Getting short reads.
Getting assembly.
command: bwa index /kb/module/work/tmp/flye.contigs.fa
[bwa_index] Pack FASTA... 0.03 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.20 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.02 sec
[bwa_index] Construct SA from BWT and Occ... 0.39 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /kb/module/work/tmp/flye.contigs.fa
[main] Real time: 1.669 sec; CPU: 1.666 sec
command: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/flye.contigs.fa /kb/module/work/tmp/04d7dd22-f2bd-4486-97c2-e7de62c328b5.fwd.fastq > /kb/module/work/tmp/alignments1_e8f1c425-7c75-4576-b2d1-314118df4731.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 67802 sequences (10000283 bp)...
[M::process] read 67816 sequences (10000044 bp)...
[M::mem_process_seqs] Processed 67802 reads in 21.553 CPU sec, 21.483 real sec
[M::process] read 67770 sequences (10000259 bp)...
[M::mem_process_seqs] Processed 67816 reads in 22.272 CPU sec, 22.148 real sec
[M::process] read 67840 sequences (10000154 bp)...
[M::mem_process_seqs] Processed 67770 reads in 21.460 CPU sec, 21.324 real sec
[M::process] read 67904 sequences (10000126 bp)...
[M::mem_process_seqs] Processed 67840 reads in 22.781 CPU sec, 22.632 real sec
[M::process] read 67838 sequences (10000162 bp)...
[M::mem_process_seqs] Processed 67904 reads in 22.851 CPU sec, 22.698 real sec
[M::process] read 67874 sequences (10000097 bp)...
[M::mem_process_seqs] Processed 67838 reads in 21.534 CPU sec, 21.369 real sec
[M::process] read 67862 sequences (10000252 bp)...
[M::mem_process_seqs] Processed 67874 reads in 21.830 CPU sec, 21.672 real sec
[M::process] read 67880 sequences (10000299 bp)...
[M::mem_process_seqs] Processed 67862 reads in 22.345 CPU sec, 22.185 real sec
[M::process] read 67840 sequences (10000084 bp)...
[M::mem_process_seqs] Processed 67880 reads in 21.698 CPU sec, 21.545 real sec
[M::process] read 67818 sequences (10000290 bp)...
[M::mem_process_seqs] Processed 67840 reads in 23.112 CPU sec, 22.952 real sec
[M::process] read 68016 sequences (10000005 bp)...
[M::mem_process_seqs] Processed 67818 reads in 21.611 CPU sec, 21.454 real sec
[M::process] read 67962 sequences (10000048 bp)...
[M::mem_process_seqs] Processed 68016 reads in 26.525 CPU sec, 26.377 real sec
[M::process] read 67822 sequences (10000035 bp)...
[M::mem_process_seqs] Processed 67962 reads in 25.561 CPU sec, 25.435 real sec
[M::process] read 67878 sequences (10000291 bp)...
[M::mem_process_seqs] Processed 67822 reads in 21.183 CPU sec, 21.027 real sec
[M::process] read 67842 sequences (10000062 bp)...
[M::mem_process_seqs] Processed 67878 reads in 21.598 CPU sec, 21.441 real sec
[M::process] read 67852 sequences (10000169 bp)...
[M::mem_process_seqs] Processed 67842 reads in 22.530 CPU sec, 22.371 real sec
[M::process] read 67902 sequences (10000057 bp)...
[M::mem_process_seqs] Processed 67852 reads in 21.911 CPU sec, 21.753 real sec
[M::process] read 67854 sequences (10000264 bp)...
[M::mem_process_seqs] Processed 67902 reads in 22.350 CPU sec, 22.195 real sec
[M::process] read 67864 sequences (10000272 bp)...
[M::mem_process_seqs] Processed 67854 reads in 21.377 CPU sec, 21.214 real sec
[M::process] read 67822 sequences (10000032 bp)...
[M::mem_process_seqs] Processed 67864 reads in 22.337 CPU sec, 22.178 real sec
[M::process] read 67882 sequences (10000068 bp)...
[M::mem_process_seqs] Processed 67822 reads in 21.682 CPU sec, 21.531 real sec
[M::process] read 67884 sequences (10000044 bp)...
