[M::mm_idx_gen::0.005*1.34] collected minimizers [M::mm_idx_gen::0.009*2.15] sorted minimizers [M::main::0.009*2.15] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.010*2.11] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.010*2.06] distinct minimizers: 5587 (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332; total length: 29903 [M::worker_pipeline::0.743*5.47] mapped 8829 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-ont -t 16 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747_filtered.fastq.gz [M::main] Real time: 0.745 sec; CPU: 4.064 sec; Peak RSS: 0.055 GB [11:40:44 - ValidArgs] Reads will be filtered to only those with RG tag: nCoV-2019_1 [11:40:44 - Predict] Reducing threads to 2, anymore is a waste. [11:40:44 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism. [11:40:44 - Predict] Setting tensorflow inter/intra-op threads to 2/1. [11:40:44 - Predict] Processing region(s): MN908947.3:0-29903 [11:40:44 - Predict] Using model: /opt/conda/lib/python3.8/site-packages/medaka/data/r1041_e82_400bps_fast_g632_model.tar.gz. [11:40:44 - Predict] Processing 1 long region(s) with batching. [11:40:45 - MdlStrTF] Model [11:40:45 - MdlStrTF] loading weights from /tmp/tmpw1xxl24r/model/variables/variables [11:40:45 - BAMFile] Creating pool of 16 BAM file sets. [11:40:45 - Sampler] Initializing sampler for consensus of region MN908947.3:0-29903. [11:40:45 - PWorker] Running inference for 0.0M draft bases. [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 45-1190. [11:40:45 - Feature] Processed MN908947.3:45.0-1190.0 (median depth 7.0) [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 2166-3256. [11:40:45 - Feature] Processed MN908947.3:2166.0-3256.0 (median depth 274.0) [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 4179-5346. [11:40:45 - Feature] Processed MN908947.3:4179.0-5346.0 (median depth 56.0) [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 6294-7391. [11:40:45 - Feature] Processed MN908947.3:6294.0-7391.0 (median depth 198.5) [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 8267-9383. [11:40:45 - Feature] Processed MN908947.3:8267.0-9383.0 (median depth 24.0) [11:40:45 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 10354-11458. [11:40:46 - Feature] Processed MN908947.3:10354.0-11458.0 (median depth 542.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 12455-13610. [11:40:46 - Feature] Processed MN908947.3:12455.0-13610.0 (median depth 162.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 14551-15723. [11:40:46 - Feature] Processed MN908947.3:14551.0-15723.0 (median depth 120.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 16634-17742. [11:40:46 - Feature] Processed MN908947.3:16634.0-17742.0 (median depth 178.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 18596-19670. [11:40:46 - Feature] Processed MN908947.3:18596.0-19670.0 (median depth 477.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 20558-21626. [11:40:46 - Feature] Processed MN908947.3:20558.0-21626.0 (median depth 231.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 22520-23620. [11:40:46 - Feature] Processed MN908947.3:22520.0-23620.0 (median depth 305.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 24642-25780. [11:40:46 - Feature] Processed MN908947.3:24642.0-25780.0 (median depth 235.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 26744-27879. [11:40:46 - Feature] Processed MN908947.3:26744.0-27879.0 (median depth 262.0) [11:40:46 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 28690-29734. [11:40:46 - Feature] Processed MN908947.3:28690.0-29734.0 (median depth 168.0) [11:40:46 - Sampler] Took 1.35s to make features. [11:40:50 - PWorker] Processed 1 batches [11:40:50 - PWorker] All done, 0 remainder regions. [11:40:50 - Predict] Finished processing all regions. [11:40:52 - DataIndx] Loaded 1/1 (100.00%) sample files. [11:40:52 - Variants] Processing MN908947.3:0-. [11:40:52 - TrimOlap] MN908947.3:454.1-1190.0 