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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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Problems with running decona on example data #48

Closed JobOudeV closed 1 year ago

JobOudeV commented 1 year ago

Hi,

I'm trying to run decona on the example data but it ends up not fully working. I'm under the impression that it has something to do with the Medaka step. I'm using this command decona -f -l 800 -m 2100 -q 10 -c 0.80 -n 25 -M -b small_database_aquarium.fasta in the example_data directory. Any help would be greatly appreciated.

Cheers,

Log:

(decona) [job@sc-prod-01 example_data]$ decona -f -l 800 -m 2100 -q 10 -c 0.80 -n 25 -M -b small_database_aquarium.fasta
Filtering data barcode83_concatenated.fastq...
Filtering data barcode84_concatenated.fastq...
Data filtered with NanoFilt
Data not demultiplexed
total raw sequences = 3426
total filtered sequences = 3424
Fastq reads are being transformed to fasta
Transforming fastq to fasta Complete
Clustering reads...
Clustering barcode83_concatenated/...
Clustering barcode84_concatenated/...
Clustering complete.
Aligning and making draft assembly of 108-27.fa...
[M::mm_idx_gen::0.001*2.12] collected minimizers
[M::mm_idx_gen::0.001*2.86] sorted minimizers
[M::main::0.001*2.84] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.77] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.72] distinct minimizers: 359 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.237
[M::worker_pipeline::0.016*3.57] mapped 108 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_108-27.fasta 108-27.fa
[M::main] Real time: 0.016 sec; CPU: 0.056 sec; Peak RSS: 0.007 GB
[racon::Polisher::initialize] loaded target sequences 0.000054 s
[racon::Polisher::initialize] loaded sequences 0.001040 s
[racon::Polisher::initialize] loaded overlaps 0.000868 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000721 s
[racon::Polisher::initialize] transformed data into windows 0.000048 s
[racon::Polisher::polish] generated consensus 0.101956 s
[racon::Polisher::] total = 0.104791 s
Aligning and making draft assembly of 130-1.fa...
[M::mm_idx_gen::0.001*2.14] collected minimizers
[M::mm_idx_gen::0.001*2.86] sorted minimizers
[M::main::0.001*2.84] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.75] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.70] distinct minimizers: 359 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.457
[M::worker_pipeline::0.017*3.56] mapped 130 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_130-1.fasta 130-1.fa
[M::main] Real time: 0.017 sec; CPU: 0.060 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000041 s
[racon::Polisher::initialize] loaded sequences 0.001275 s
[racon::Polisher::initialize] loaded overlaps 0.001116 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.001040 s
[racon::Polisher::initialize] transformed data into windows 0.000054 s
[racon::Polisher::polish] generated consensus 0.119443 s
[racon::Polisher::] total = 0.123069 s
Aligning and making draft assembly of 136-21.fa...
[M::mm_idx_gen::0.001*2.07] collected minimizers
[M::mm_idx_gen::0.001*2.83] sorted minimizers
[M::main::0.001*2.81] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.73] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.66] distinct minimizers: 350 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.631
[M::worker_pipeline::0.019*3.61] mapped 136 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_136-21.fasta 136-21.fa
[M::main] Real time: 0.019 sec; CPU: 0.069 sec; Peak RSS: 0.006 GB
[racon::Polisher::initialize] loaded target sequences 0.000041 s
[racon::Polisher::initialize] loaded sequences 0.001313 s
[racon::Polisher::initialize] loaded overlaps 0.001174 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000761 s
[racon::Polisher::initialize] transformed data into windows 0.000057 s
[racon::Polisher::polish] generated consensus 0.172866 s
[racon::Polisher::] total = 0.176323 s
Aligning and making draft assembly of 190-18.fa...