[M::mem_process_seqs] Processed 67882 reads in 21.246 CPU sec, 21.108 real sec
[M::process] read 67838 sequences (10000124 bp)...
[M::mem_process_seqs] Processed 67884 reads in 22.071 CPU sec, 21.913 real sec
[M::process] read 67906 sequences (10000113 bp)...
[M::mem_process_seqs] Processed 67838 reads in 21.105 CPU sec, 20.950 real sec
[M::process] read 67840 sequences (10000037 bp)...
[M::mem_process_seqs] Processed 67906 reads in 21.844 CPU sec, 21.685 real sec
[M::process] read 67844 sequences (10000090 bp)...
[M::mem_process_seqs] Processed 67840 reads in 21.019 CPU sec, 20.859 real sec
[M::process] read 67924 sequences (10000262 bp)...
[M::mem_process_seqs] Processed 67844 reads in 20.922 CPU sec, 20.761 real sec
[M::process] read 67966 sequences (10000014 bp)...
[M::mem_process_seqs] Processed 67924 reads in 21.922 CPU sec, 21.762 real sec
[M::process] read 67874 sequences (10000246 bp)...
[M::mem_process_seqs] Processed 67966 reads in 22.650 CPU sec, 22.491 real sec
[M::process] read 67952 sequences (10000115 bp)...
[M::mem_process_seqs] Processed 67874 reads in 20.967 CPU sec, 20.803 real sec
[M::process] read 67978 sequences (10000030 bp)...
[M::mem_process_seqs] Processed 67952 reads in 22.030 CPU sec, 21.879 real sec
[M::process] read 67858 sequences (10000286 bp)...
[M::mem_process_seqs] Processed 67978 reads in 21.960 CPU sec, 21.853 real sec
[M::process] read 67896 sequences (10000298 bp)...
[M::mem_process_seqs] Processed 67858 reads in 21.352 CPU sec, 21.194 real sec
[M::process] read 67904 sequences (10000188 bp)...
[M::mem_process_seqs] Processed 67896 reads in 21.214 CPU sec, 21.060 real sec
[M::process] read 67854 sequences (10000119 bp)...
[M::mem_process_seqs] Processed 67904 reads in 21.766 CPU sec, 21.607 real sec
[M::process] read 67962 sequences (10000202 bp)...
[M::mem_process_seqs] Processed 67854 reads in 20.838 CPU sec, 20.676 real sec
[M::process] read 67928 sequences (10000240 bp)...
[M::mem_process_seqs] Processed 67962 reads in 21.334 CPU sec, 21.165 real sec
[M::process] read 67856 sequences (10000102 bp)...
[M::mem_process_seqs] Processed 67928 reads in 21.812 CPU sec, 21.653 real sec
[M::process] read 67858 sequences (10000150 bp)...
[M::mem_process_seqs] Processed 67856 reads in 20.623 CPU sec, 20.511 real sec
[M::process] read 67932 sequences (10000205 bp)...
[M::mem_process_seqs] Processed 67858 reads in 20.988 CPU sec, 20.830 real sec
[M::process] read 67856 sequences (10000101 bp)...
[M::mem_process_seqs] Processed 67932 reads in 21.885 CPU sec, 21.731 real sec
[M::process] read 67872 sequences (10000023 bp)...
[M::mem_process_seqs] Processed 67856 reads in 21.482 CPU sec, 21.324 real sec
[M::process] read 67978 sequences (10000070 bp)...
[M::mem_process_seqs] Processed 67872 reads in 21.349 CPU sec, 21.203 real sec
[M::process] read 67968 sequences (10000032 bp)...
[M::mem_process_seqs] Processed 67978 reads in 21.772 CPU sec, 21.612 real sec
[M::process] read 67916 sequences (10000259 bp)...
[M::mem_process_seqs] Processed 67968 reads in 21.072 CPU sec, 20.914 real sec
[M::process] read 67944 sequences (10000199 bp)...
[M::mem_process_seqs] Processed 67916 reads in 21.329 CPU sec, 21.177 real sec
[M::process] read 67912 sequences (10000027 bp)...
