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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Nanopolish error #89

Open CrimsonTyphoon1727 opened 2 years ago

CrimsonTyphoon1727 commented 2 years ago

Hello everyone,

New user here. I have been trying to run artic pipeline here.

Right after align_trim, I get lines and lines of error message and assembly finishes. Even though I have viral assembly, I don't get any vcf outputs pulling out variants.

006: H5PL.c line 475 in H5PLfind(): can't open directory: /home/saisankar/miniconda3/envs/artic-ncov2019/lib/hdf5/plugin major: Plugin for dynamically loaded library minor: Can't open directory or file HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140321979332352: #000: H5Dio.c line 173 in H5Dread(): can't read data major: Dataset minor: Read failed #001: H5Dio.c line 554 in H5Dread(): can't read data major: Dataset minor: Read failed #002: H5Dchunk.c line 1875 in H5Dchunk_read(): unable to read raw data chunk major: Low-level I/O minor: Read failed #003: H5Dchunk.c line 2905 in H5D__chunk_lock(): data pipeline read failed major: Data filters minor: Filter operation failed #004: H5Z.c line 1347 in H5Z_pipeline(): required filter 'vbz' is not registered major: Data filters minor: Read failed #005: H5PL.c line 358 in H5PL_load(): search in paths failed major: Plugin for dynamically loaded library minor: Can't get value #006: H5PL.c line 475 in H5PLfind(): can't open directory: /home/saisankar/miniconda3/envs/artic-ncov2019/lib/hdf5/plugin major: Plugin for dynamically loaded library minor: Can't open directory or file HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 140322105222912: #000: H5Dio.c line 173 in H5Dread(): can't read data major: Dataset minor: Read failed #001: H5Dio.c line 554 in H5Dread(): can't read data major: Dataset minor: Read failed #002: H5Dchunk.c line 1875 in H5Dchunk_read(): unable to read raw data chunk major: Low-level I/O minor: Read failed #003: H5Dchunk.c line 2905 in H5D__chunk_lock(): data pipeline read failed major: Data filters minor: Filter operation failed #004: H5Z.c line 1347 in H5Z_pipeline(): required filter 'vbz' is not registered major: Data filters minor: Read failed #005: H5PL.c line 358 in H5PL_load(): search in paths failed major: Plugin for dynamically loaded library minor: Can't get value

At the end, I get the following message:

006: H5PL.c line 475 in H5PL__find(): can't open directory: /home/saisankar/miniconda3/envs/artic-ncov2019/lib/hdf5/plugin major: Plugin for dynamically loaded library minor: Can't open directory or file [post-run summary] total reads: 37688, unparseable: 0, qc fail: 0, could not calibrate: 0, no alignment: 0, bad fast5: 18844 Running: artic_vcf_merge Virus /home/saisankar/Tools/artic-ncov2019/primer_schemes//nCoV-2019/V3/nCoV-2019.scheme.bed 2> Virus.primersitereport.txt nCoV-2019_1:Virus.nCoV-2019_1.vcf nCoV-2019_2:Virus.nCoV-2019_2.vcf Running: artic_vcf_filter --nanopolish Virus.merged.vcf Virus.pass.vcf Virus.fail.vcf Running: bgzip -f Virus.pass.vcf Running: tabix -p vcf Virus.pass.vcf.gz Running: artic_make_depth_mask --store-rg-depths /home/saisankar/Tools/artic-ncov2019/primer_schemes//nCoV-2019/V3/nCoV-2019.reference.fasta Virus.primertrimmed.rg.sorted.bam Virus.coverage_mask.txt Running: artic_mask /home/saisankar/Tools/artic-ncov2019/primer_schemes//nCoV-2019/V3/nCoV-2019.reference.fasta Virus.coverage_mask.txt Virus.fail.vcf Virus.preconsensus.fasta Running: bcftools consensus -f Virus.preconsensus.fasta Virus.pass.vcf.gz -m Virus.coverage_mask.txt -o Virus.consensus.fasta Note: the --sample option not given, applying all records regardless of the genotype Warning: Sequence "MN908947.3" not in Virus.pass.vcf.gz Applied 0 variants Running: artic_fasta_header Virus.consensus.fasta "Virus/ARTIC/nanopolish" Running: cat Virus.consensus.fasta /home/saisankar/Tools/artic-ncov2019/primer_schemes//nCoV-2019/V3/nCoV-2019.reference.fasta > Virus.muscle.in.fasta Running: muscle -in Virus.muscle.in.fasta -out Virus.muscle.out.fasta MUSCLE v3.8.1551 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. Virus.muscle.in 2 seqs, lengths min 29903, max 29903, avg 29903 00:00:00 20 MB(1%) Iter 1 100.00% K-mer dist pass 1 00:00:00 20 MB(1%) Iter 1 100.00% K-mer dist pass 2 00:00:13 1004 MB(62%) Iter 1 100.00% Align node 00:00:13 1004 MB(62%) Iter 1 100.00% Root alignment

Please let me know how I can proceed to overcome this error!

Thanks everyone!

herman-roev commented 2 years ago

I have the same problem. There is no hdf5 directory in miniconda3/envs/artic-ncov2019/lib/

AnyaKovalenko commented 2 years ago

Hi. No worries, you just need to copy/move the hdf5 plugin from /usr/local/hdf5/lib/plugin into the miniconda/envs/artic-ncov2019/lib/hdf5.
Before do this, create the 'hdf5' folder inside miniconda/envs/artic-ncov2019/lib/ Good luck.

CrimsonTyphoon1727 commented 2 years ago

I have the same problem. There is no hdf5 directory in miniconda3/envs/artic-ncov2019/lib/

Hey! Sorry, I forgot to update the answer. ARTIC uses gzip-compressed files. My fast5 files were .vbz compressed files. I used ont-fast5-api to convert the compression format from .vbz to gzip. That helped with the analysis.