[M::mm_idx_gen::0.001*2.23] collected minimizers
[M::mm_idx_gen::0.001*2.99] sorted minimizers
[M::main::0.001*2.97] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.89] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.83] distinct minimizers: 351 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.573
[M::worker_pipeline::0.024*3.65] mapped 190 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_190-18.fasta 190-18.fa
[M::main] Real time: 0.024 sec; CPU: 0.088 sec; Peak RSS: 0.006 GB
[racon::Polisher::initialize] loaded target sequences 0.000047 s
[racon::Polisher::initialize] loaded sequences 0.001810 s
[racon::Polisher::initialize] loaded overlaps 0.001427 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.001055 s
[racon::Polisher::initialize] transformed data into windows 0.000076 s
[racon::Polisher::polish] generated consensus 0.210641 s
[racon::Polisher::] total = 0.215187 s
Aligning and making draft assembly of 244-12.fa...
[M::mm_idx_gen::0.001*2.11] collected minimizers
[M::mm_idx_gen::0.001*2.86] sorted minimizers
[M::main::0.001*2.84] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.76] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.71] distinct minimizers: 367 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.335
[M::worker_pipeline::0.029*3.66] mapped 244 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_244-12.fasta 244-12.fa
[M::main] Real time: 0.029 sec; CPU: 0.107 sec; Peak RSS: 0.006 GB
[racon::Polisher::initialize] loaded target sequences 0.000046 s
[racon::Polisher::initialize] loaded sequences 0.002352 s
[racon::Polisher::initialize] loaded overlaps 0.001868 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.001518 s
[racon::Polisher::initialize] transformed data into windows 0.000095 s
[racon::Polisher::polish] generated consensus 0.230490 s
[racon::Polisher::] total = 0.236529 s
Aligning and making draft assembly of 29-9.fa...
[M::mm_idx_gen::0.001*2.20] collected minimizers
[M::mm_idx_gen::0.001*2.92] sorted minimizers
[M::main::0.001*2.90] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.83] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.77] distinct minimizers: 376 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.271
[M::worker_pipeline::0.006*3.24] mapped 29 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_29-9.fasta 29-9.fa
[M::main] Real time: 0.006 sec; CPU: 0.019 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000040 s
[racon::Polisher::initialize] loaded sequences 0.000310 s
[racon::Polisher::initialize] loaded overlaps 0.000239 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000344 s
[racon::Polisher::initialize] transformed data into windows 0.000019 s
[racon::Polisher::polish] generated consensus 0.015804 s
[racon::Polisher::] total = 0.016815 s
Aligning and making draft assembly of 38-17.fa...
[M::mm_idx_gen::0.001*2.05] collected minimizers
[M::mm_idx_gen::0.001*2.87] sorted minimizers
[M::main::0.001*2.84] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.76] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.71] distinct minimizers: 342 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.433
[M::worker_pipeline::0.007*3.34] mapped 38 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_38-17.fasta 38-17.fa
[M::main] Real time: 0.007 sec; CPU: 0.023 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000045 s
[racon::Polisher::initialize] loaded sequences 0.000370 s
[racon::Polisher::initialize] loaded overlaps 0.000298 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000356 s
[racon::Polisher::initialize] transformed data into windows 0.000023 s
[racon::Polisher::polish] generated consensus 0.019769 s
[racon::Polisher::] total = 0.020916 s
Aligning and making draft assembly of 42-15.fa...
[M::mm_idx_gen::0.001*2.10] collected minimizers
[M::mm_idx_gen::0.001*2.88] sorted minimizers
[M::main::0.001*2.86] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.77] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.71] distinct minimizers: 374 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.227
[M::worker_pipeline::0.007*3.34] mapped 42 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_42-15.fasta 42-15.fa
[M::main] Real time: 0.007 sec; CPU: 0.024 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000039 s
[racon::Polisher::initialize] loaded sequences 0.000412 s
[racon::Polisher::initialize] loaded overlaps 0.000345 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000407 s
[racon::Polisher::initialize] transformed data into windows 0.000024 s
[racon::Polisher::polish] generated consensus 0.030298 s
[racon::Polisher::] total = 0.031594 s
Aligning and making draft assembly of 43-38.fa...
[M::mm_idx_gen::0.001*2.12] collected minimizers
[M::mm_idx_gen::0.001*2.87] sorted minimizers
[M::main::0.001*2.85] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.77] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.71] distinct minimizers: 367 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.264
[M::worker_pipeline::0.007*3.35] mapped 43 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_43-38.fasta 43-38.fa
[M::main] Real time: 0.007 sec; CPU: 0.024 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000039 s
[racon::Polisher::initialize] loaded sequences 0.000419 s
[racon::Polisher::initialize] loaded overlaps 0.000375 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000391 s
[racon::Polisher::initialize] transformed data into windows 0.000024 s
[racon::Polisher::polish] generated consensus 0.022495 s
[racon::Polisher::] total = 0.023812 s
Aligning and making draft assembly of 45-24.fa...
