Update Minipolish to 0.2.1 by cwoodside1278 · Pull Request #1592 · StaPH-B/docker-builds

cwoodside1278 · 2026-03-11T23:28:15Z

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/build-files/samtools/1.15 )
Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
- (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/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

Description

Updated minipolish to 0.2.1 version from 0.2.0

created new directory structure minipolish/0.2.1
Updated the ubuntu to noble
Updated the container-specific read me to minipolish/0.2.1
Updated the main read me to include the new version

Diff Output

diff -r build-files/minipolish/0.2.1/Dockerfile build-files/minipolish/0.2.0/Dockerfile
1c1
< ARG MINIPOLISH_VER=0.2.1
---
> ARG MINIPOLISH_VER=0.2.0
6c6,7
< FROM ubuntu:noble AS builder
---
> 
> FROM ubuntu:jammy AS builder
57c58
< FROM ubuntu:noble AS app
---
> FROM ubuntu:jammy AS app
62c63
< LABEL base.image="ubuntu:noble"
---
> LABEL base.image="ubuntu:jammy"
85c86
<   pip install --break-system-packages v${MINIPOLISH_VER}.tar.gz && \
---
>   pip install v${MINIPOLISH_VER}.tar.gz && \
110c111
< RUN miniasm_and_minipolish.sh long_reads_high_depth.fastq.gz 4 > test.gfa && head test.gfa
---
> RUN miniasm_and_minipolish.sh long_reads_high_depth.fastq.gz 4 > test.gfa && head test.gfa
\ No newline at end of file

Test build

[+] Building 9.5s (20/20) FINISHED                                                                                                                                    docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 3.12kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [builder 1/6] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                   0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => CACHED [app 2/6] RUN apt-get update && apt-get install -y --no-install-recommends   wget   ca-certificates   python3-pip &&   apt-get autoclean && rm -rf /var/lib/apt/lis  0.0s
 => CACHED [builder 2/6] RUN apt-get update && apt-get install --no-install-recommends -y   perl   default-jre   gnuplot   libgomp1   maven   git   wget   python3   build-ess  0.0s
 => CACHED [builder 3/6] RUN wget https://github.com/lbcb-sci/racon/archive/refs/tags/1.5.0.tar.gz &&   tar -xvf 1.5.0.tar.gz &&   cd racon-1.5.0 &&   mkdir build &&   cd bui  0.0s
 => CACHED [builder 4/6] RUN racon_test                                                                                                                                         0.0s
 => CACHED [builder 5/6] RUN curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner &&     mv minimap2-  0.0s
 => CACHED [builder 6/6] RUN wget https://github.com/lh3/miniasm/archive/v0.3.tar.gz &&   mkdir miniasm &&   tar -xzvf v0.3.tar.gz -C miniasm --strip-components 1 &&   rm v0.  0.0s
 => CACHED [app 3/6] COPY --from=builder /racon-1.5.0/build/bin/* /usr/local/bin/                                                                                               0.0s
 => CACHED [app 4/6] COPY --from=builder /usr/local/bin/* /usr/local/bin/                                                                                                       0.0s
 => [app 5/6] RUN wget https://github.com/rrwick/Minipolish/archive/refs/tags/v0.2.1.tar.gz &&   tar -vxf v0.2.1.tar.gz &&   pip install --break-system-packages v0.2.1.tar.gz  2.1s
 => [app 6/6] WORKDIR /data                                                                                                                                                     0.0s 
 => [test 1/5] RUN minipolish --help                                                                                                                                            0.2s 
 => [test 2/5] RUN minimap2 --version && racon --help && miniasm -V                                                                                                             0.2s 
 => [test 3/5] WORKDIR /test                                                                                                                                                    0.0s 
 => [test 4/5] RUN wget https://github.com/rrwick/Unicycler/raw/refs/heads/main/sample_data/long_reads_high_depth.fastq.gz                                                      1.0s 
 => [test 5/5] RUN miniasm_and_minipolish.sh long_reads_high_depth.fastq.gz 4 > test.gfa && head test.gfa                                                                       1.3s 
 => exporting to image                                                                                                                                                          4.3s 
 => => exporting layers                                                                                                                                                         3.2s 
 => => exporting manifest sha256:c1a51d3dc08c66a752d7fb01a1a4e481d5f501b0b7789a9cfa4924d6c3353712                                                                               0.0s 
 => => exporting config sha256:f8cc4d68c391554127b0a0c43e9b12d6ae3dde2afddd2f48aee2a29a29ae38d9                                                                                 0.0s 
 => => exporting attestation manifest sha256:6e864b9cff00fa2b98ed524d7ecc052e17b3f9c097330eaab7825a0c62ea4efb                                                                   0.0s 
 => => exporting manifest list sha256:1609b8ed1b6134b3a99659651c19ceb97b8fcc542628d7243f58c212be96ed55                                                                          0.0s 
 => => naming to docker.io/library/minipolish:0.2.1                                                                                                                             0.0s
 => => unpacking to docker.io/library/minipolish:0.2.1

