search

parklab / PaSDqc

A python library for single cell whole-genome sequencing quality evaluation
MIT License
9 stars 3 forks source link

invalid value encountered in true_divide #7

Closed tamaraprieto closed 6 years ago

tamaraprieto commented 6 years ago

Hi,

I am getting the following error when running the program.

This is the command: PaSDqc QC \ -d test/ \ -c PaSDqc-1.1.0-source/PaSDqc/db/categorical_spectra_0.1x.txt \ -q 30 \ -r TEST

This is the std error ` Processing: 1 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr1.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 1 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 1 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr1.map.pos Processing: 2 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr2.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 2 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 2 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr2.map.pos Processing: 3 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr3.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 3 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 3 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr3.map.pos Processing: 4 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr4.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 4 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 4 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr4.map.pos Processing: 5 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr5.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 5 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 5 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr5.map.pos Processing: 6 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr6.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 6 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 6 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr6.map.pos Processing: 7 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr7.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 7 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 7 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr7.map.pos Processing: 8 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr8.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 8 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 8 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr8.map.pos Processing: 9 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr9.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 9 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 9 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr9.map.pos Processing: 10 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr10.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 10 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 10 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr10.map.pos Processing: 11 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr11.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 11 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 11 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr11.map.pos Processing: 12 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr12.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 12 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 12 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr12.map.pos Processing: 13 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr13.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 13 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 13 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr13.map.pos Processing: 14 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr14.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 14 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 14 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr14.map.pos Processing: 15 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr15.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 15 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 15 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr15.map.pos Processing: 16 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr16.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 16 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 16 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr16.map.pos Processing: 17 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr17.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 17 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 17 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr17.map.pos Processing: 18 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr18.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 18 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 18 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr18.map.pos Processing: 19 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr19.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 19 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 19 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr19.map.pos Processing: 20 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr20.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 20 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 20 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr20.map.pos Processing: 21 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr21.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 21 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 21 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos Processing: 22 Executing: samtools view -q 30 -L /PaSDqc/lib/python3.5/site-packages/PaSDqc/db/grch37.chr22.map.bed /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 22 | cut -f 3,4 | uniq > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos Executing: samtools view -uh -q 30 /mnt/gluster/distributed/home/uvi/be/Single-Cell/RESULTS/PaSDqc/PaSDqc/TP-ML-F3-IP.dedup.ps.bam 22 | samtools depth -b PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos - > PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos.cov; rm PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr22.map.pos PaSDqc/psd/TP-ML-F3-IP.dedup.ps.chroms.spec 1.p arm /home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:93: RuntimeWarning:

divide by zero encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:93: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:104: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/astropy/stats/lombscargle/implementations/fast_impl.py:122: RuntimeWarning:

invalid value encountered in true_divide

/home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 3226 results

1.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 1 results

10.p arm 10.q arm 11.p arm 11.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 6986 results

12.p arm 12.q arm 13.p arm 13.q arm 14.p arm 14.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7999 results

15.p arm 15.q arm 16.p arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 3221 results

16.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 5056 results

17.p arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 6323 results

17.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7648 results

18.p arm 18.q arm 19.p arm 19.q arm 2.p arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 8000 results

2.q arm /home/uvi/be/.local/lib/python3.5/site-packages/numpy/lib/function_base.py:4035: RuntimeWarning:

Invalid value encountered in median for 7759 results

20.p arm 20.q arm 21.p arm multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/PaSDqc/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/PaSDqc/bin/PaSDqc", line 102, in _build_and_save psd = PaSDqc.PSDTools.SamplePSD.build_from_dir(str(dir_in), sample=sample, clean=clean) File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 268, in build_from_dir df = cls._build_dataframe(file_list, build) File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 318, in _build_dataframe [psd.PSD_LS_chrom(f_cent, freq=freq) for psd in psd_list] File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 318, in [psd.PSD_LS_chrom(f_cent, freq=freq) for psd in psd_list] File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 207, in PSD_LS_chrom pwr_p, count_p = self.PSD_LS_manual(df_p, freq, l_seg, p_overlap, verbose=verbose) File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 164, in PSD_LS_manual starts, ends = ChromPSD._welch_seg_bounds(df.pos, l_seg, p_overlap) File "/PaSDqc/lib/python3.5/site-packages/PaSDqc/PSDTools.py", line 59, in _welch_seg_bounds ends[-1] = pos.iloc[-1] IndexError: index -1 is out of bounds for axis 0 with size 0 """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/PaSDqc/bin/PaSDqc", line 265, in args.func(args) File "/PaSDqc/bin/PaSDqc", line 210, in QC PSD(args) File "/PaSDqc/bin/PaSDqc", line 95, in PSD [p.get() for p in res] File "/PaSDqc/bin/PaSDqc", line 95, in [p.get() for p in res] File "/PaSDqc/lib/python3.5/multiprocessing/pool.py", line 644, in get raise self._value IndexError: index -1 is out of bounds for axis 0 with size 0`

Do you have any idea about what can be happening here? I just find this error for some of the single-cells, not all of them. Thanks in advance

maxwellsh commented 6 years ago

Hmm, looks like it's failing when trying to analyze 21p. The problem appears to be that there is no depth information for that chromosome arm. My guess is you may have very little (or no) coverage of that chromosome arm. You can check this by loading PaSDqc/cov/TP-ML-F3-IP.dedup.ps.chr21.map.pos.cov and plotting the pos column vs the depth column. I expect you will find virtually no reads on 22p.

Please let me know if this is the case. If not, we can troubleshoot further.

tamaraprieto commented 6 years ago

Coverage is quite low indeed. Here you are the plot:

chr21 depth

Is it not possible to run PaSDqc in such conditions?

maxwellsh commented 6 years ago

Unfortunately not. With such sparse coverage, the amplification patterns cannot be accurately inferred. Indeed, if the cell was sequenced to e.g. 1X average coverage, but one chromosome has such low coverage PaSDqc cannot function, that itself is indicative of a low quality sample.

On Wed, May 2, 2018, 6:17 AM tamaraprieto notifications@github.com wrote:

Coverage is quite low indeed. Here you are the plot:

[image: chr21 depth] https://user-images.githubusercontent.com/7628968/39518042-f8a075e4-4e01-11e8-89f3-ed53eaab3094.png

Is it not possible to run PaSDqc in such conditions?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/parklab/PaSDqc/issues/7#issuecomment-385931123, or mute the thread https://github.com/notifications/unsubscribe-auth/AZAmIFAmutCPyseHZwV8qQ7Kd6GgbmS3ks5tuYevgaJpZM4Tqr3h .

tamaraprieto commented 6 years ago

OK, thank you. Could you please consider to issue a warning under these circumstances so the user knows what is going on?

maxwellsh commented 6 years ago

Yes, I will do. Thank you for pointing out this issue!

On Thu, May 3, 2018, 5:52 AM tamaraprieto notifications@github.com wrote:

OK, thank you. Could you please consider to issue a warning under these circumstances so the user knows what is going on?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/parklab/PaSDqc/issues/7#issuecomment-386244342, or mute the thread https://github.com/notifications/unsubscribe-auth/AZAmIAbKZV4KPCDa27c8dD3Yt1y4w8h9ks5tutNegaJpZM4Tqr3h .