[M::mm_idx_gen::0.001*2.06] collected minimizers
[M::mm_idx_gen::0.001*2.89] sorted minimizers
[M::main::0.001*2.87] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.80] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.74] distinct minimizers: 369 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.238
[M::worker_pipeline::0.007*3.40] mapped 45 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_45-24.fasta 45-24.fa
[M::main] Real time: 0.007 sec; CPU: 0.025 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000038 s
[racon::Polisher::initialize] loaded sequences 0.000432 s
[racon::Polisher::initialize] loaded overlaps 0.000334 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000499 s
[racon::Polisher::initialize] transformed data into windows 0.000024 s
[racon::Polisher::polish] generated consensus 0.039120 s
[racon::Polisher::] total = 0.040504 s
Aligning and making draft assembly of 63-8.fa...
[M::mm_idx_gen::0.001*2.15] collected minimizers
[M::mm_idx_gen::0.001*2.97] sorted minimizers
[M::main::0.001*2.94] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.87] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.82] distinct minimizers: 357 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.401
[M::worker_pipeline::0.010*3.48] mapped 63 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_63-8.fasta 63-8.fa
[M::main] Real time: 0.010 sec; CPU: 0.034 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000038 s
[racon::Polisher::initialize] loaded sequences 0.000601 s
[racon::Polisher::initialize] loaded overlaps 0.000572 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000347 s
[racon::Polisher::initialize] transformed data into windows 0.000030 s
[racon::Polisher::polish] generated consensus 0.043605 s
[racon::Polisher::] total = 0.045262 s
Aligning and making draft assembly of 74-19.fa...
[M::mm_idx_gen::0.001*2.11] collected minimizers
[M::mm_idx_gen::0.001*2.89] sorted minimizers
[M::main::0.001*2.87] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.79] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.72] distinct minimizers: 367 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.341
[M::worker_pipeline::0.011*3.48] mapped 74 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_74-19.fasta 74-19.fa
[M::main] Real time: 0.011 sec; CPU: 0.038 sec; Peak RSS: 0.006 GB
[racon::Polisher::initialize] loaded target sequences 0.000040 s
[racon::Polisher::initialize] loaded sequences 0.000722 s
[racon::Polisher::initialize] loaded overlaps 0.000614 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000533 s
[racon::Polisher::initialize] transformed data into windows 0.000034 s
[racon::Polisher::polish] generated consensus 0.049516 s
[racon::Polisher::] total = 0.051526 s
Done
Aligning and making draft assembly of 110-36.fa...
[M::mm_idx_gen::0.001*2.05] collected minimizers
[M::mm_idx_gen::0.001*2.85] sorted minimizers
[M::main::0.001*2.83] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.76] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.71] distinct minimizers: 371 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.278
[M::worker_pipeline::0.014*3.53] mapped 110 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_110-36.fasta 110-36.fa
[M::main] Real time: 0.015 sec; CPU: 0.051 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000042 s
[racon::Polisher::initialize] loaded sequences 0.001068 s
[racon::Polisher::initialize] loaded overlaps 0.000897 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000803 s
[racon::Polisher::initialize] transformed data into windows 0.000046 s
[racon::Polisher::polish] generated consensus 0.103744 s
[racon::Polisher::] total = 0.106693 s
Aligning and making draft assembly of 120-3.fa...
[M::mm_idx_gen::0.001*2.14] collected minimizers
[M::mm_idx_gen::0.001*2.93] sorted minimizers
[M::main::0.001*2.91] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.83] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.78] distinct minimizers: 355 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.504
[M::worker_pipeline::0.016*3.57] mapped 120 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_120-3.fasta 120-3.fa
[M::main] Real time: 0.016 sec; CPU: 0.056 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000039 s
[racon::Polisher::initialize] loaded sequences 0.001141 s
[racon::Polisher::initialize] loaded overlaps 0.000873 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000870 s
[racon::Polisher::initialize] transformed data into windows 0.000049 s
[racon::Polisher::polish] generated consensus 0.139825 s
[racon::Polisher::] total = 0.142897 s
Aligning and making draft assembly of 122-13.fa...
