JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa"

[liliaevgeniou]

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

[leepc12]

This pipeline has been deprecated. Please use a new pipeline. https://github.com/ENCODE-DCC/chip-seq-pipeline2

Or try with new pipeline's conda environment. This old pipeline's requirements.txt is too old and there has been tons of update on Conda's side.