added pip install --break-system-packages v${MINIPOLISH_VER}.tar.gz && \

erinyoung · 2026-03-12T16:32:59Z

Looks like this one failed

#20 [test 5/5] RUN miniasm_and_minipolish.sh long_reads_high_depth.fastq.gz 4 > test.gfa && head test.gfa
#20 0.246 [M::mm_idx_gen::0.195*1.01] collected minimizers
#20 0.319 [M::mm_idx_gen::0.267*1.79] sorted minimizers
#20 0.319 [M::main::0.267*1.79] loaded/built the index for 620 target sequence(s)
#20 0.344 [M::mm_mapopt_update::0.292*1.72] mid_occ = 12
#20 0.344 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 620
#20 0.362 [M::mm_idx_stat::0.311*1.68] distinct minimizers: 1668886 (95.40% are singletons); average occurrences: 1.072; average spacing: 2.939; total length: 5259229
#20 0.562 [M::worker_pipeline::0.511*2.27] mapped 620 sequences
#20 0.569 [M::main] Version: 2.30-r1287
#20 0.569 [M::main] CMD: minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz
#20 0.569 [M::main] Real time: 0.517 sec; CPU: 1.165 sec; Peak RSS: 0.085 GB
#20 0.576 [M::main] ===> Step 1: reading read mappings <===
#20 0.579 [M::ma_hit_read::0.002*1.35] read 3616 hits; stored 6933 hits and 609 sequences (5215569 bp)
#20 0.579 [M::main] ===> Step 2: 1-pass (crude) read selection <===
#20 0.579 [M::ma_hit_sub::0.003*1.29] 54 query sequences remain after sub
#20 0.579 [M::ma_hit_cut::0.003*1.29] 168 hits remain after cut
#20 0.579 [M::ma_hit_flt::0.003*1.29] 168 hits remain after filtering; crude coverage after filtering: 3.69
#20 0.579 [M::main] ===> Step 3: 2-pass (fine) read selection <===
#20 0.579 [M::ma_hit_sub::0.003*1.28] 12 query sequences remain after sub
#20 0.579 [M::ma_hit_cut::0.003*1.28] 34 hits remain after cut
#20 0.579 [M::ma_hit_contained::0.003*1.28] 3 sequences and 4 hits remain after containment removal
#20 0.579 [M::main] ===> Step 4: graph cleaning <===
#20 0.579 [M::ma_sg_gen] read 4 arcs
#20 0.579 [M::main] ===> Step 4.1: transitive reduction <===
#20 0.579 [M::asg_arc_del_trans] transitively reduced 0 arcs
#20 0.579 [M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
#20 0.579 [M::asg_cut_tip] cut 1 tips
#20 0.579 [M::asg_arc_del_multi] removed 0 multi-arcs
#20 0.579 [M::asg_arc_del_asymm] removed 0 asymmetric arcs
#20 0.579 [M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
#20 0.579 [M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===
#20 0.579 [M::asg_arc_del_short] removed 0 short overlaps
#20 0.579 [M::asg_arc_del_short] removed 0 short overlaps
#20 0.579 [M::asg_arc_del_short] removed 0 short overlaps
