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add bwa to polypolish 0.6.0 #1113

Merged
merged 1 commit into from
Dec 12, 2024
Merged

add bwa to polypolish 0.6.0 #1113

merged 1 commit into from
Dec 12, 2024

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sage-wright
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This PR adds BWA to polypolish 0.6.0 so that only a single container is needed.

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@kapsakcj kapsakcj self-requested a review November 26, 2024 17:19
@erinyoung
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It looks like the tests worked

#15 [test 1/4] RUN polypolish --help && polypolish --version
#15 0.068   _____        _                       _  _       _     
#15 0.068  |  __ \      | |                     | |(_)     | |    
#15 0.068  | |__) |___  | | _   _  _ __    ___  | | _  ___ | |__  
#15 0.068  |  ___// _ \ | || | | || '_ \  / _ \ | || |/ __|| '_ \ 
#15 0.068  | |   | (_) || || |_| || |_) || (_) || || |\__ \| | | |
#15 0.068  |_|    \___/ |_| \__, || .__/  \___/ |_||_||___/|_| |_|
#15 0.068                    __/ || |                             
#15 0.068                   |___/ |_|
#15 0.068 
#15 0.068 short-read polishing of long-read assemblies
#15 0.068 
#15 0.068 Usage: polypolish <COMMAND>
#15 0.068 
#15 0.068 Commands:
#15 0.068   filter  filter paired-end alignments based on insert size
#15 0.068   polish  polish a long-read assembly using short-read alignments
#15 0.068 
#15 0.068 Options:
#15 0.068   -h, --help     Print help
#15 0.068   -V, --version  Print version
#15 0.070 Polypolish 0.6.0
#15 DONE 0.1s