and MN908947.3:2166.0-2495.3 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:2917.0-3256.0 and MN908947.3:4179.0-4727.2 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:4815.0-5346.0 and MN908947.3:6294.0-6653.2 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:7011.0-7391.0 and MN908947.3:8267.0-8885.1 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:8762.1-9383.0 and MN908947.3:10354.0-10632.2 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:11150.0-11458.0 and MN908947.3:12455.0-12862.0 cannot be concatenated as there is no overlap and they do not abut. /opt/conda/lib/python3.8/site-packages/medaka/labels.py:387: RuntimeWarning: divide by zero encountered in log10 q = -10 * np.log10(err) [11:40:52 - TrimOlap] MN908947.3:13223.0-13610.0 and MN908947.3:14551.0-14985.0 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:15290.0-15723.0 and MN908947.3:16634.0-17028.1 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:17354.1-17742.0 and MN908947.3:18596.0-18893.5 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:19363.1-19670.0 and MN908947.3:20558.0-20937.0 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:21259.1-21626.0 and MN908947.3:22520.0-22875.2 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:23273.3-23620.0 and MN908947.3:24642.0-25019.0 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:25422.0-25780.0 and MN908947.3:26744.0-27070.1 cannot be concatenated as there is no overlap and they do not abut. [11:40:52 - TrimOlap] MN908947.3:27533.3-27879.0 and MN908947.3:28690.0-29109.1 cannot be concatenated as there is no overlap and they do not abut. [11:40:54 - ValidArgs] Reads will be filtered to only those with RG tag: nCoV-2019_1 [11:40:54 - Annotate] Getting chrom coordinates [11:40:54 - Annotate] Processing chunk with coordinates: MN908947.3:240-29510 [11:40:54 - BAMFile] Creating pool of 16 BAM file sets. [11:40:56 - ValidArgs] Reads will be filtered to only those with RG tag: nCoV-2019_2 [11:40:56 - Predict] Reducing threads to 2, anymore is a waste. [11:40:56 - Predict] It looks like you are running medaka without a GPU and attempted to set a high number of threads. We have scaled this down to an optimal number. If you wish to improve performance please see https://nanoporetech.github.io/medaka/installation.html#improving-parallelism. [11:40:56 - Predict] Setting tensorflow inter/intra-op threads to 2/1. [11:40:56 - Predict] Processing region(s): MN908947.3:0-29903 [11:40:56 - Predict] Using model: /opt/conda/lib/python3.8/site-packages/medaka/data/r1041_e82_400bps_fast_g632_model.tar.gz. [11:40:56 - Predict] Processing 1 long region(s) with batching. [11:40:56 - MdlStrTF] Model [11:40:56 - MdlStrTF] loading weights from /tmp/tmpzd_dlods/model/variables/variables [11:40:56 - BAMFile] Creating pool of 16 BAM file sets. [11:40:56 - Sampler] Initializing sampler for consensus of region MN908947.3:0-29903. [11:40:56 - PWorker] Running inference for 0.0M draft bases. [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 1114-2257. [11:40:57 - Feature] Processed MN908947.3:1114.0-2257.0 (median depth 128.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 3144-4250. [11:40:57 - Feature] Processed MN908947.3:3144.0-4250.0 (median depth 393.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 5267-6364. [11:40:57 - Feature] Processed MN908947.3:5267.0-6364.0 (median depth 70.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 7312-8371. [11:40:57 - Feature] Processed MN908947.3:7312.0-8371.0 (median depth 18.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 9315-10436. [11:40:57 - Feature] Processed MN908947.3:9315.0-10436.0 (median depth 45.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 11383-12552. [11:40:57 - Feature] Processed MN908947.3:11383.0-12552.0 (median depth 515.0) [11:40:57 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 13517-14628. [11:40:58 - Feature] Processed MN908947.3:13517.0-14628.0 (median depth 395.