Have never had trouble using the chip-seq pipeline but with newly generated sequencing reads for a TF the pipeline fails. If I run this pipeline without input controls using histone pipeline type it works fine. Any help would be greatly appreciated and happy to fill in missing gaps of info to solve the issue.
OS/Platform
OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
Conda version: If you used Conda ($ conda --version).
Pipeline version: [e.g. v1.6.0]
Caper version: [e.g. v1.2.0]
chip-seq-pipeline-v1.2.0
using the UCSD TSCC cluster - TSCC uses the TORQUE Resource Manager (also known by its historical name Portable Batch System, or PBS) with the Maui Cluster Scheduler to define and manage job queues
If you ran caper run without Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.
If you ran caper submit with a running Caper server then first find your workflow ID (1st column) with caper list and run caper debug [WORKFLOW_ID].
Paste troubleshooting result.
[2021-11-15 20:46:44,13] [error] WorkflowManagerActor Workflow 3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd failed (during ExecutingWorkflowState): Job chip.spp_pooled:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/execution/stderr.
Traceback (most recent call last):
File "/software/chip-seq-pipeline/src/encode_spp.py", line 115, in <module>
main()
File "/software/chip-seq-pipeline/src/encode_spp.py", line 90, in main
args.fraglen, args.cap_num_peak, args.nth, args.out_dir)
File "/software/chip-seq-pipeline/src/encode_spp.py", line 67, in spp
run_shell_cmd(cmd0)
File "/software/chip-seq-pipeline/src/encode_common.py", line 252, in run_shell_cmd
raise Exception(err_str)
Exception: PID=55953, PGID=55953, RC=1
STDERR=Loading required package: caTools
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 0
Calls: find.binding.positions ... calculate.enrichment.estimates -> lapply -> FUN -> cbind -> cbind -> data.frame
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
STDOUT=################
ChIP data: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/inputs/1290795626/A1_S29_L003_R1_001.merged.nodup.pooled.tagAlign.gz
Control data: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/inputs/-70684730/A12input_S33_L003_R1_001.merged.nodup.pooled.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 278
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: NA
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/execution
narrowPeak output file name: NA
regionPeak output file name: A1_S29_L003_R1_001.merged.nodup.pooled_x_A12input_S33_L003_R1_001.merged.nodup.pooled.300K.regionPeak.gz.tmp
Rdata filename: NA
plot pdf filename: NA
result filename: NA
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/inputs/1290795626/A1_S29_L003_R1_001.merged.nodup.pooled.tagAlign.gz
opened /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/tmp.b0c01532/RtmpjDCQfz/A1_S29_L003_R1_001.merged.nodup.pooled.tagAlignda9341e2f0e1
done. read 34521764 fragments
ChIP data read length 101
[1] TRUE
Reading Control tagAlign/BAM file /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/inputs/-70684730/A12input_S33_L003_R1_001.merged.nodup.pooled.tagAlign.gz
opened /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pooled/tmp.b0c01532/RtmpjDCQfz/A12input_S33_L003_R1_001.merged.nodup.pooled.tagAlignda934c2e4208
done. read 3842312 fragments
Control data read length 101
Calculating peak characteristics
Minimum cross-correlation value 0.3530526
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.38962993307496
Top 3 estimates for fragment length 278
Window half size 585
Phantom peak location 105
Phantom peak Correlation 0.3735254
Normalized Strand cross-correlation coefficient (NSC) 1.103603
Relative Strand cross-correlation Coefficient (RSC) 1.786629
Phantom Peak Quality Tag 2
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.01381287 processing chr1 in 5 steps [.....] done ( 2254 positions)
processing chr10 in 4 steps [....] done ( 2062 positions)
processing chr11 in 3 steps [...] done ( 3013 positions)
processing chr12 in 3 steps [...] done ( 1651 positions)
processing chr13 in 3 steps [...] done ( 1418 positions)
processing chr14 in 4 steps [....] done ( 1393 positions)
processing chr15 in 3 steps [...] done ( 1715 positions)
