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Sequence correction provided by ONT Research
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missing the bam file when running medaka_consensus #511

Closed hungweichen0327 closed 2 weeks ago

hungweichen0327 commented 2 weeks ago

Hi,

Describe the bug I can not successfully run the medaka_consensus due to missing the bam file.

I used the script below: nohup medaka_consensus -m r1041_e82_400bps_sup_v5.0.0 -i reads.fq -d assembly_rmdup.fasta -t 64 1> medaka.err 2> medaka.out &

TF_CPP_MIN_LOG_LEVEL is set to '3'
Checking program versions
This is medaka 1.12.0
Program    Version    Required   Pass     
bcftools   1.14       1.11       True     
bgzip      1.14       1.11       True     
minimap2   2.17       2.11       True     
samtools   1.14       1.11       True     
tabix      1.14       1.11       True     
Aligning basecalls to draft

Logging

[10:12:40 - MdlStrTF] Successfully removed temporary files from /tmp/tmplwg4msas.
[10:12:41 - MdlStrTF] Successfully removed temporary files from /tmp/tmp49qse9ur.
Creating fai index file /Nextdenovo/v5.0_reads/1gb_dx1_dx0/run2/polishing/assembly_rmdup.fasta.fai
Creating mmi index file /Nextdenovo/v5.0_reads/1gb_dx1_dx0/run2/polishing/assembly_rmdup.fasta.map-ont.mmi
[M::mm_idx_gen::12.594*1.53] collected minimizers
[M::mm_idx_gen::16.141*1.85] sorted minimizers
[M::main::17.866*1.77] loaded/built the index for 251 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 251
[M::mm_idx_stat::18.230*1.75] distinct minimizers: 50138088 (51.18% are singletons); average occurrences: 3.929; average spacing: 5.271
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -I 16G -x map-ont -d /Nextdenovo/v5.0_reads/1gb_dx1_dx0/run2/polishing/assembly_rmdup.fasta.map-ont.mmi /Nextdenovo/v5.0_reads/1gb_dx1_dx0/run2/polishing/assembly_rmdup.fasta
[M::main] Real time: 44.116 sec; CPU: 32.376 sec; Peak RSS: 6.186 GB
[M::main::35.395*0.16] loaded/built the index for 251 target sequence(s)
[M::mm_mapopt_update::36.941*0.19] mid_occ = 512
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 251
[M::mm_idx_stat::37.636*0.21] distinct minimizers: 50138088 (51.18% are singletons); average occurrences: 3.929; average spacing: 5.271
[M::worker_pipeline::116.648*19.67] mapped 123183 sequences
[M::worker_pipeline::197.759*17.13] mapped 126751 sequences
[M::worker_pipeline::274.859*16.90] mapped 109141 sequences

(I skip similar information above)

[M::worker_pipeline::4355.078*21.82] mapped 49174 sequences
[M::worker_pipeline::4421.203*21.79] mapped 47107 sequences
to_draft.bam.tmp.0034.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0030.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0045.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0009.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0050.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0032.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0003.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0035.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0033.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0005.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0018.bam" : No such file or directory
[E::hts_open_format] [E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0013.bam" : No such file or directory
Failed to open file "calls_to_draft.bam.tmp.0026.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0012.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0002.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0007.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0040.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0052.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0004.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0028.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0015.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0001.bam" : No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0001.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0002.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0003.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0004.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0005.bam": No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0038.bam" : No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0051.bam" : No such file or directory

(I skip similar information above)

samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0056.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0057.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0058.bam": No such file or directory
[E::hts_open_format] Failed to open file "calls_to_draft.bam.tmp.0059.bam" : No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0059.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0060.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0061.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0062.bam": No such file or directory
samtools sort: failed to create temporary file "calls_to_draft.bam.tmp.0063.bam": No such file or directory
Alignment pipeline failed.

Environment: No GPU

Thank you for the help.

hungweichen0327 commented 2 weeks ago

When I add -o ./medaka, it solved.