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 15622-16710. [11:40:58 - Feature] Processed MN908947.3:15622.0-16710.0 (median depth 187.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 17632-18693. [11:40:58 - Feature] Processed MN908947.3:17632.0-18693.0 (median depth 55.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 19582-20681. [11:40:58 - Feature] Processed MN908947.3:19582.0-20681.0 (median depth 62.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 21544-22602. [11:40:58 - Feature] Processed MN908947.3:21544.0-22602.0 (median depth 242.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 23529-24724. [11:40:58 - Feature] Processed MN908947.3:23529.0-24724.0 (median depth 291.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 25692-26853. [11:40:58 - Feature] Processed MN908947.3:25692.0-26853.0 (median depth 255.0) [11:40:58 - Feature] Pileup counts do not span requested region, requested MN908947.3:0-29903, received 27796-28995. [11:40:58 - Feature] Processed MN908947.3:27796.0-28995.0 (median depth 25.0) [11:40:58 - Sampler] Took 1.41s to make features. [11:41:01 - PWorker] Processed 1 batches [11:41:01 - PWorker] All done, 0 remainder regions. [11:41:01 - Predict] Finished processing all regions. [11:41:03 - DataIndx] Loaded 1/1 (100.00%) sample files. [11:41:03 - Variants] Processing MN908947.3:0-. [11:41:03 - TrimOlap] MN908947.3:1829.0-2257.0 and MN908947.3:3144.0-3473.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:3918.1-4250.0 and MN908947.3:5267.0-5761.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:5835.2-6364.0 and MN908947.3:7312.0-7968.1 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:7723.0-8371.0 and MN908947.3:9315.0-9885.1 cannot be concatenated as there is no overlap and they do not abut. /opt/conda/lib/python3.8/site-packages/medaka/labels.py:387: RuntimeWarning: divide by zero encountered in log10 q = -10 * np.log10(err) [11:41:03 - TrimOlap] MN908947.3:9897.1-10436.0 and MN908947.3:11383.0-11675.2 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:12250.2-12552.0 and MN908947.3:13517.0-13848.1 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:14299.1-14628.0 and MN908947.3:15622.0-16002.1 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:16318.1-16710.0 and MN908947.3:17632.0-18149.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:18188.0-18693.0 and MN908947.3:19582.0-20083.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:20186.0-20681.0 and MN908947.3:21544.0-21906.1 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:22243.1-22602.0 and MN908947.3:23529.0-23905.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:24379.2-24724.0 and MN908947.3:25692.0-26061.1 cannot be concatenated as there is no overlap and they do not abut. [11:41:03 - TrimOlap] MN908947.3:26486.2-26853.0 and MN908947.3:27796.0-28407.0 cannot be concatenated as there is no overlap and they do not abut. [11:41:05 - ValidArgs] Reads will be filtered to only those with RG tag: nCoV-2019_2 [11:41:05 - Annotate] Getting chrom coordinates [11:41:05 - Annotate] Processing chunk with coordinates: MN908947.3:2245-28881 [11:41:05 - BAMFile] Creating pool of 16 BAM file sets. Lines total/split/realigned/skipped: 98/0/0/0 Note: the --sample option not given, applying all records regardless of the genotype The site MN908947.3:12510 overlaps with another variant, skipping... The site MN908947.3:22577 overlaps with another variant, skipping... The site MN908947.3:23599 overlaps with another variant, skipping... The site MN908947.3:23604 overlaps with another variant, skipping... The site MN908947.3:28881 overlaps with another variant, skipping... Applied 93 variants 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. 