assembly patches and alternate loci (haplotypes). These were needed for mapping purposes."

Command error:
  Loading required package: parallel
  
  Attaching package: ‘BiocGenerics’
  
  The following objects are masked from ‘package:parallel’:
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from ‘package:stats’:
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from ‘package:base’:
  
      anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
      colnames, colSums, dirname, do.call, duplicated, eval, evalq,
      Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
      lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
      pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
      rowSums, sapply, setdiff, sort, table, tapply, union, unique,
      unsplit, which, which.max, which.min
  
  Loading required package: S4Vectors
  Loading required package: stats4
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: GenomicRanges
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Loading required package: rtracklayer
  Error in `$<-.data.frame`(`*tmp*`, "Event_type", value = "CA") : 
    replacement has 1 row, data has 0
  Calls: get_postprocessing_table -> $<- -> $<-.data.frame
  Execution halted

Work dir:
  /projects/Splicing_Analysis/work/22/6a90cabac1c18c65e004da3ca843f5

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`