annotation bed has incorrect number of fields

[slsevilla]

• Rule:
  • rule peak_ExonIntron
• project:

  /data/RBL_NCI/Wolin/mESC_clip_3_clip3_v2.0

• error log:

  /data/RBL_NCI/Wolin/mESC_clip_3_clip3_v2.0/log/20220613_1244/16_peak_ExonIntron.41785323.AnnoStrand=SameStrand,sp=YKO_Clip.err

• error:

  Error: line number 925339 of file /data/RBL_NCI/Wolin/mESC_clip_3_clip3_v2.0/04_annotation/02_peaks/YKO_Clip_annotable.bed has 4 fields, but 8 were expected.
  Error in names(x) <- value : 
  'names' attribute [15] must be the same length as the vector [0]
  Calls: system.time -> IE_calling -> colnames<- -> colnames<-
  In addition: Warning message:
  In fread(paste0(tmp_dir, file_id, "peaks_OLexon.txt"), header = F,  :
  File '/lscratch/41785323/YKO_Clip_peaks_OLexon.txt' has size 0. Returning a NULL data.frame.
  Timing stopped at: 9.575 0.498 10.26

[slsevilla]

Interestingly another project had similar failures, but then went on to finish with no intervention after a second attempt through the code. I assume something is being created or edited during the failure but this is weird.

• project:
  • 11-30-21_7849iCLIP_v2.0
• log file (FAILED):

  /data/RBL_NCI/Wolin/11-30-21_7849iCLIP_v2.0/log/20220613_1246/16_peak_ExonIntron.41785454.AnnoStrand=OppoStrand,sp=KO.out

• error:

  Error: line number 1428360 of file /data/RBL_NCI/Wolin/11-30-21_7849iCLIP_v2.0/04_annotation/02_peaks/KO_annotable.bed has 6 fields, but 8 were expected.
  Error in names(x) <- value : 
  'names' attribute [15] must be the same length as the vector [0]
  Calls: system.time -> IE_calling -> colnames<- -> colnames<-
  In addition: Warning message:

• log file (COMPLETED):

  /data/RBL_NCI/Wolin/11-30-21_7849iCLIP_v2.0/log/20220613_1246/16_peak_ExonIntron.41785454.AnnoStrand=OppoStrand,sp=KO.err

[slsevilla]

Another project had this error.

• Rule:
  • rule peak_ExonIntron
• project
  • /data/RBL_NCI/Wolin/mESC_clip_2_v2.0
• log file
  • /data/RBL_NCI/Wolin/mESC_clip_2_v2.0/log/20220613_1248/16_peak_ExonIntron.42033870.AnnoStrand=SameStrand,sp=Ro_Clip_2.err
• error

  Error line number 1353130 of file /data/RBL_NCI/Wolin/mESC_clip_2_v2.0/04_annotation/02_peaks/Ro_Clip_2_annotable.bed has 3 fields, but 8 were expected.
  Error in names(x) <- value : 
  'names' attribute [15] must be the same length as the vector [0]
  Calls: system.time -> IE_calling -> colnames<- -> colnames<-
  In addition: Warning message:
  In fread(paste0(tmp_dir, file_id, "peaks_OLexon.txt"), header = F,  :
  File '/lscratch/42033870/Ro_Clip_2_peaks_OLexon.txt' has size 0. Returning a NULL data.frame.
  Timing stopped at: 9.894 0.555 10.53

[slsevilla]

issue is that both "same" and "opp" strand files were running simultaneously and overwriting one another in the output dir. will merge both files into one rule to avoid this issue

completed with commit 0c88461913b62c954b06752699cfbed6f7f805ab