[M::mem_process_seqs] Processed 67944 reads in 22.315 CPU sec, 22.156 real sec
[M::process] read 67920 sequences (10000242 bp)...
[M::mem_process_seqs] Processed 67912 reads in 20.944 CPU sec, 20.808 real sec
[M::process] read 67918 sequences (10000095 bp)...
[M::mem_process_seqs] Processed 67920 reads in 21.139 CPU sec, 20.987 real sec
[M::process] read 28078 sequences (4135774 bp)...
[M::mem_process_seqs] Processed 67918 reads in 21.158 CPU sec, 21.029 real sec
[M::mem_process_seqs] Processed 28078 reads in 8.751 CPU sec, 8.642 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/flye.contigs.fa /kb/module/work/tmp/04d7dd22-f2bd-4486-97c2-e7de62c328b5.fwd.fastq
[main] Real time: 1093.442 sec; CPU: 1101.070 sec
command: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/flye.contigs.fa /kb/module/work/tmp/6320cbfd-f262-4d10-8b88-fde478a032fb.rev.fastq > /kb/module/work/tmp/alignments2_e0f0137e-ee24-4bb9-ad3b-9116cbb26d77.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 67868 sequences (10000255 bp)...
[M::process] read 67956 sequences (10000237 bp)...
[M::mem_process_seqs] Processed 67868 reads in 24.510 CPU sec, 24.436 real sec
[M::process] read 67888 sequences (10000075 bp)...
[M::mem_process_seqs] Processed 67956 reads in 26.292 CPU sec, 26.161 real sec
[M::process] read 67966 sequences (10000158 bp)...
[M::mem_process_seqs] Processed 67888 reads in 25.842 CPU sec, 25.657 real sec
[M::process] read 68052 sequences (10000139 bp)...
[M::mem_process_seqs] Processed 67966 reads in 27.091 CPU sec, 26.963 real sec
[M::process] read 67920 sequences (10000230 bp)...
[M::mem_process_seqs] Processed 68052 reads in 27.955 CPU sec, 27.794 real sec
[M::process] read 68054 sequences (10000285 bp)...
[M::mem_process_seqs] Processed 67920 reads in 24.873 CPU sec, 24.715 real sec
[M::process] read 67972 sequences (10000066 bp)...
[M::mem_process_seqs] Processed 68054 reads in 26.334 CPU sec, 26.209 real sec
[M::process] read 68176 sequences (10000202 bp)...
[M::mem_process_seqs] Processed 67972 reads in 26.479 CPU sec, 26.318 real sec
[M::process] read 68010 sequences (10000221 bp)...
[M::mem_process_seqs] Processed 68176 reads in 26.812 CPU sec, 26.643 real sec
[M::process] read 67964 sequences (10000296 bp)...
[M::mem_process_seqs] Processed 68010 reads in 26.975 CPU sec, 26.806 real sec
[M::process] read 68322 sequences (10000096 bp)...
[M::mem_process_seqs] Processed 67964 reads in 26.157 CPU sec, 25.994 real sec
[M::process] read 68166 sequences (10000183 bp)...
[M::mem_process_seqs] Processed 68322 reads in 31.459 CPU sec, 31.290 real sec
[M::process] read 67916 sequences (10000126 bp)...
[M::mem_process_seqs] Processed 68166 reads in 29.468 CPU sec, 29.296 real sec
[M::process] read 68032 sequences (10000044 bp)...
[M::mem_process_seqs] Processed 67916 reads in 24.646 CPU sec, 24.486 real sec
[M::process] read 68000 sequences (10000127 bp)...
[M::mem_process_seqs] Processed 68032 reads in 26.392 CPU sec, 26.230 real sec
[M::process] read 67928 sequences (10000206 bp)...
[M::mem_process_seqs] Processed 68000 reads in 27.312 CPU sec, 27.195 real sec
[M::process] read 68012 sequences (10000049 bp)...
[M::mem_process_seqs] Processed 67928 reads in 26.202 CPU sec, 26.045 real sec
[M::process] read 67910 sequences (10000035 bp)...