#20 0.579 [M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
#20 0.579 [M::asg_cut_internal] cut 0 internal sequences
#20 0.579 [M::asg_cut_biloop] cut 0 small bi-loops
#20 0.579 [M::asg_cut_tip] cut 0 tips
#20 0.579 [M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
#20 0.579 [M::main] ===> Step 4.5: aggressively cutting short overlaps <===
#20 0.579 [M::asg_arc_del_short] removed 0 short overlaps
#20 0.579 [M::main] ===> Step 5: generating unitigs <===
#20 0.623 [M::main] Version: 0.3-r179
#20 0.623 [M::main] CMD: miniasm -f long_reads_high_depth.fastq.gz /tmp/tmp.M7POmWMu1e.paf
#20 0.623 [M::main] Real time: 0.047 sec; CPU: 0.047 sec
#20 0.664 
#20 0.664 Checking requirements
#20 0.664     Minipolish requires Minimap2 and Racon to run, so it checks for these tools
#20 0.664 now.
#20 0.664 
#20 0.667 Minimap2 found: /usr/local/bin/minimap2 (v2.30-r1287)
#20 0.670 Racon found:    /usr/local/bin/racon (v1.5.0)
#20 0.670 
#20 0.670 
#20 0.670 Loading graph
#20 0.670     Loading the miniasm GFA graph into memory.
#20 0.670 
#20 0.670 /tmp/tmp.tE3n2Xbvst.gfa
#20 0.670   0 segments (0 bp)
#20 0.670   0 links
#20 0.670 
#20 0.671 
#20 0.671 Initial polishing round
#20 0.671     The first round of polishing is done on a per-segment basis and only uses
#20 0.671 reads which are definitely associated with the segment (because the GFA
#20 0.671 indicated that they were used to make the segment).
#20 0.671 
#20 0.716 Warning: No matching per-segment reads ("a" lines) were found in the GFA. Skipping initial polishing round. Use --skip_initial to suppress this warning.
#20 0.716 
#20 0.716 
#20 0.716 Full polishing rounds
#20 0.716     The assembly graph is now polished using all of the reads. Multiple rounds
#20 0.716 of polishing are done, and circular contigs are rotated between rounds.
#20 0.716 
#20 0.716 
#20 0.762 Running Racon on round_1:
#20 0.762   reads:      long_reads_high_depth.fastq.gz (620 reads)
#20 0.762   input:      /tmp/tmptq4lme1s/round_1.fasta (0 bp)
#20 0.847   alignments: /tmp/tmptq4lme1s/round_1.paf (0 alignments)
#20 0.847 
#20 0.847 Error: minimap2 produced no alignments for round_1.
#20 DONE 0.9s

cwoodside1278 · 2026-03-12T17:37:53Z

Oh weird. I will look into the error. Could it be that the samples used to test are not good anymore?

The very last line is the new code to test and try without a wrapper script

cwoodside1278 · 2026-03-12T18:06:39Z

@erinyoung where did you get that output from? I want to make sure I can replicate the error to debug it. Was it when you ran the docker?