[M::mm_idx_gen::0.001*2.22] collected minimizers
[M::mm_idx_gen::0.001*2.98] sorted minimizers
[M::main::0.001*2.96] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.88] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.83] distinct minimizers: 359 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.343
[M::worker_pipeline::0.017*3.59] mapped 122 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_122-13.fasta 122-13.fa
[M::main] Real time: 0.017 sec; CPU: 0.061 sec; Peak RSS: 0.007 GB
[racon::Polisher::initialize] loaded target sequences 0.000044 s
[racon::Polisher::initialize] loaded sequences 0.001171 s
[racon::Polisher::initialize] loaded overlaps 0.000974 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000902 s
[racon::Polisher::initialize] transformed data into windows 0.000056 s
[racon::Polisher::polish] generated consensus 0.104031 s
[racon::Polisher::] total = 0.107273 s
Aligning and making draft assembly of 155-7.fa...
[M::mm_idx_gen::0.001*2.21] collected minimizers
[M::mm_idx_gen::0.001*2.92] sorted minimizers
[M::main::0.001*2.90] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.82] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.77] distinct minimizers: 368 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.329
[M::worker_pipeline::0.023*3.67] mapped 155 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_155-7.fasta 155-7.fa
[M::main] Real time: 0.023 sec; CPU: 0.085 sec; Peak RSS: 0.009 GB
[racon::Polisher::initialize] loaded target sequences 0.000040 s
[racon::Polisher::initialize] loaded sequences 0.001498 s
[racon::Polisher::initialize] loaded overlaps 0.001248 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000844 s
[racon::Polisher::initialize] transformed data into windows 0.000070 s
[racon::Polisher::polish] generated consensus 0.206973 s
[racon::Polisher::] total = 0.210788 s
Aligning and making draft assembly of 198-26.fa...
[M::mm_idx_gen::0.001*2.13] collected minimizers
[M::mm_idx_gen::0.002*2.89] sorted minimizers
[M::main::0.002*2.87] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.80] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.75] distinct minimizers: 377 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.215
[M::worker_pipeline::0.024*3.63] mapped 198 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_198-26.fasta 198-26.fa
[M::main] Real time: 0.024 sec; CPU: 0.087 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000042 s
[racon::Polisher::initialize] loaded sequences 0.001928 s
[racon::Polisher::initialize] loaded overlaps 0.001616 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.001089 s
[racon::Polisher::initialize] transformed data into windows 0.000080 s
[racon::Polisher::polish] generated consensus 0.187380 s
[racon::Polisher::] total = 0.192257 s
Aligning and making draft assembly of 25-18.fa...
[M::mm_idx_gen::0.001*2.15] collected minimizers
[M::mm_idx_gen::0.001*2.89] sorted minimizers
[M::main::0.001*2.88] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.80] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.75] distinct minimizers: 372 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.296
[M::worker_pipeline::0.005*3.19] mapped 25 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_25-18.fasta 25-18.fa
[M::main] Real time: 0.005 sec; CPU: 0.016 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000039 s
[racon::Polisher::initialize] loaded sequences 0.000250 s
[racon::Polisher::initialize] loaded overlaps 0.000201 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000365 s
[racon::Polisher::initialize] transformed data into windows 0.000017 s
[racon::Polisher::polish] generated consensus 0.013751 s
[racon::Polisher::] total = 0.014682 s
Aligning and making draft assembly of 27-14.fa...