[M::mem_process_seqs] Processed 68012 reads in 26.931 CPU sec, 26.804 real sec
[M::process] read 68006 sequences (10000186 bp)...
[M::mem_process_seqs] Processed 67910 reads in 25.511 CPU sec, 25.344 real sec
[M::process] read 67912 sequences (10000014 bp)...
[M::mem_process_seqs] Processed 68006 reads in 26.773 CPU sec, 26.654 real sec
[M::process] read 67968 sequences (10000196 bp)...
[M::mem_process_seqs] Processed 67912 reads in 25.717 CPU sec, 25.572 real sec
[M::process] read 67960 sequences (10000130 bp)...
[M::mem_process_seqs] Processed 67968 reads in 24.564 CPU sec, 24.398 real sec
[M::process] read 67900 sequences (10000194 bp)...
[M::mem_process_seqs] Processed 67960 reads in 24.882 CPU sec, 24.717 real sec
[M::process] read 67974 sequences (10000213 bp)...
[M::mem_process_seqs] Processed 67900 reads in 23.738 CPU sec, 23.561 real sec
[M::process] read 67882 sequences (10000268 bp)...
[M::mem_process_seqs] Processed 67974 reads in 24.063 CPU sec, 23.884 real sec
[M::process] read 67838 sequences (10000288 bp)...
[M::mem_process_seqs] Processed 67882 reads in 22.888 CPU sec, 22.754 real sec
[M::process] read 67890 sequences (10000123 bp)...
[M::mem_process_seqs] Processed 67838 reads in 21.879 CPU sec, 21.716 real sec
[M::process] read 67928 sequences (10000188 bp)...
[M::mem_process_seqs] Processed 67890 reads in 22.971 CPU sec, 22.797 real sec
[M::process] read 67892 sequences (10000274 bp)...
[M::mem_process_seqs] Processed 67928 reads in 23.881 CPU sec, 23.708 real sec
[M::process] read 67948 sequences (10000019 bp)...
[M::mem_process_seqs] Processed 67892 reads in 21.871 CPU sec, 21.706 real sec
[M::process] read 67954 sequences (10000178 bp)...
[M::mem_process_seqs] Processed 67948 reads in 24.159 CPU sec, 24.003 real sec
[M::process] read 67796 sequences (10000062 bp)...
[M::mem_process_seqs] Processed 67954 reads in 23.506 CPU sec, 23.387 real sec
[M::process] read 67890 sequences (10000294 bp)...
[M::mem_process_seqs] Processed 67796 reads in 22.636 CPU sec, 22.469 real sec
[M::process] read 67902 sequences (10000049 bp)...
[M::mem_process_seqs] Processed 67890 reads in 22.939 CPU sec, 22.768 real sec
[M::process] read 67870 sequences (10000211 bp)...
[M::mem_process_seqs] Processed 67902 reads in 23.512 CPU sec, 23.344 real sec
[M::process] read 67966 sequences (10000289 bp)...
[M::mem_process_seqs] Processed 67870 reads in 22.135 CPU sec, 21.969 real sec
[M::process] read 68004 sequences (10000222 bp)...
[M::mem_process_seqs] Processed 67966 reads in 22.924 CPU sec, 22.755 real sec
[M::process] read 67816 sequences (10000168 bp)...
[M::mem_process_seqs] Processed 68004 reads in 24.403 CPU sec, 24.252 real sec
[M::process] read 67836 sequences (10000122 bp)...
[M::mem_process_seqs] Processed 67816 reads in 177.567 CPU sec, 177.389 real sec
[M::process] read 67882 sequences (10000271 bp)...
[M::mem_process_seqs] Processed 67836 reads in 99.553 CPU sec, 99.438 real sec
[M::process] read 67844 sequences (10000083 bp)...
[M::mem_process_seqs] Processed 67882 reads in 21.748 CPU sec, 21.585 real sec
[M::process] read 67836 sequences (10000139 bp)...
[M::mem_process_seqs] Processed 67844 reads in 21.638 CPU sec, 21.476 real sec
[M::process] read 67890 sequences (10000053 bp)...