I made a small update and my docker build ran fine again:

[+] Building 2.7s (20/20) FINISHED                                                                                                                                    docker:default
 => [internal] load build definition from Dockerfile                                                                                                                            0.0s
 => => transferring dockerfile: 3.48kB                                                                                                                                          0.0s
 => [internal] load metadata for docker.io/library/ubuntu:noble                                                                                                                 0.0s
 => [internal] load .dockerignore                                                                                                                                               0.0s
 => => transferring context: 2B                                                                                                                                                 0.0s
 => [builder 1/6] FROM docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                   0.0s
 => => resolve docker.io/library/ubuntu:noble@sha256:d1e2e92c075e5ca139d51a140fff46f84315c0fdce203eab2807c7e495eff4f9                                                           0.0s
 => CACHED [app 2/6] RUN apt-get update && apt-get install -y --no-install-recommends   wget   ca-certificates   python3-pip &&   apt-get autoclean && rm -rf /var/lib/apt/lis  0.0s
 => CACHED [builder 2/6] RUN apt-get update && apt-get install --no-install-recommends -y   perl   default-jre   gnuplot   libgomp1   maven   git   wget   python3   build-ess  0.0s
 => CACHED [builder 3/6] RUN wget https://github.com/lbcb-sci/racon/archive/refs/tags/1.5.0.tar.gz &&   tar -xvf 1.5.0.tar.gz &&   cd racon-1.5.0 &&   mkdir build &&   cd bui  0.0s
 => CACHED [builder 4/6] RUN racon_test                                                                                                                                         0.0s
 => CACHED [builder 5/6] RUN curl -L https://github.com/lh3/minimap2/releases/download/v2.30/minimap2-2.30_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner &&     mv minimap2-  0.0s
 => CACHED [builder 6/6] RUN wget https://github.com/lh3/miniasm/archive/v0.3.tar.gz &&   mkdir miniasm &&   tar -xzvf v0.3.tar.gz -C miniasm --strip-components 1 &&   rm v0.  0.0s
 => CACHED [app 3/6] COPY --from=builder /racon-1.5.0/build/bin/* /usr/local/bin/                                                                                               0.0s
 => CACHED [app 4/6] COPY --from=builder /usr/local/bin/* /usr/local/bin/                                                                                                       0.0s
 => CACHED [app 5/6] RUN wget https://github.com/rrwick/Minipolish/archive/refs/tags/v0.2.1.tar.gz &&   tar -vxf v0.2.1.tar.gz &&   pip install --break-system-packages v0.2.1  0.0s
 => CACHED [app 6/6] WORKDIR /data                                                                                                                                              0.0s
 => CACHED [test 1/5] RUN minipolish --help                                                                                                                                     0.0s
 => CACHED [test 2/5] RUN minimap2 --version && racon --help && miniasm -V                                                                                                      0.0s
 => CACHED [test 3/5] WORKDIR /test                                                                                                                                             0.0s
 => CACHED [test 4/5] RUN wget https://github.com/rrwick/Unicycler/raw/refs/heads/main/sample_data/long_reads_high_depth.fastq.gz                                               0.0s
 => [test 5/5] RUN minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz > overlaps.paf &&     miniasm -f long_reads_high_depth.fastq.gz over  2.3s
 => exporting to image                                                                                                                                                          0.2s
 => => exporting layers                                                                                                                                                         0.1s
 => => exporting manifest sha256:25da24b225f1b7386cd07f46365044b7a77afa3fe197ba58a0c2c13618e6ec0a                                                                               0.0s 
 => => exporting config sha256:7066d1897ba2729fce02b7ee0e4bdee56ea4c88441ebd13b7e3beafae89c08fa                                                                                 0.0s 
 => => exporting attestation manifest sha256:d33227fcca0797426d21cc53ce3a05acf1ba23dff7c536a178b0303e47005d1c                                                                   0.0s 
 => => exporting manifest list sha256:390d87814b1060b57e37dfb2e817fc86835c9f6a5a27c3e7018480492d0ea16d                                                                          0.0s 
 => => naming to docker.io/library/minipolish:0.2.1                                                                                                                             0.0s
 => => unpacking to docker.io/library/minipolish:0.2.1

erinyoung · 2026-03-13T15:28:35Z

I would recommend you go into your docker image after you build it and see the output.