[M::mm_idx_gen::0.001*2.14] collected minimizers
[M::mm_idx_gen::0.001*2.90] sorted minimizers
[M::main::0.001*2.88] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.80] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.74] distinct minimizers: 357 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.577
[M::worker_pipeline::0.005*3.25] mapped 27 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_27-14.fasta 27-14.fa
[M::main] Real time: 0.005 sec; CPU: 0.017 sec; Peak RSS: 0.003 GB
[racon::Polisher::initialize] loaded target sequences 0.000047 s
[racon::Polisher::initialize] loaded sequences 0.000265 s
[racon::Polisher::initialize] loaded overlaps 0.000212 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000364 s
[racon::Polisher::initialize] transformed data into windows 0.000017 s
[racon::Polisher::polish] generated consensus 0.018189 s
[racon::Polisher::] total = 0.019156 s
Aligning and making draft assembly of 27-34.fa...
[M::mm_idx_gen::0.001*2.22] collected minimizers
[M::mm_idx_gen::0.001*2.97] sorted minimizers
[M::main::0.001*2.95] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.87] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.81] distinct minimizers: 362 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.378
[M::worker_pipeline::0.005*3.28] mapped 27 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_27-34.fasta 27-34.fa
[M::main] Real time: 0.005 sec; CPU: 0.017 sec; Peak RSS: 0.003 GB
[racon::Polisher::initialize] loaded target sequences 0.000038 s
[racon::Polisher::initialize] loaded sequences 0.000269 s
[racon::Polisher::initialize] loaded overlaps 0.000233 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000367 s
[racon::Polisher::initialize] transformed data into windows 0.000016 s
[racon::Polisher::polish] generated consensus 0.014254 s
[racon::Polisher::] total = 0.015241 s
Aligning and making draft assembly of 36-42.fa...
[M::mm_idx_gen::0.001*2.12] collected minimizers
[M::mm_idx_gen::0.001*2.90] sorted minimizers
[M::main::0.001*2.88] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.80] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.74] distinct minimizers: 359 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.368
[M::worker_pipeline::0.006*3.35] mapped 36 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_36-42.fasta 36-42.fa
[M::main] Real time: 0.006 sec; CPU: 0.020 sec; Peak RSS: 0.003 GB
[racon::Polisher::initialize] loaded target sequences 0.000038 s
[racon::Polisher::initialize] loaded sequences 0.000355 s
[racon::Polisher::initialize] loaded overlaps 0.000282 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000379 s
[racon::Polisher::initialize] transformed data into windows 0.000023 s
[racon::Polisher::polish] generated consensus 0.022946 s
[racon::Polisher::] total = 0.024077 s
Aligning and making draft assembly of 38-30.fa...
[M::mm_idx_gen::0.001*2.11] collected minimizers
[M::mm_idx_gen::0.001*2.94] sorted minimizers
[M::main::0.001*2.92] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.84] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.78] distinct minimizers: 362 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.395
[M::worker_pipeline::0.006*3.31] mapped 38 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_38-30.fasta 38-30.fa
[M::main] Real time: 0.007 sec; CPU: 0.022 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000037 s
[racon::Polisher::initialize] loaded sequences 0.000384 s
[racon::Polisher::initialize] loaded overlaps 0.000306 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000414 s
[racon::Polisher::initialize] transformed data into windows 0.000022 s
[racon::Polisher::polish] generated consensus 0.030840 s
[racon::Polisher::] total = 0.032056 s
Aligning and making draft assembly of 38-51.fa...
[M::mm_idx_gen::0.001*2.23] collected minimizers
[M::mm_idx_gen::0.001*2.98] sorted minimizers
[M::main::0.001*2.96] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.87] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.81] distinct minimizers: 359 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.390
[M::worker_pipeline::0.007*3.35] mapped 38 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_38-51.fasta 38-51.fa
[M::main] Real time: 0.007 sec; CPU: 0.022 sec; Peak RSS: 0.005 GB
[racon::Polisher::initialize] loaded target sequences 0.000041 s
[racon::Polisher::initialize] loaded sequences 0.000381 s
[racon::Polisher::initialize] loaded overlaps 0.000305 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000378 s
[racon::Polisher::initialize] transformed data into windows 0.000023 s
[racon::Polisher::polish] generated consensus 0.020085 s
[racon::Polisher::] total = 0.021279 s
Aligning and making draft assembly of 41-56.fa...
