Error converting BAM to tagalign file

[CLAIRE-cuhk]

Description of the bug

Hello,
I have a problem with TMP where the chipseq pipeline stops at process > PHANTOMPEAKQUALTOOLS with an error message: "No space left on device". Could you please help me?

Error in log file:

Command used and terminal output

Error in log file:
[6d/b3ee0a] process > CHECK_DESIGN (design_combin... [100%] 1 of 1 ✔
[b1/eee33d] process > MAKE_GENOME_FILTER (genome.fa) [100%] 1 of 1 ✔
[64/50722f] process > FASTQC (HL60-MYB_IP_R1_T1)     [100%] 14 of 14 ✔
[8f/e2f715] process > TRIMGALORE (HL60-MYB_IP_R1_T1) [100%] 14 of 14 ✔
[23/d890f2] process > BWA_MEM (HL60-MYB_IP_R1_T1)    [100%] 14 of 14 ✔
[fc/22232a] process > SORT_BAM (HL60-MYB_IP_R1_T1)   [100%] 14 of 14 ✔
[99/9f93ec] process > MERGED_BAM (MOLM16-MYB_INPU... [100%] 14 of 14 ✔
[bf/44ffb8] process > MERGED_BAM_FILTER (MOLM16-M... [100%] 14 of 14 ✔
[14/d7f26d] process > MERGED_BAM_REMOVE_ORPHAN (M... [100%] 14 of 14 ✔
[99/4ada7b] process > PRESEQ (MOLM16-MYB_INPUT_R1)   [100%] 14 of 14 ✔
[64/68a15a] process > PICARD_METRICS (MOLM16-MYB_R1) [100%] 13 of 13
[ce/daab22] process > BIGWIG (MOLM16-MYB_R1)         [100%] 13 of 13
[2e/c74049] process > PLOTPROFILE (TF1-MYB_INPUT_R1) [100%] 9 of 9
[67/759571] process > PHANTOMPEAKQUALTOOLS (MOLM1... [100%] 13 of 13, failed: 1
[ae/bf3836] process > PLOTFINGERPRINT (THP1-MYB_I... [100%] 6 of 6
[76/286600] process > MACS2 (THP1-MYB_IP_R1 vs TH... [100%] 6 of 6
[ef/28e5d2] process > MACS2_ANNOTATE (AML3-MYB_R1... [100%] 1 of 1
[-        ] process > MACS2_QC                       -
[-        ] process > CONSENSUS_PEAKS                -
[-        ] process > CONSENSUS_PEAKS_ANNOTATE       -
[-        ] process > CONSENSUS_PEAKS_COUNTS         -
[-        ] process > CONSENSUS_PEAKS_DESEQ2         -
[-        ] process > IGV                            -
[c2/2b91a4] process > get_software_versions          [100%] 1 of 1 ✔
[-        ] process > MULTIQC                        -
[8e/e07af9] process > output_documentation           [100%] 1 of 1 ✔
-[nf-core/chipseq] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'PHANTOMPEAKQUALTOOLS (TF1-MYB_INPUT_R1)'

Caused by:
  Process `PHANTOMPEAKQUALTOOLS (TF1-MYB_INPUT_R1)` terminated with an error exit status (1)
Command executed:

  RUN_SPP=`which run_spp.R`
  Rscript -e "library(caTools); source(\"$RUN_SPP\")" -c="TF1-MYB_INPUT_R1.mLb.clN.sorted.bam" -savp="TF1-MYB_INPUT_R1.spp.pdf" -savd="TF1-MYB_INPUT_R1.spp.Rdata" -out="TF1-M
  cp spp_correlation_header.txt TF1-MYB_INPUT_R1_spp_correlation_mqc.tsv
  Rscript -e "load('TF1-MYB_INPUT_R1.spp.Rdata'); write.table(crosscorr\$cross.correlation, file=\"TF1-MYB_INPUT_R1_spp_correlation_mqc.tsv\", sep=",", quote=FALSE, row.names
  
  awk -v OFS='  ' '{print "TF1-MYB_INPUT_R1", $9}' TF1-MYB_INPUT_R1.spp.out | cat spp_nsc_header.txt - > TF1-MYB_INPUT_R1_spp_nsc_mqc.tsv
  awk -v OFS='  ' '{print "TF1-MYB_INPUT_R1", $10}' TF1-MYB_INPUT_R1.spp.out | cat spp_rsc_header.txt - > TF1-MYB_INPUT_R1_spp_rsc_mqc.tsv

Command exit status:
  1

Command output:
  ################
  ChIP data: TF1-MYB_INPUT_R1.mLb.clN.sorted.bam 
  Control data: NA 
  strandshift(min): -500 
  strandshift(step): 5 
  strandshift(max) 1500 
  user-defined peak shift NA 
  exclusion(min): 10 
  exclusion(max): NaN 
  num parallel nodes: 6 
  FDR threshold: 0.01 
  NumPeaks Threshold: NA 
  Output Directory: . 
  narrowPeak output file name: NA 
  regionPeak output file name: NA 
  Rdata filename: TF1-MYB_INPUT_R1.spp.Rdata 
  plot pdf filename: TF1-MYB_INPUT_R1.spp.pdf 
  result filename: TF1-MYB_INPUT_R1.spp.out 
  Overwrite files?: FALSE
  
  Reading ChIP tagAlign/BAM file TF1-MYB_INPUT_R1.mLb.clN.sorted.bam 

Command error:
  Loading required package: Rcpp
   awk: cmd. line:1: (FILENAME=- FNR=14759004) fatal: print to "standard output" failed: No space left on device
   Error converting BAM to tagalign file: /tmp/Rtmp3bSeIf/TF1-MYB_INPUT_R1.mLb.clN.sorted.bam1a6a66c63125
 
 Work dir:
   /lustre/scratch/scratch/ucnvlw0/Other_projects/AML_LOF_enhancer/MYB_chipseq_analysis/try1/work/cc/9963e5e05180da251118639151a4e8
 
 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Relevant files

No response

System information

No response

[JoseEspinosa]

This is probably because there is not enough space in TMP. You could try redirecting the $TMPDIR to somewhere where you have space in your working area on the cluster.

[JoseEspinosa]

You can also skip this step using --skip_spp.

[JoseEspinosa]

Actually, the parameter has been removed by mistake in the last iteration. It will add back when #339 is merged

[JoseEspinosa]

Will close it now. Feel free to reach out if you have any further questions.