processing chr16 in 3 steps [...] done ( 1190 positions)
processing chr17 in 3 steps [...] done ( 1868 positions)
processing chr18 in 3 steps [...] done ( 1124 positions)
processing chr19 in 2 steps [..] done ( 1217 positions)
processing chr1_GL456210_random in 1 steps [.] done ( positions)
processing chr1_GL456211_random in 1 steps [.] done ( 1 positions)
processing chr1_GL456212_random in 1 steps [.] done ( 0 positions)
processing chr1_GL456221_random in 1 steps [.] done ( 0 positions)
processing chr2 in 5 steps [.....] done ( 2931 positions)
processing chr3 in 4 steps [....] done ( 1707 positions)
processing chr4 in 4 steps [....] done ( 2771 positions)
processing chr4_GL456216_random in 1 steps [.] done ( 9 positions)
processing chr4_JH584295_random in 1 steps [.] done ( 1 positions)
processing chr5 in 4 steps [....] done ( 2749 positions)
processing chr5_GL456354_random in 1 steps [.] done ( 0 positions)
processing chr5_JH584299_random in 1 steps [.] done ( positions)
processing chr6 in 4 steps [....] done ( 1828 positions)
processing chr7 in 4 steps [....] done ( 2744 positions)
processing chr8 in 4 steps [....] done ( 2387 positions)
processing chr9 in 4 steps [....] done ( 2157 positions)
processing chrUn_GL456239 in 1 steps [.] done ( 6 positions)
processing chrUn_GL456360 in 1 steps [.] done ( positions)
processing chrUn_GL456366 in 1 steps [.] done ( positions)
processing chrUn_GL456367 in 1 steps [.] done ( 0 positions)
processing chrUn_GL456368 in 1 steps [.] done ( positions)
processing chrUn_GL456370 in 1 steps [.] done ( 5 positions)
processing chrUn_GL456378 in 1 steps [.] done ( 1 positions)
processing chrUn_GL456379 in 1 steps [.] done ( 0 positions)
processing chrUn_GL456383 in 1 steps [.] done ( 18 positions)
processing chrUn_GL456389 in 1 steps [.] done ( 25 positions)
processing chrUn_GL456390 in 1 steps [.] done ( 12 positions)
processing chrUn_GL456392 in 1 steps [.] done ( 17 positions)
processing chrUn_GL456393 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456394 in 1 steps [.] done ( positions)
processing chrUn_GL456396 in 1 steps [.] done ( 8 positions)
processing chrUn_JH584304 in 1 steps [.] done ( 87 positions)
processing chrX in 5 steps [.....] done ( 1097 positions)
processing chrX_GL456233_random in 1 steps [.] done ( 1 positions)
processing chrY in 3 steps [...] done ( 14 positions)
excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 72.39624 processing chr1 in 5 steps [.....] done ( 133720 positions)
processing chr10 in 4 steps [....] done ( 91669 positions)
processing chr11 in 3 steps [...] done ( 106641 positions)
processing chr12 in 3 steps [...] done ( 84280 positions)
processing chr13 in 3 steps [...] done ( 84632 positions)
processing chr14 in 4 steps [....] done ( 80282 positions)
processing chr15 in 3 steps [...] done ( 76517 positions)
processing chr16 in 3 steps [...] done ( 65592 positions)
processing chr17 in 3 steps [...] done ( 75258 positions)
processing chr18 in 3 steps [...] done ( 63538 positions)
processing chr19 in 2 steps [..] done ( 47433 positions)
processing chr1_GL456210_random in 1 steps [.] done ( 52 positions)
processing chr1_GL456211_random in 1 steps [.] done ( 89 positions)
processing chr1_GL456212_random in 1 steps [.] done ( 37 positions)
processing chr1_GL456221_random in 1 steps [.] done ( 52 positions)
processing chr2 in 5 steps [.....] done ( 136143 positions)
processing chr3 in 4 steps [....] done ( 102345 positions)
processing chr4 in 4 steps [....] done ( 116627 positions)
processing chr4_GL456216_random in 1 steps [.] done ( 33 positions)
processing chr4_JH584292_random in 1 steps [.] done ( 9 positions)
processing chr4_JH584295_random in 1 steps [.] done ( 2 positions)
processing chr5 in 4 steps [....] done ( 119629 positions)
processing chr5_GL456354_random in 1 steps [.] done ( 4 positions)
processing chr5_JH584296_random in 1 steps [.] done ( 1 positions)
processing chr5_JH584297_random in 1 steps [.] done ( 3 positions)
processing chr5_JH584299_random in 1 steps [.] done ( 61 positions)
processing chr6 in 4 steps [....] done ( 104701 positions)
processing chr7 in 4 steps [....] done ( 110894 positions)
processing chr8 in 4 steps [....] done ( 99332 positions)