The text I copy into these PR are the results from the GitHub Actions (GA). The link is https://github.com/StaPH-B/docker-builds/actions/runs/23016665625/job/66841744349?pr=1592

cwoodside1278 · 2026-03-13T16:06:56Z

So it appears my code fix worked! After I ran the image and checked it looks like all the tests were successful.

root@1672533d4e72:/test# cd /test
minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz > overlaps.paf
miniasm -f long_reads_high_depth.fastq.gz overlaps.paf -s 50 -e 1 > test.gfa
minipolish --threads 4 long_reads_high_depth.fastq.gz test.gfa > polished.gfa
head polished.gfa
[M::mm_idx_gen::0.281*1.00] collected minimizers
[M::mm_idx_gen::0.378*1.75] sorted minimizers
[M::main::0.378*1.75] loaded/built the index for 620 target sequence(s)
[M::mm_mapopt_update::0.409*1.69] mid_occ = 12
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 620
[M::mm_idx_stat::0.431*1.66] distinct minimizers: 1668886 (95.40% are singletons); average occurrences: 1.072; average spacing: 2.939; total length: 5259229
[M::worker_pipeline::0.730*2.34] mapped 620 sequences
[M::main] Version: 2.30-r1287
[M::main] CMD: minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz
[M::main] Real time: 0.740 sec; CPU: 1.721 sec; Peak RSS: 0.083 GB
[M::main] ===> Step 1: reading read mappings <===
[M::ma_hit_read::0.003*1.45] read 3616 hits; stored 7231 hits and 611 sequences (5221350 bp)
[M::main] ===> Step 2: 1-pass (crude) read selection <===
[M::ma_hit_sub::0.004*1.39] 81 query sequences remain after sub
[M::ma_hit_cut::0.004*1.38] 724 hits remain after cut
[M::ma_hit_flt::0.004*1.38] 710 hits remain after filtering; crude coverage after filtering: 6.40
[M::main] ===> Step 3: 2-pass (fine) read selection <===
[M::ma_hit_sub::0.004*1.38] 48 query sequences remain after sub
[M::ma_hit_cut::0.004*1.37] 466 hits remain after cut
[M::ma_hit_contained::0.004*1.37] 7 sequences and 20 hits remain after containment removal
[M::main] ===> Step 4: graph cleaning <===
[M::ma_sg_gen] read 18 arcs
[M::main] ===> Step 4.1: transitive reduction <===
[M::asg_arc_del_trans] transitively reduced 4 arcs
[M::asg_arc_del_multi] removed 0 multi-arcs
[M::asg_arc_del_asymm] removed 0 asymmetric arcs
[M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
[M::asg_cut_tip] cut 2 tips
[M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips
[M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===
[M::asg_arc_del_short] removed 0 short overlaps
[M::asg_arc_del_short] removed 0 short overlaps
[M::asg_arc_del_short] removed 0 short overlaps
[M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
[M::asg_cut_internal] cut 0 internal sequences
[M::asg_cut_biloop] cut 0 small bi-loops
[M::asg_cut_tip] cut 0 tips
[M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
[M::main] ===> Step 4.5: aggressively cutting short overlaps <===
[M::asg_arc_del_short] removed 0 short overlaps
[M::main] ===> Step 5: generating unitigs <===
[M::main] Version: 0.3-r179
[M::main] CMD: miniasm -f long_reads_high_depth.fastq.gz -s 50 -e 1 overlaps.paf
[M::main] Real time: 0.054 sec; CPU: 0.055 sec