[M::mm_idx_gen::0.001*2.09] collected minimizers
[M::mm_idx_gen::0.001*2.91] sorted minimizers
[M::main::0.001*2.89] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.82] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.76] distinct minimizers: 352 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.520
[M::worker_pipeline::0.007*3.37] mapped 41 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_41-56.fasta 41-56.fa
[M::main] Real time: 0.007 sec; CPU: 0.024 sec; Peak RSS: 0.007 GB
[racon::Polisher::initialize] loaded target sequences 0.000037 s
[racon::Polisher::initialize] loaded sequences 0.000391 s
[racon::Polisher::initialize] loaded overlaps 0.000346 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000441 s
[racon::Polisher::initialize] transformed data into windows 0.000025 s
[racon::Polisher::polish] generated consensus 0.023599 s
[racon::Polisher::] total = 0.024898 s
Aligning and making draft assembly of 42-9.fa...
[M::mm_idx_gen::0.001*2.09] collected minimizers
[M::mm_idx_gen::0.001*2.88] sorted minimizers
[M::main::0.001*2.87] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.78] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.72] distinct minimizers: 379 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.240
[M::worker_pipeline::0.007*3.32] mapped 42 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_42-9.fasta 42-9.fa
[M::main] Real time: 0.007 sec; CPU: 0.023 sec; Peak RSS: 0.003 GB
[racon::Polisher::initialize] loaded target sequences 0.000035 s
[racon::Polisher::initialize] loaded sequences 0.000408 s
[racon::Polisher::initialize] loaded overlaps 0.000315 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000450 s
[racon::Polisher::initialize] transformed data into windows 0.000023 s
[racon::Polisher::polish] generated consensus 0.022456 s
[racon::Polisher::] total = 0.023749 s
Aligning and making draft assembly of 49-46.fa...
[M::mm_idx_gen::0.001*2.18] collected minimizers
[M::mm_idx_gen::0.001*2.95] sorted minimizers
[M::main::0.001*2.92] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.84] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.79] distinct minimizers: 367 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.308
[M::worker_pipeline::0.007*3.40] mapped 49 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_49-46.fasta 49-46.fa
[M::main] Real time: 0.008 sec; CPU: 0.025 sec; Peak RSS: 0.003 GB
[racon::Polisher::initialize] loaded target sequences 0.000038 s
[racon::Polisher::initialize] loaded sequences 0.000474 s
[racon::Polisher::initialize] loaded overlaps 0.000376 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000394 s
[racon::Polisher::initialize] transformed data into windows 0.000025 s
[racon::Polisher::polish] generated consensus 0.036520 s
[racon::Polisher::] total = 0.037888 s
Aligning and making draft assembly of 52-25.fa...
[M::mm_idx_gen::0.001*2.00] collected minimizers
[M::mm_idx_gen::0.001*2.83] sorted minimizers
[M::main::0.001*2.81] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.74] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.69] distinct minimizers: 362 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.340
[M::worker_pipeline::0.008*3.34] mapped 52 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_52-25.fasta 52-25.fa
[M::main] Real time: 0.008 sec; CPU: 0.027 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000036 s
[racon::Polisher::initialize] loaded sequences 0.000496 s
[racon::Polisher::initialize] loaded overlaps 0.000448 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000494 s
[racon::Polisher::initialize] transformed data into windows 0.000026 s
[racon::Polisher::polish] generated consensus 0.039681 s
[racon::Polisher::] total = 0.041249 s
Aligning and making draft assembly of 60-35.fa...
[M::mm_idx_gen::0.001*2.15] collected minimizers
[M::mm_idx_gen::0.001*2.93] sorted minimizers
[M::main::0.001*2.91] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.83] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.77] distinct minimizers: 361 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.341
[M::worker_pipeline::0.009*3.46] mapped 60 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_60-35.fasta 60-35.fa
[M::main] Real time: 0.009 sec; CPU: 0.032 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000041 s
[racon::Polisher::initialize] loaded sequences 0.000572 s
[racon::Polisher::initialize] loaded overlaps 0.000521 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000397 s
[racon::Polisher::initialize] transformed data into windows 0.000029 s
[racon::Polisher::polish] generated consensus 0.042420 s
[racon::Polisher::] total = 0.044046 s
Aligning and making draft assembly of 62-29.fa...