processing chr9 in 4 steps [....] done ( 99253 positions)
processing chrUn_GL456239 in 1 steps [.] done ( 47 positions)
processing chrUn_GL456359 in 1 steps [.] done ( 14 positions)
processing chrUn_GL456360 in 1 steps [.] done ( 20 positions)
processing chrUn_GL456366 in 1 steps [.] done ( 20 positions)
processing chrUn_GL456367 in 1 steps [.] done ( 27 positions)
processing chrUn_GL456368 in 1 steps [.] done ( 6 positions)
processing chrUn_GL456370 in 1 steps [.] done ( 14 positions)
processing chrUn_GL456372 in 1 steps [.] done ( 16 positions)
processing chrUn_GL456378 in 1 steps [.] done ( 23 positions)
processing chrUn_GL456379 in 1 steps [.] done ( 36 positions)
processing chrUn_GL456381 in 1 steps [.] done ( 30 positions)
processing chrUn_GL456382 in 1 steps [.] done ( 10 positions)
processing chrUn_GL456383 in 1 steps [.] done ( 17 positions)
processing chrUn_GL456385 in 1 steps [.] done ( 16 positions)
processing chrUn_GL456387 in 1 steps [.] done ( 29 positions)
processing chrUn_GL456389 in 1 steps [.] done ( 15 positions)
processing chrUn_GL456390 in 1 steps [.] done ( 9 positions)
processing chrUn_GL456392 in 1 steps [.] done ( 15 positions)
processing chrUn_GL456393 in 1 steps [.] done ( 61 positions)
processing chrUn_GL456394 in 1 steps [.] done ( 14 positions)
processing chrUn_GL456396 in 1 steps [.] done ( 20 positions)
processing chrUn_JH584304 in 1 steps [.] done ( 31 positions)
processing chrX in 5 steps [.....] done ( 81422 positions)
processing chrX_GL456233_random in 1 steps [.] done ( 164 positions)
processing chrY in 3 steps [...] done ( 37 positions)
excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000003
Job chip.spp:1:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/execution/stderr.
Traceback (most recent call last):
File "/software/chip-seq-pipeline/src/encode_spp.py", line 115, in <module>
main()
File "/software/chip-seq-pipeline/src/encode_spp.py", line 90, in main
args.fraglen, args.cap_num_peak, args.nth, args.out_dir)
File "/software/chip-seq-pipeline/src/encode_spp.py", line 67, in spp
run_shell_cmd(cmd0)
File "/software/chip-seq-pipeline/src/encode_common.py", line 252, in run_shell_cmd
raise Exception(err_str)
Exception: PID=53985, PGID=53985, RC=1
STDERR=Loading required package: caTools
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 0
Calls: find.binding.positions ... calculate.enrichment.estimates -> lapply -> FUN -> cbind -> cbind -> data.frame
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
STDOUT=################
ChIP data: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/inputs/-955210546/A2_S30_L003_R1_001.merged.nodup.tagAlign.gz
Control data: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/inputs/-1497687848/ctl_for_rep2.tagAlign.gz
strandshift(min): -500
strandshift(step): 5
strandshift(max) 1500
user-defined peak shift 250
exclusion(min): 10
exclusion(max): NaN
num parallel nodes: NA
FDR threshold: 0.01
NumPeaks Threshold: 3e+05
Output Directory: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/execution
narrowPeak output file name: NA
regionPeak output file name: A2_S30_L003_R1_001.merged.nodup_x_ctl_for_rep2.300K.regionPeak.gz.tmp
Rdata filename: NA
plot pdf filename: NA
result filename: NA
Overwrite files?: TRUE
Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/inputs/-955210546/A2_S30_L003_R1_001.merged.nodup.tagAlign.gz
opened /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/tmp.fa0bca6f/RtmpYou8In/A2_S30_L003_R1_001.merged.nodup.tagAlignd2ee2fc15669
done. read 10737662 fragments
ChIP data read length 101
[1] TRUE
Reading Control tagAlign/BAM file /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/inputs/-1497687848/ctl_for_rep2.tagAlign.gz
opened /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp/shard-1/tmp.fa0bca6f/RtmpYou8In/ctl_for_rep2.tagAlignd2ee5221dea4
done. read 3842312 fragments
Control data read length 101
Calculating peak characteristics
Minimum cross-correlation value 0.1539102
Minimum cross-correlation shift 1500
Top 3 cross-correlation values 0.18106679260315
Top 3 estimates for fragment length 250
Window half size 545
Phantom peak location 105
Phantom peak Correlation 0.1672511
Normalized Strand cross-correlation coefficient (NSC) 1.176444
