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Sequence correction provided by ONT Research
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Medaka fails to complete. #385

Closed tnn111 closed 2 years ago

tnn111 commented 2 years ago

Medaka version 1.7.1 fails with the attached message. It's a CentOS system with an A100, Driver Version: 460.32.03 CUDA Version: 11.2.

Any suggestions? The command line is:

/usr/bin/time medaka_consensus -i Ashby0005_nano.fastq -d results_flye/assembly.fasta -o medaka -t 24 -m r941_min_sup_g507 &> medaka.log &

[21:51:27 - TrimOlap] contig_14166:0.0-5179.0 and contig_14166:5210.0-5855.0 cannot be concatenated as there is no overlap and they do not abut. [21:51:27 - TrimOlap] contig_14166:5210.0-5855.0 and contig_14166:6204.0-7699.0 cannot be concatenated as there is no overlap and they do not abut. [21:51:27 - DataIndx] Loaded 1/1 (100.00%) sample files. [21:51:27 - TrimOlap] contig_8404:0.0-1108.0 and contig_8404:1416.0-4745.0 cannot be concatenated as there is no overlap and they do not abut. [E::fai_retrieve] Failed to retrieve block: unexpected end of file Traceback (most recent call last): File "/home/torben/opt/mambaforge/envs/medaka/bin/medaka", line 11, in sys.exit(main()) File "/home/torben/opt/mambaforge/envs/medaka/lib/python3.8/site-packages/medaka/medaka.py", line 724, in main args.func(args) File "/home/torben/opt/mambaforge/envs/medaka/lib/python3.8/site-packages/medaka/stitch.py", line 229, in stitch contigs, gt = fill_gaps(contigs, args.draft, args.fill_char) File "/home/torben/opt/mambaforge/envs/medaka/lib/python3.8/site-packages/medaka/stitch.py", line 128, in fill_gaps draft_seq = draft.fetch(ref_name) File "pysam/libcfaidx.pyx", line 317, in pysam.libcfaidx.FastaFile.fetch BlockingIOError: [Errno 11] b'Resource temporarily unavailable' Failed to stitch consensus chunks. Command exited with non-zero status 1 42173.47user 5962.48system 1:25:21elapsed 939%CPU (0avgtext+0avgdata 19757920maxresident)k 5763728inputs+88325544outputs (381major+1071758484minor)pagefaults 0swaps

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tnn111 commented 2 years ago

I redid my conda setup and the problem went away. It looks like a Python issue.

DanaBlu commented 8 months ago

Hi @tnn111! I have exactly the same problem with the latest version of Medaka (1.11.3). I also tried it with an older version of Medaka (1.7.2) in combination with an old version of Python (3.8). Do you remember what exactly you did with your conda setup to solve the problem? Best, Dana!

michoug commented 6 months ago

Hi @DanaBlu Use the -x option to regenerate the indexes at the start, it was the issue for me Best Greg