#16 [test 2/4] RUN wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/assembly.fasta &&     wget -q https://raw.githubusercontent.com/wiki/rrwick/Polypolish/files/toy_example/alignments.sam &&     polypolish polish assembly.fasta alignments.sam > polished.fasta
#16 0.285 
#16 0.285 Starting Polypolish polish (2024-11-26 17:18:52)
#16 0.285     Polypolish is a tool for polishing genome assemblies with short reads.
#16 0.285 Unlike other tools in this category, Polypolish uses SAM files where each read
#16 0.285 has been aligned to all possible locations (not just a single best location).
#16 0.285 This allows it to repair errors in repeat regions that other alignment-based
#16 0.285 polishers cannot fix.
#16 0.285 
#16 0.285 Polypolish version: 0.6.0
#16 0.285 
#16 0.285 Input assembly:
#16 0.285   assembly.fasta
#16 0.285 
#18 159.3 [M::mem_pestat] mean and std.dev: (511.12, 216.93)
#18 159.3 [M::mem_pestat] low and high boundaries for proper pairs: (1, 1515)
#18 159.3 [M::mem_pestat] skip orientation RF as there are not enough pairs
#18 159.3 [M::mem_pestat] skip orientation RR as there are not enough pairs
#18 159.3 [M::mem_pestat] skip orientation FF
#18 160.4 [M::mem_process_seqs] Processed 40690 reads in 4.992 CPU sec, 4.857 real sec
#18 163.7 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 15[785](https://github.com/StaPH-B/docker-builds/actions/runs/12035719339/job/33555364646?pr=1113#step:8:791), 1, 4)
#18 163.7 [M::mem_pestat] skip orientation FF as there are not enough pairs
#18 163.7 [M::mem_pestat] analyzing insert size distribution for orientation FR...
#18 163.7 [M::mem_pestat] (25, 50, 75) percentile: (355, 474, 643)
#18 163.7 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1219)
#18 163.7 [M::mem_pestat] mean and std.dev: (511.53, 216.86)
#18 163.7 [M::mem_pestat] low and high boundaries for proper pairs: (1, 1507)
#18 163.7 [M::mem_pestat] skip orientation RF as there are not enough pairs
#18 163.7 [M::mem_pestat] skip orientation RR as there are not enough pairs
#18 164.5 [M::mem_process_seqs] Processed 34532 reads in 4.188 CPU sec, 4.145 real sec
#18 164.7 [main] Version: 0.7.18-r1243-dirty
#18 164.7 [main] CMD: bwa mem ref.fa r1.fq.gz r2.fq.gz
#18 164.7 [main] Real time: 163.313 sec; CPU: 168.103 sec
#18 164.7 @SQ	SN:NC_003197.2	LN:4857450
#18 164.7 @SQ	SN:NC_003277.2	LN:93933
#18 164.7 @HD	VN:1.5	SO:unsorted	GO:query
#18 164.7 @PG	ID:bwa	PN:bwa	VN:0.7.18-r1243-dirty	CL:bwa mem ref.fa r1.fq.gz r2.fq.gz
#18 164.7 SRR6082043.1	121	NC_003197.2	2689535	60	65S182M	=	2689535	0	AAGACGGAAAACGAGAAGAAGAGAGGACACGGGGGAAAGGAGAAGTGAAAAAGAGACAGGGAAAACGTTAGCGAGGTAACCGCCGCCAACGCCAGTACCGACGCCATTCCCCAGCTAAAAACGCCAAACACTATACTGAATAACAGCACCATTAACGCGCCGGAACAGGGCCGCATCCCCATAGACAGAACGATCATGAGTCGCGCGCGCCAGTCAACGCCGCTATGCAATTGTTCCTGCGTCGGTA	9:-9-//-:-9-/9/9///9/9/9/-------/9//////;/://///;/B;/B/;/9/9/-;;--/--9--/;99--------/--;---//;--9---:-//0;..-./0;0/.FFCC;-/./;;00=0000=00<D=0D=0<00=01>..>--/////22F?0F<<///0/?//012B2F>B1?>/B/1B21B1>>>//////////1DA//A//A00A12F1DBGGBBGFCDDDDDDAAAAAA	NM:i:9	MD:Z:12T0C9T38T4T21T33T10A16T30	MQ:i:0	AS:i:137	XS:i:0
#18 164.7 SRR6082043.1	181	NC_003197.2	2689535	0	*	=	2689535	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGGCAGAAAAAGAAGAGAAAAAGAAAAAGAAACGAAGAAGGAAAAAATGAAAAGAGGAGAAGACAGGCGAGAGAGAAAAATGAACGTACTGTATATGGGGATGCGGCAATGAACCGGAGCGATAAAGGTGCTGATAATCAGAAAAGAGATAGGAGTAAATAGCAGGGGAATGGAGACGGTAATGGAGAAGGAGGAGGGAAAAACGAAAACGAAAAAA	--------;-99----9------9--90;000000000;/000000;000/0=0=</0000=/.</.0<111>10<>1=<1111?1?<1<111<11?/////1112210B222B10B0/12B122220B0//0<?///112221///////0//2B1BB0/01122222D222@21DBDA11B11111222221B//00122BD1100///112B111A11B0000001110AA0001311BB11>11>11	MC:Z:65S182M	MQ:i:60	AS:i:0	XS:i:0