Relative Strand cross-correlation Coefficient (RSC) 2.035596
Phantom Peak Quality Tag 2
Removing read stacks
Finding peaks
finding background exclusion regions ... done
determining peaks on provided 1 control datasets:
using reversed signal for FDR calculations
bg.weight= 0.04478349 processing chr1 in 5 steps [.....] done ( 2157 positions)
processing chr10 in 4 steps [....] done ( 1976 positions)
processing chr11 in 3 steps [...] done ( 2909 positions)
processing chr12 in 3 steps [...] done ( 1599 positions)
processing chr13 in 3 steps [...] done ( 1364 positions)
processing chr14 in 4 steps [....] done ( 1347 positions)
processing chr15 in 3 steps [...] done ( 1688 positions)
processing chr16 in 3 steps [...] done ( 1138 positions)
processing chr17 in 3 steps [...] done ( 1817 positions)
processing chr18 in 3 steps [...] done ( 1074 positions)
processing chr19 in 2 steps [..] done ( 1191 positions)
processing chr1_GL456210_random in 1 steps [.] done ( positions)
processing chr1_GL456211_random in 1 steps [.] done ( 1 positions)
processing chr1_GL456212_random in 1 steps [.] done ( 0 positions)
processing chr1_GL456221_random in 1 steps [.] done ( 0 positions)
processing chr2 in 5 steps [.....] done ( 2803 positions)
processing chr3 in 4 steps [....] done ( 1629 positions)
processing chr4 in 4 steps [....] done ( 2678 positions)
processing chr4_GL456216_random in 1 steps [.] done ( 9 positions)
processing chr4_JH584295_random in 1 steps [.] done ( 1 positions)
processing chr5 in 4 steps [....] done ( 2655 positions)
processing chr5_GL456354_random in 1 steps [.] done ( 0 positions)
processing chr5_JH584299_random in 1 steps [.] done ( positions)
processing chr6 in 4 steps [....] done ( 1759 positions)
processing chr7 in 4 steps [....] done ( 2680 positions)
processing chr8 in 4 steps [....] done ( 2290 positions)
processing chr9 in 4 steps [....] done ( 2075 positions)
processing chrUn_GL456239 in 1 steps [.] done ( 6 positions)
processing chrUn_GL456360 in 1 steps [.] done ( positions)
processing chrUn_GL456366 in 1 steps [.] done ( positions)
processing chrUn_GL456367 in 1 steps [.] done ( 0 positions)
processing chrUn_GL456368 in 1 steps [.] done ( positions)
processing chrUn_GL456370 in 1 steps [.] done ( 4 positions)
processing chrUn_GL456378 in 1 steps [.] done ( 1 positions)
processing chrUn_GL456379 in 1 steps [.] done ( 0 positions)
processing chrUn_GL456383 in 1 steps [.] done ( 16 positions)
processing chrUn_GL456389 in 1 steps [.] done ( 20 positions)
processing chrUn_GL456390 in 1 steps [.] done ( 12 positions)
processing chrUn_GL456392 in 1 steps [.] done ( 16 positions)
processing chrUn_GL456393 in 1 steps [.] done ( 8 positions)
processing chrUn_GL456394 in 1 steps [.] done ( positions)
processing chrUn_GL456396 in 1 steps [.] done ( 9 positions)
processing chrUn_JH584304 in 1 steps [.] done ( 83 positions)
processing chrX in 5 steps [.....] done ( 1057 positions)
processing chrX_GL456233_random in 1 steps [.] done ( 1 positions)
processing chrY in 3 steps [...] done ( 12 positions)
excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 22.32966 processing chr1 in 5 steps [.....] done ( 65134 positions)
processing chr10 in 4 steps [....] done ( 45853 positions)
processing chr11 in 3 steps [...] done ( 62439 positions)
processing chr12 in 3 steps [...] done ( 43166 positions)
processing chr13 in 3 steps [...] done ( 42334 positions)
processing chr14 in 4 steps [....] done ( 39377 positions)
processing chr15 in 3 steps [...] done ( 41042 positions)
processing chr16 in 3 steps [...] done ( 32583 positions)
processing chr17 in 3 steps [...] done ( 41752 positions)
processing chr18 in 3 steps [...] done ( 31887 positions)
processing chr19 in 2 steps [..] done ( 26155 positions)
processing chr1_GL456210_random in 1 steps [.] done ( 19 positions)
processing chr1_GL456211_random in 1 steps [.] done ( 37 positions)
processing chr1_GL456212_random in 1 steps [.] done ( 19 positions)
processing chr1_GL456221_random in 1 steps [.] done ( 17 positions)
processing chr2 in 5 steps [.....] done ( 72896 positions)
processing chr3 in 4 steps [....] done ( 47152 positions)
processing chr4 in 4 steps [....] done ( 64085 positions)
processing chr4_GL456216_random in 1 steps [.] done ( 10 positions)