[M::mem_process_seqs] Processed 67836 reads in 21.450 CPU sec, 21.285 real sec
[M::process] read 67940 sequences (10000281 bp)...
[M::mem_process_seqs] Processed 67890 reads in 22.143 CPU sec, 22.012 real sec
[M::process] read 67896 sequences (10000217 bp)...
[M::mem_process_seqs] Processed 67940 reads in 22.063 CPU sec, 21.890 real sec
[M::process] read 67896 sequences (10000158 bp)...
[M::mem_process_seqs] Processed 67896 reads in 22.027 CPU sec, 21.865 real sec
[M::process] read 67888 sequences (10000182 bp)...
[M::mem_process_seqs] Processed 67896 reads in 22.894 CPU sec, 22.724 real sec
[M::process] read 67896 sequences (10000084 bp)...
[M::mem_process_seqs] Processed 67888 reads in 22.305 CPU sec, 22.135 real sec
[M::process] read 67908 sequences (10000286 bp)...
[M::mem_process_seqs] Processed 67896 reads in 22.491 CPU sec, 22.325 real sec
[M::process] read 25236 sequences (3717432 bp)...
[M::mem_process_seqs] Processed 67908 reads in 23.115 CPU sec, 22.976 real sec
[M::mem_process_seqs] Processed 25236 reads in 8.955 CPU sec, 8.871 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -a -k1 -T7 -A1 -B1 -O1 -E1 -L100 /kb/module/work/tmp/flye.contigs.fa /kb/module/work/tmp/6320cbfd-f262-4d10-8b88-fde478a032fb.rev.fastq
[main] Real time: 1456.969 sec; CPU: 1464.824 sec
command: polypolish filter --in1 /kb/module/work/tmp/alignments1_e8f1c425-7c75-4576-b2d1-314118df4731.sam --in2 /kb/module/work/tmp/alignments2_e0f0137e-ee24-4bb9-ad3b-9116cbb26d77.sam --out1 /kb/module/work/tmp/filtered1_8a8da3f1-2325-4470-93d3-f50b87edbd2d.sam --out2 /kb/module/work/tmp/filtered2_2016b69f-e84a-449d-97d9-76d2cdca2390.sam
[1;4;93mStarting Polypolish filter[0m [2m(2024-06-24 15:55:44)[0m
[2m This runs a pre-processing filter on SAM alignments before they are used to
polish. It looks at each read pair and flags alignments that do not seem to be
part of a concordant pair. This can improve the accuracy Polypolish, especially
near the edges of repeats.[0m
Polypolish version: 0.6.0
Input alignments:
/kb/module/work/tmp/alignments1_e8f1c425-7c75-4576-b2d1-314118df4731.sam
/kb/module/work/tmp/alignments2_e0f0137e-ee24-4bb9-ad3b-9116cbb26d77.sam
Output alignments:
/kb/module/work/tmp/filtered1_8a8da3f1-2325-4470-93d3-f50b87edbd2d.sam
/kb/module/work/tmp/filtered2_2016b69f-e84a-449d-97d9-76d2cdca2390.sam
Settings:
--orientation auto
--low 0.1
--high 99.9
[1;4;93mLoading alignments[0m [2m(2024-06-24 15:55:44)[0m
/kb/module/work/tmp/alignments1_e8f1c425-7c75-4576-b2d1-314118df4731.sam: 4,353,982 alignments from 3,422,356 reads
/kb/module/work/tmp/alignments2_e0f0137e-ee24-4bb9-ad3b-9116cbb26d77.sam: 8,915,677 alignments from 3,422,356 reads
[1;4;93mFinding insert size thresholds[0m [2m(2024-06-24 15:56:21)[0m
[2m Read pairs with exactly one alignment per read are used to determine the
orientation and insert size thresholds for the read set.[0m
fr: 3,252,504 pairs
rf: 9 pairs
ff: 33 pairs
rr: 39 pairs
Automatically determined correct orientation: fr
Low threshold: 43 (0.1st percentile)
High threshold: 853 (99.9th percentile)
[1;4;93mFiltering SAM files[0m [2m(2024-06-24 15:56:29)[0m
[2m Read alignments that are part of a good pair (correct orientation and