#18 164.7 SRR6082043.2	73	NC_003197.2	3108932	54	204M45S	=	3108932	0	ATCTTCAATCCGAATGCAACGCTCGACTGGCATCTTGCGCTCCGCCTTTCTGCCGGTTTGCCCGTTCTGTCACGGGTTATGCTGCTTATGCTGATTGTTTTTCTGCCGTTTGTGCGCAACAAATTTGTAGTACAACTGTTGGGTGTATTTCCCAACGTCCTGGTCGATCTGATCCATAATCTACACGGGAGCTGCGGCTATAGCTTCTTACCGCGTTTGTTTTTCCTTTTCCAGCTTTTTGTGCATCAG	1AAAAFFFFFFAC1FCB11A0AA000AB00001ADF21//A///////11B211//A///111//B>?12221////?/B11B11112B11B11BB11BBFF0F211///0/B01/////0/01@@222221<11??01?1///.-111><1110.....<0/<<--<:;00::00;0000;0:0/.--.-.;//---;.9000009/;///-----9------//;:B//////;9/9;---//////	NM:i:27	MD:Z:32G13A0G0G8A0A5A4G1G4A8A0A10A10G0A0A12A3A2A7G4A1A1A0A8G13G7G24	MQ:i:0	AS:i:69	XS:i:0
#18 164.7 SRR6082043.2	133	NC_003197.2	3108932	0	*	=	3108932	0	TCTTTTTTTTTTTCCTTTTTTTTCTTTCTCTCCTCCTTCCTTCTTTTTTCATCCTTTTTTCTTCTTCTCTTCTCTCTCTTCTTTTTCCTTCTCTTCCTTCTTCTCCTTTTACTCTTTCTCCTTCTCCTTTTCTTTTTCTCCGCTTCTTTGCTGTTTCTCTTTTTTCTTGCTTTTTTTCTTCTTCCTCTTTACTCCCCTTTTTCCTCATCTTCCGTTTTTCTTTTTTTTCTTTTCTTCCTTTCCTTTTTGTT	11>111B>1>00001122B1///011A2222101000A10121111@1>0222@B2211>0BB2BB221@B12121111212BB1B011>1<12>11121112>11112121B12112>21111@11<12@21@1110111/////11111=1=<11<111<11-/<00000000:-/;;00:000000;0000/..9.000/0000000000.009../9:/9/--9////9///////////:///-99	MC:Z:204M45S	MQ:i:54	AS:i:0	XS:i:0
#18 164.7 SRR6082043.3	73	NC_003197.2	2325618	60	241M10S	=	2325618	0	GGCAACCCGCACGACCTGTATGCCCCGGAGGTCGGTAGCCCGAAGGGTAAAAGCGTTAACGTCCCTGTCCAGGTATTTTGCCCGGCCTGCGGCTTTGCCAACACCTTCTGTGGGAAAACCACTGCCGACTGCACGCTGATTGAACACTTTGTCCGTCGCTGCCAGGGCTGGTTTGTGGATGACGACGGCCATCTCGAGCTGTGCGATTTTCGCTTTCGCTTCATTAACTGCCCGCTGTGTATTTCCGAAAT	3AABBBFBBBBBGCEEEBGBGCFEEE22220BA00A11A3A000011133533111B1141B11>B3B@@433B4BEEG433?///<?/0//<<<F22<22//<<?F<F1110//1/0<..<<11<--<-./0<.-<..;C00000/;CG00:0.:.--9.../0..9;..;BC.//./;///..------;///./.../;//..:.AFB-.;9A9..99.//////;///9.---;/9//;///...-.	NM:i:11	MD:Z:47A7A54G18G21G23A17G5A23A0A10A5	MQ:i:0	AS:i:186	XS:i:0
#18 164.7 SRR6082043.3	133	NC_003197.2	2325618	0	*	=	2325618	0	TTCTTATCCTTCCCATTCTGCATCGTCTTTCCTCTTCTGCTCTGTTCTATCTCTTCCTTTTTCCTTATCTCCGCTTTTATCATTTCGTCCGTTTCGTCCTGTTTTTCGTCTCATTCTCTTCTTCTTCTTTCGTCTTTTTCTTTTTCTTCTTTACACTGCTGTCTGTTTTTTTATCTTAATCGTTTTTCTCTCTTCTCTCTTTTGTCGTCGTCTTCCTCTATCCTTCCTTTGCTTCTTCTCTCTTTTTGTTT	1>1>13B13B31111A13B313D31AA0AD3131B113111111222B222122BA1BD21101D2211221//AAAF2122D2A20B////1>1/0/>/111@0/0/B//02B22222212122B22112/0///B1B01>1BB01122BB2121B11111121B@@FC///11111111///..<01111>1<=11100=00/0.<.-<..;00;00000/000:0:000000000000000000-;9/	MC:Z:241M10S	MQ:i:60	AS:i:0	XS:i:0
#18 DONE 164.7s

@erinyoung
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@kapsakcj , I don't have any changes to recommend for this PR, so I've approved it. I noticed that you selected yourself as a reviewer, so I'll hold off on merging and deploying.

@erinyoung erinyoung merged commit db42d7f into StaPH-B:master Dec 12, 2024
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@erinyoung
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I've deployed this image with the tag "0.6.0-bwa"

You can check the status here : https://github.com/StaPH-B/docker-builds/actions/runs/12305604973

Let us know if you run into any issues!

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@erinyoung erinyoung erinyoung approved these changes

@kapsakcj kapsakcj Awaiting requested review from kapsakcj

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@sage-wright @erinyoung