[M::mm_idx_gen::0.001*2.09] collected minimizers
[M::mm_idx_gen::0.001*2.90] sorted minimizers
[M::main::0.001*2.89] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*2.82] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.76] distinct minimizers: 368 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.337
[M::worker_pipeline::0.009*3.48] mapped 62 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_62-29.fasta 62-29.fa
[M::main] Real time: 0.009 sec; CPU: 0.031 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000043 s
[racon::Polisher::initialize] loaded sequences 0.000599 s
[racon::Polisher::initialize] loaded overlaps 0.000501 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000501 s
[racon::Polisher::initialize] transformed data into windows 0.000029 s
[racon::Polisher::polish] generated consensus 0.056607 s
[racon::Polisher::] total = 0.058340 s
Aligning and making draft assembly of 66-2.fa...
[M::mm_idx_gen::0.001*2.17] collected minimizers
[M::mm_idx_gen::0.001*2.99] sorted minimizers
[M::main::0.001*2.97] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.89] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*2.83] distinct minimizers: 358 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.441
[M::worker_pipeline::0.011*3.48] mapped 66 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_66-2.fasta 66-2.fa
[M::main] Real time: 0.011 sec; CPU: 0.037 sec; Peak RSS: 0.006 GB
[racon::Polisher::initialize] loaded target sequences 0.000039 s
[racon::Polisher::initialize] loaded sequences 0.000640 s
[racon::Polisher::initialize] loaded overlaps 0.000547 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000697 s
[racon::Polisher::initialize] transformed data into windows 0.000031 s
[racon::Polisher::polish] generated consensus 0.042786 s
[racon::Polisher::] total = 0.044818 s
Aligning and making draft assembly of 86-0.fa...
[M::mm_idx_gen::0.001*2.11] collected minimizers
[M::mm_idx_gen::0.001*2.90] sorted minimizers
[M::main::0.001*2.88] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*2.78] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*2.73] distinct minimizers: 390 (100.00% are singletons); average occurrences: 1.000; average spacing: 4.972
[M::worker_pipeline::0.011*3.50] mapped 86 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax map-ont -k15 -t 4 ref_86-0.fasta 86-0.fa
[M::main] Real time: 0.012 sec; CPU: 0.040 sec; Peak RSS: 0.004 GB
[racon::Polisher::initialize] loaded target sequences 0.000036 s
[racon::Polisher::initialize] loaded sequences 0.000821 s
[racon::Polisher::initialize] loaded overlaps 0.000678 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.000675 s
[racon::Polisher::initialize] transformed data into windows 0.000039 s
[racon::Polisher::polish] generated consensus 0.057179 s
[racon::Polisher::] total = 0.059516 s
Done
polishing 108-27.fa Racon sequence with Medaka...
2023-02-15 15:11:06.331413: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Checking program versions
This is medaka 1.1.2
Program    Version    Required   Pass
bcftools   1.10.2     1.9        True
bgzip      1.10.2     1.9        True
minimap2   2.17       2.11       True
samtools   1.10       1.9        True
tabix      1.10.2     1.9        True
2023-02-15 15:11:08.378409: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-02-15 15:11:10.213318: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Aligning basecalls to draft
Removing previous index file /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/polished_108-27.fasta.mmi
Removing previous index file /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/polished_108-27.fasta.fai
Constructing minimap index.
[M::mm_idx_gen::0.001*1.93] collected minimizers
[M::mm_idx_gen::0.002*2.35] sorted minimizers
[M::main::0.003*1.91] loaded/built the index for 1 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.003*1.89] distinct minimizers: 365 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.466
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -I 16G -x map-ont --MD -d /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/polished_108-27.fasta.mmi /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/polished_108-27.fasta
[M::main] Real time: 0.003 sec; CPU: 0.005 sec; Peak RSS: 0.003 GB
[M::main::0.001*1.47] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.001*1.43] mid_occ = 2
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.001*1.42] distinct minimizers: 365 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.466
[M::worker_pipeline::0.016*3.26] mapped 108 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x map-ont --MD -t 4 -a -A 2 -B 4 -O 4,24 -E 2,1 /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/polished_108-27.fasta.mmi /data/job/decona/example_data/data/barcode83_concatenated/multi-seq/108-27.fa
[M::main] Real time: 0.016 sec; CPU: 0.052 sec; Peak RSS: 0.006 GB
Running medaka consensus
2023-02-15 15:11:12.109782: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[15:11:13 - Predict] Processing region(s): 96859a13-4f5a-43ce-b014-2a55fa5efc31:0-1995
[15:11:13 - Predict] Using model: /kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5.