processing chr4_JH584292_random in 1 steps [.] done ( 3 positions)
processing chr4_JH584295_random in 1 steps [.] done ( 1 positions)
processing chr5 in 4 steps [....] done ( 67255 positions)
processing chr5_GL456354_random in 1 steps [.] done ( 1 positions)
processing chr5_JH584296_random in 1 steps [.] done ( 1 positions)
processing chr5_JH584297_random in 1 steps [.] done ( 0 positions)
processing chr5_JH584299_random in 1 steps [.] done ( 15 positions)
processing chr6 in 4 steps [....] done ( 52499 positions)
processing chr7 in 4 steps [....] done ( 62334 positions)
processing chr8 in 4 steps [....] done ( 53691 positions)
processing chr9 in 4 steps [....] done ( 54463 positions)
processing chrUn_GL456239 in 1 steps [.] done ( 31 positions)
processing chrUn_GL456359 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456360 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456366 in 1 steps [.] done ( 11 positions)
processing chrUn_GL456367 in 1 steps [.] done ( 11 positions)
processing chrUn_GL456368 in 1 steps [.] done ( 3 positions)
processing chrUn_GL456370 in 1 steps [.] done ( 4 positions)
processing chrUn_GL456372 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456378 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456379 in 1 steps [.] done ( 14 positions)
processing chrUn_GL456381 in 1 steps [.] done ( 19 positions)
processing chrUn_GL456382 in 1 steps [.] done ( 4 positions)
processing chrUn_GL456383 in 1 steps [.] done ( 6 positions)
processing chrUn_GL456385 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456387 in 1 steps [.] done ( 26 positions)
processing chrUn_GL456389 in 1 steps [.] done ( 9 positions)
processing chrUn_GL456390 in 1 steps [.] done ( 7 positions)
processing chrUn_GL456392 in 1 steps [.] done ( 8 positions)
processing chrUn_GL456393 in 1 steps [.] done ( 35 positions)
processing chrUn_GL456394 in 1 steps [.] done ( 13 positions)
processing chrUn_GL456396 in 1 steps [.] done ( 9 positions)
processing chrUn_JH584304 in 1 steps [.] done ( 36 positions)
processing chrX in 5 steps [.....] done ( 29988 positions)
processing chrX_GL456233_random in 1 steps [.] done ( 57 positions)
processing chrY in 3 steps [...] done ( 10 positions)
excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= 2.000105
Job chip.spp_pr1:1:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /projects/ps-yeolab4/t_cell_p01_project/home/jkanbar/rawdata/chipseq/ezh2/malat1KD/cromwell-executions/chip/3a5fa5c7-1e1d-43b2-a9b1-a232ea7882fd/call-spp_pr1/shard-1/execution/stderr.
Traceback (most recent call last):
File "/software/chip-seq-pipeline/src/encode_spp.py", line 115, in <module>
main()
File "/software/chip-seq-pipeline/src/encode_spp.py", line 90, in main
args.fraglen, args.cap_num_peak, args.nth, args.out_dir)
File "/software/chip-seq-pipeline/src/encode_spp.py", line 67, in spp
run_shell_cmd(cmd0)
File "/software/chip-seq-pipeline/src/encode_common.py", line 252, in run_shell_cmd
raise Exception(err_str)
Exception: PID=53986, PGID=53986, RC=1
STDERR=Loading required package: caTools
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 0
Calls: find.binding.positions ... calculate.enrichment.estimates -> lapply -> FUN -> cbind -> cbind -> data.frame
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
Describe the bug
Have never had trouble using the chip-seq pipeline but with newly generated sequencing reads for a TF the pipeline fails. If I run this pipeline without input controls using histone pipeline type it works fine. Any help would be greatly appreciated and happy to fill in missing gaps of info to solve the issue.
OS/Platform
$ conda --version).chip-seq-pipeline-v1.2.0 using the UCSD TSCC cluster - TSCC uses the TORQUE Resource Manager (also known by its historical name Portable Batch System, or PBS) with the Maui Cluster Scheduler to define and manage job queues
Caper configuration file
Paste contents of
~/.caper/default.conf.Input JSON file
Paste contents of your input JSON file.
Troubleshooting result
If you ran
caper runwithout Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.If you ran
caper submitwith a running Caper server then first find your workflow ID (1st column) withcaper listand runcaper debug [WORKFLOW_ID].Paste troubleshooting result.