JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa" #50
Description
Got an error at the JSD step. I used nth=1 (I tried with more but they somehow did not work either, or said "not enough resources"), and on a server with 1 core, 80gb memory.
I think the pipeline install_dependencies.sh installed numpy 1.18.5.
Error pasted below:
03:18:53.464 ExecutionerLocal 'Local[28]': Task selected 'chipseq.bds.20200801_100653_737/task.postalign_bam.jsd.line_812.id_32' on host 'localhost'
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa
Traceback (most recent call last):
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/bin/plotFingerprint", line 4, in <module>
from deeptools.plotFingerprint import main
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/deeptools/plotFingerprint.py", line 15, in <module>
import deeptools.countReadsPerBin as countR
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 13, in <module>
import pyBigWig
ImportError: numpy.core.multiarray failed to import
Task failed:
Program & line : '/home/unix/levgenio/software/TF_chipseq_pipeline/modules/postalign_bam.bds', line 812
Task Name : 'jsd'
Task ID : 'chipseq.bds.20200801_100653_737/task.postalign_bam.jsd.line_812.id_32'
Task PID : '22031'
Task hint : 'plotFingerprint -b /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep1/10222853_Microglia_H3K27ac1_161020Tsa_D16-11125_hg19_bestmap.nodup.bam /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep2/10222853_Microglia_H3K27ac2_161020Tsa_D16-11126_hg19_bestmap'
Task resources : 'cpus: 1 mem: -1.0 B wall-timeout: 8640000'
State : 'ERROR'
Dependency state : 'ERROR'
Retries available : '1'
Input files : '[/home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep1/10222853_Microglia_H3K27ac1_161020Tsa_D16-11125_hg19_bestmap.nodup.bam, /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep2/10222853_Microglia_H3K27ac2_161020Tsa_D16-11126_hg19_bestmap.nodup.bam, /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/ctl1/10222853_Microglia_Input1_161020Tsa_D16-11119_hg19_bestmap.nodup.bam]'
Output files : '[/home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/qc/10222853_Microglia_out_jsd.png, /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/qc/10222853_Microglia_out_jsd.qc]'
Script file : '/broad/compbio/levgenio/code/AQUAS_pipeline/chipseq.bds.20200801_100653_737/task.postalign_bam.jsd.line_812.id_32.sh'
Exit status : '1'
Program :
# SYS command. line 813
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=/home/unix/levgenio/software/TF_chipseq_pipeline/.:/home/unix/levgenio/software/TF_chipseq_pipeline/modules:/home/unix/levgenio/software/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
# SYS command. line 814
plotFingerprint -b /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep1/10222853_Microglia_H3K27ac1_161020Tsa_D16-11125_hg19_bestmap.nodup.bam /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/rep2/10222853_Microglia_H3K27ac2_161020Tsa_D16-11126_hg19_bestmap.nodup.bam /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/ctl1/10222853_Microglia_Input1_161020Tsa_D16-11119_hg19_bestmap.nodup.bam --JSDsample /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/align/ctl1/10222853_Microglia_Input1_161020Tsa_D16-11119_hg19_bestmap.nodup.bam \
--labels rep1 rep2 ctl1 \
--outQualityMetrics /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/qc/10222853_Microglia_out_jsd.qc \
--minMappingQuality 30 \
-T "Fingerprints of different samples" \
--blackListFileName /home/unix/levgenio/data/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
--numberOfProcessors 1 \
--plotFile /home/unix/levgenio/data/AQUAS/AQUAS_out/10222853_Microglia_out/qc/10222853_Microglia_out_jsd.png
# SYS command. line 823
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
StdErr (100000000 lines) :
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa
Traceback (most recent call last):
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/bin/plotFingerprint", line 4, in <module>
from deeptools.plotFingerprint import main
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/deeptools/plotFingerprint.py", line 15, in <module>
import deeptools.countReadsPerBin as countR
File "/home/unix/levgenio/software/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/deeptools/countReadsPerBin.py", line 13, in <module>
import pyBigWig
ImportError: numpy.core.multiarray failed to import
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.jsd.line_812.id_32' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_2_rep1.line_205.id_12, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_2_rep1.line_205.id_12' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_xcor.xcor_rep1.line_102.id_16, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_xcor.xcor_rep1.line_102.id_16' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.markdup_bam_picard_ctl1.line_409.id_25, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.markdup_bam_picard_ctl1.line_409.id_25' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_2_ctl2.line_205.id_30, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_2_ctl2.line_205.id_30' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_1_ctl2.line_155.id_28, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.dedup_bam_1_ctl2.line_155.id_28' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.bam_to_tag_rep1.line_595.id_14, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.bam_to_tag_rep1.line_595.id_14' finished.
03:19:03.543 Wait: Waiting for task to finish: chipseq.bds.20200801_100653_737/task.postalign_bam.bam_to_tag_rep1.line_595.id_13, state: FINISHED
03:19:03.543 Wait: Task 'chipseq.bds.20200801_100653_737/task.postalign_bam.bam_to_tag_rep1.line_595.id_13' finished.
Fatal error: /home/unix/levgenio/software/TF_chipseq_pipeline/chipseq.bds, line 414, pos 3. Task/s failed.
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
03:19:03.705 Writing report file 'chipseq.bds.20200801_100653_737.report.html'
03:19:03.739 Program 'chipseq.bds.20200801_100653_737' finished, exit value: 1, tasks executed: 23, tasks failed: 1, tasks failed names: jsd.
03:19:03.739 Finished. Exit code: 1
03:19:03.739 ExecutionerLocal 'Local[28]': Killed