insert size) pass the filter and are written unaltered to the output file. Read
alignments which are not part of good pair are written to the output file with a
"ZP:Z:fail" tag so Polypolish will not use them.[0m
Filtering /kb/module/work/tmp/alignments1_e8f1c425-7c75-4576-b2d1-314118df4731.sam:
4,151,616 pass
202,366 fail
Filtering /kb/module/work/tmp/alignments2_e0f0137e-ee24-4bb9-ad3b-9116cbb26d77.sam:
4,162,185 pass
4,753,492 fail
[1;4;93mFinished![0m [2m(2024-06-24 16:00:42)[0m
Alignments before filtering: 13,269,659
Alignments after filtering: 8,313,801
Time to run: 0:04:57.606467
command: polypolish polish --fraction_invalid 0.2 --fraction_valid 0.5 --max_errors 10 --min_depth 5 /kb/module/work/tmp/flye.contigs.fa /kb/module/work/tmp/filtered1_8a8da3f1-2325-4470-93d3-f50b87edbd2d.sam /kb/module/work/tmp/filtered2_2016b69f-e84a-449d-97d9-76d2cdca2390.sam > /kb/module/work/tmp/polypolish_output_3a5fe691-28a1-4e6a-a76e-d9f3ae4054c5.fasta
[1;4;93mStarting Polypolish polish[0m [2m(2024-06-24 16:00:56)[0m
[2m Polypolish is a tool for polishing genome assemblies with short reads.
Unlike other tools in this category, Polypolish uses SAM files where each read
has been aligned to all possible locations (not just a single best location).
This allows it to repair errors in repeat regions that other alignment-based
polishers cannot fix.[0m
Polypolish version: 0.6.0
Input assembly:
/kb/module/work/tmp/flye.contigs.fa
Input short-read alignments:
/kb/module/work/tmp/filtered1_8a8da3f1-2325-4470-93d3-f50b87edbd2d.sam
/kb/module/work/tmp/filtered2_2016b69f-e84a-449d-97d9-76d2cdca2390.sam
Settings:
--fraction_invalid 0.2
--fraction_valid 0.5
--max_errors 10
--min_depth 5
not logging debugging information
[1;4;93mLoading assembly[0m [2m(2024-06-24 16:00:56)[0m
contig_1 (6,657 bp)
contig_2 (4,043,281 bp)
[1;4;93mLoading alignments[0m [2m(2024-06-24 16:00:56)[0m
/kb/module/work/tmp/filtered1_8a8da3f1-2325-4470-93d3-f50b87edbd2d.sam: 4,353,982 alignments from 3,422,356 reads
/kb/module/work/tmp/filtered2_2016b69f-e84a-449d-97d9-76d2cdca2390.sam: 8,915,677 alignments from 3,422,356 reads
Filtering for high-quality end-to-end alignments:
8,190,926 alignments kept
5,078,733 alignments discarded
[1;4;93mPolishing assembly sequences[0m [2m(2024-06-24 16:01:55)[0m
[2m For each position in the assembly, Polypolish determines the read depth
at that position and collects all aligned bases. It then polishes the assembly
by looking for positions where the pileup unambiguously supports a different
sequence than the assembly.[0m
Polishing contig_1 (6,657 bp):
mean read depth: 264.4x
3 bp have a depth of zero (99.9549% coverage)
1 position changed (0.0150% of total positions)
estimated pre-polishing sequence accuracy: 99.9850% (Q38.23)
Polishing contig_2 (4,043,281 bp):
mean read depth: 244.4x
2 bp have a depth of zero (100.0000% coverage)
30 positions changed (0.0007% of total positions)
estimated pre-polishing sequence accuracy: 99.9993% (Q51.30)
[1;4;93mFinished![0m [2m(2024-06-24 16:01:57)[0m
Polished sequence (to stdout):
contig_1_polypolish (6,657 bp)
contig_2_polypolish (4,043,312 bp)
Time to run: 0:01:01.011620
Generating and saving report.
Polypolish results saved.