[15:11:13 - Predict] Setting tensorflow threads to 4.
[15:11:13 - Predict] Processing 1 long region(s) with batching.
[15:11:13 - ModelStore] filepath /kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5
[15:11:14 - DLoader] Initializing data loader
[15:11:14 - PWorker] Running inference for 0.0M draft bases.
[15:11:14 - Sampler] Initializing sampler for consensus of region 96859a13-4f5a-43ce-b014-2a55fa5efc31:0-1995.
[15:11:14 - Feature] Processed 96859a13-4f5a-43ce-b014-2a55fa5efc31:0.0-1994.0 (median depth 108.0)
[15:11:14 - Sampler] Took 0.01s to make features.
[15:11:14 - Sampler] Region 96859a13-4f5a-43ce-b014-2a55fa5efc31:0.0-1994.0 (3622 positions) is smaller than inference chunk length 10000, quarantining.
[15:11:14 - PWorker] All done, 1 remainder regions.
[15:11:14 - Predict] Processing 1 short region(s).
[15:11:14 - ModelStore] filepath /kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/data/r941_min_high_g360_model.hdf5
[15:11:14 - DLoader] Initializing data loader
[15:11:14 - PWorker] Running inference for 0.0M draft bases.
[15:11:14 - Sampler] Initializing sampler for consensus of region 96859a13-4f5a-43ce-b014-2a55fa5efc31:0-1995.
[15:11:14 - Feature] Processed 96859a13-4f5a-43ce-b014-2a55fa5efc31:0.0-1994.0 (median depth 108.0)
[15:11:14 - Sampler] Took 0.01s to make features.
[15:11:17 - PWorker] All done, 0 remainder regions.
[15:11:17 - Predict] Finished processing all regions.
Using medaka stitch to create consensus.
2023-02-15 15:11:17.976901: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  SSE4.1 SSE4.2 AVX AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
[15:11:19 - DataIndex] Loaded 1/1 (100.00%) sample files.
[15:11:19 - Stitch] Stitching regions: ['96859a13-4f5a-43ce-b014-2a55fa5efc31:0-']
[15:11:19 - DataIndex] Loaded 1/1 (100.00%) sample files.
[15:11:19 - Stitch] Processing 96859a13-4f5a-43ce-b014-2a55fa5efc31:0-.
[15:11:19 - Stitch] Used heuristic 0 times for 96859a13-4f5a-43ce-b014-2a55fa5efc31:0-.
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/process.py", line 239, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/process.py", line 198, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/process.py", line 198, in <listcomp>
    return [fn(*args) for args in chunk]
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/stitch.py", line 133, in _stitcher
    return fill_gaps(contigs, draft)
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/stitch.py", line 117, in fill_gaps
    draft_seq = draft.fetch(ref_name)
  File "pysam/libcfaidx.pyx", line 303, in pysam.libcfaidx.FastaFile.fetch
KeyError: "sequence 'b'96859a13-4f5a-43ce-b014-2a55fa5efc31'' not present"
"""

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

Traceback (most recent call last):
  File "/kusers/ancillary/job/.conda/envs/decona/bin/medaka", line 11, in <module>
    sys.exit(main())
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/medaka.py", line 669, in main
    args.func(args)
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/site-packages/medaka/stitch.py", line 152, in stitch
    for contigs, gap_tree in executor.map(worker, rgrps):
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator
    yield fs.pop().result()
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/_base.py", line 444, in result
    return self.__get_result()
  File "/kusers/ancillary/job/.conda/envs/decona/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result
    raise self._exception
KeyError: "sequence 'b'96859a13-4f5a-43ce-b014-2a55fa5efc31'' not present"
Failed to stitch consensus chunks.
khoojj commented 1 year ago

Hi, I came across similar error - any idea how to solve it? Thanks