817747.muscle.in 2 seqs, lengths min 29880, max 29903, avg 29891 00:00:00 16 MB(-1%) Iter 1 33.33% K-mer dist pass 1 00:00:00 16 MB(-1%) Iter 1 100.00% K-mer dist pass 1 00:00:00 16 MB(-1%) Iter 1 33.33% K-mer dist pass 2 00:00:00 16 MB(-1%) Iter 1 100.00% K-mer dist pass 2 00:00:00 33 MB(-2%) Iter 1 100.00% Align node 00:00:16 999 MB(-51%) Iter 1 100.00% Align node 00:00:16 999 MB(-51%) Iter 1 50.00% Root alignment 00:00:16 999 MB(-51%) Iter 1 100.00% Root alignment 00:00:16 999 MB(-51%) Iter 1 100.00% Root alignment Running: minimap2 -a -x map-ont -t 16 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747_filtered.fastq.gz | samtools view -bS -F 4 - | samtools sort -o 817747.sorted.bam - Running: samtools index 817747.sorted.bam Running: align_trim --normalise 500 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --start --remove-incorrect-pairs --report 817747.alignreport.txt < 817747.sorted.bam 2> 817747.alignreport.er | samtools sort -T 817747 - -o 817747.trimmed.rg.sorted.bam Running: align_trim --normalise 500 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --remove-incorrect-pairs --report 817747.alignreport.txt < 817747.sorted.bam 2> 817747.alignreport.er | samtools sort -T 817747 - -o 817747.primertrimmed.rg.sorted.bam Running: samtools index 817747.trimmed.rg.sorted.bam Running: samtools index 817747.primertrimmed.rg.sorted.bam Running: medaka consensus --model r1041_e82_400bps_fast_g632 --threads 16 --chunk_len 800 --chunk_ovlp 400 --RG nCoV-2019_1 817747.trimmed.rg.sorted.bam 817747.nCoV-2019_1.hdf Running: medaka variant external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.nCoV-2019_1.hdf 817747.nCoV-2019_1.vcf Running: medaka tools annotate --pad 25 --RG nCoV-2019_1 817747.nCoV-2019_1.vcf external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.trimmed.rg.sorted.bam 817747.medaka-annotate.vcf Running: mv 817747.medaka-annotate.vcf 817747.nCoV-2019_1.vcf Running: medaka consensus --model r1041_e82_400bps_fast_g632 --threads 16 --chunk_len 800 --chunk_ovlp 400 --RG nCoV-2019_2 817747.trimmed.rg.sorted.bam 817747.nCoV-2019_2.hdf Running: medaka variant external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.nCoV-2019_2.hdf 817747.nCoV-2019_2.vcf Running: medaka tools annotate --pad 25 --RG nCoV-2019_2 817747.nCoV-2019_2.vcf external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.trimmed.rg.sorted.bam 817747.medaka-annotate.vcf Running: mv 817747.medaka-annotate.vcf 817747.nCoV-2019_2.vcf Running: artic_vcf_merge 817747 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed 2> 817747.primersitereport.txt nCoV-2019_1:817747.nCoV-2019_1.vcf nCoV-2019_2:817747.nCoV-2019_2.vcf Running: bgzip -f 817747.merged.vcf Running: tabix -p vcf 817747.merged.vcf.gz Running: artic-tools check_vcf --summaryOut 817747.vcfreport.txt 817747.merged.vcf.gz external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed 2> 817747.vcfcheck.log Running: artic_vcf_filter --medaka --min-depth 20 --min-qual 20 --nanopolish-qual-cov-ratio 3.0 817747.merged.vcf.gz 817747.pass.vcf 817747.fail.vcf Running: artic_make_depth_mask --depth 20 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.primertrimmed.rg.sorted.bam 817747.coverage_mask.txt Running: artic_mask external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.coverage_mask.txt 817747.fail.vcf 817747.preconsensus.fasta Running: bcftools norm --check-ref x --fasta-ref 817747.preconsensus.fasta -O z -o 817747.pass.vcf.gz 817747.pass.vcf Running: tabix -p vcf 817747.pass.vcf.gz Running: bcftools consensus -f 817747.preconsensus.fasta 817747.pass.vcf.gz -m 817747.coverage_mask.txt -o 817747.consensus.fasta Running: artic_fasta_header 817747.consensus.fasta "817747/ARTIC/medaka" Running: cat 817747.consensus.fasta external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta > 817747.muscle.in.fasta Running: muscle -in 817747.muscle.in.fasta -out 817747.muscle.out.fasta Running: artic_get_stats --min-depth 20 --scheme external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --align-report 817747.alignreport.txt --vcf-report 817747.vcfreport.txt 817747 sed: couldn't open temporary file ./sedi4f8Y8: Permission denied