search

phasebook / phasebook

Haplotype aware de novo assembly of diploid genome from long reads
GNU General Public License v3.0
53 stars 11 forks source link

crash during cluster processing #27

Open HMPNK opened 2 years ago

HMPNK commented 2 years ago

Hi I am trying to assemble a 1Gb genome. Phasebook stopped with:

..... 2022-05-19 01:01:12,129 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9593 variant calling started... 2022-05-19 01:01:12,617 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9595 variant calling started... 2022-05-19 01:01:12,617 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9596 variant calling started... 2022-05-19 01:01:12,680 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9593 reads phasing started... 2022-05-19 01:01:13,084 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9596 reads phasing started... 2022-05-19 01:01:13,198 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9595 reads phasing started... 2022-05-19 01:01:13,242 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9597 variant calling started... 2022-05-19 01:01:13,295 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9594 variant calling started... 2022-05-19 01:01:13,411 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9600 variant calling started... 2022-05-19 01:01:13,485 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9601 variant calling started... 2022-05-19 01:01:13,486 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9598 variant calling started... 2022-05-19 01:01:13,797 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9594 reads phasing started... 2022-05-19 01:01:13,868 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9597 reads phasing started... 2022-05-19 01:01:13,907 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9600 reads phasing started... 2022-05-19 01:01:13,991 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9601 reads phasing started... 2022-05-19 01:01:14,063 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9598 reads phasing started... [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". 2022-05-19 01:01:48,951 - /home/kuhl/phasebook/scripts/assembly.py[line:150] - INFO: cluster:9410 variant calling started... 2022-05-19 01:01:49,521 - /home/kuhl/phasebook/scripts/assembly.py[line:153] - INFO: cluster:9410 reads phasing started... [main_samview] fail to read the header from "-". multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/kuhl/miniconda2/envs/phasebook/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, *kwds)) File "/home/kuhl/miniconda2/envs/phasebook/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/kuhl/phasebook/scripts/assembly.py", line 154, in get_superead hap2reads = phase_reads(i, vcf, bam, ref, outdir, True,binpath) File "/home/kuhl/phasebook/scripts/phasing.py", line 74, in phase_reads read = line.strip().split()[0] IndexError: list index out of range """

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

Traceback (most recent call last): File "/home/kuhl/phasebook/scripts/phasebook.py", line 379, in sys.exit(main()) File "/home/kuhl/phasebook/scripts/phasebook.py", line 312, in main args.correct_mode) File "/home/kuhl/phasebook/scripts/parallel.py", line 17, in run_on_local pool.map(get_superead, params, chunksize=1) # ordered File "/home/kuhl/miniconda2/envs/phasebook/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/kuhl/miniconda2/envs/phasebook/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value IndexError: list index out of range

How to fix this? How can I restart from here?

HMPNK commented 2 years ago

Same issue happens when running the example file.

HMPNK commented 2 years ago

I just found that this issue is due to Installation problems. I was unable to use python3.7 because it was conflicting with my CUDA Version according to bioconda. I installed everything on another System without CUDA and it worked (at least the example)