erinyoung · 2026-03-13T16:20:22Z

You are completely correct! It looks like it's working now

21 [test 5/5] RUN minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz > overlaps.paf &&     miniasm -f long_reads_high_depth.fastq.gz overlaps.paf -s 50 -e 1 > test.gfa &&     minipolish --threads 4 long_reads_high_depth.fastq.gz test.gfa > polished.gfa &&     head polished.gfa
#21 0.245 [M::mm_idx_gen::0.193*1.01] collected minimizers
#21 0.321 [M::mm_idx_gen::0.269*1.82] sorted minimizers
#21 0.321 [M::main::0.269*1.82] loaded/built the index for 620 target sequence(s)
#21 0.345 [M::mm_mapopt_update::0.294*1.75] mid_occ = 12
#21 0.345 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 620
#21 0.365 [M::mm_idx_stat::0.313*1.71] distinct minimizers: 1668886 (95.40% are singletons); average occurrences: 1.072; average spacing: 2.939; total length: 5259229
#21 0.561 [M::worker_pipeline::0.509*2.28] mapped 620 sequences
#21 0.567 [M::main] Version: 2.30-r1287
#21 0.567 [M::main] CMD: minimap2 -x ava-ont -t 4 long_reads_high_depth.fastq.gz long_reads_high_depth.fastq.gz
#21 0.567 [M::main] Real time: 0.515 sec; CPU: 1.169 sec; Peak RSS: 0.081 GB
#21 0.573 [M::main] ===> Step 1: reading read mappings <===
#21 0.575 [M::ma_hit_read::0.003*1.25] read 3616 hits; stored 7231 hits and 611 sequences (5221350 bp)
#21 0.575 [M::main] ===> Step 2: 1-pass (crude) read selection <===
#21 0.575 [M::ma_hit_sub::0.003*1.21] 81 query sequences remain after sub
#21 0.576 [M::ma_hit_cut::0.003*1.21] 724 hits remain after cut
#21 0.576 [M::ma_hit_flt::0.003*1.20] 710 hits remain after filtering; crude coverage after filtering: 6.40
#21 0.576 [M::main] ===> Step 3: 2-pass (fine) read selection <===
#21 0.576 [M::ma_hit_sub::0.003*1.19] 48 query sequences remain after sub
#21 0.576 [M::ma_hit_cut::0.003*1.18] 466 hits remain after cut
#21 0.576 [M::ma_hit_contained::0.003*1.18] 7 sequences and 20 hits remain after containment removal
#21 0.576 [M::main] ===> Step 4: graph cleaning <===
#21 0.576 [M::ma_sg_gen] read 18 arcs
#21 0.576 [M::main] ===> Step 4.1: transitive reduction <===
#21 0.576 [M::asg_arc_del_trans] transitively reduced 4 arcs
#21 0.576 [M::asg_arc_del_multi] removed 0 multi-arcs
#21 0.576 [M::asg_arc_del_asymm] removed 0 asymmetric arcs
#21 0.576 [M::main] ===> Step 4.2: initial tip cutting and bubble popping <===
#21 0.576 [M::asg_cut_tip] cut 2 tips
#21 0.576 [M::asg_pop_bubble] popped 1 bubbles and trimmed 0 tips
#21 0.576 [M::main] ===> Step 4.3: cutting short overlaps (3 rounds in total) <===
#21 0.576 [M::asg_arc_del_short] removed 0 short overlaps
#21 0.576 [M::asg_arc_del_short] removed 0 short overlaps
#21 0.576 [M::asg_arc_del_short] removed 0 short overlaps
#21 0.576 [M::main] ===> Step 4.4: removing short internal sequences and bi-loops <===
#21 0.576 [M::asg_cut_internal] cut 0 internal sequences
#21 0.576 [M::asg_cut_biloop] cut 0 small bi-loops
#21 0.576 [M::asg_cut_tip] cut 0 tips
#21 0.576 [M::asg_pop_bubble] popped 0 bubbles and trimmed 0 tips
#21 0.576 [M::main] ===> Step 4.5: aggressively cutting short overlaps <===
#21 0.576 [M::asg_arc_del_short] removed 0 short overlaps
#21 1.028   input:      /tmp/tmpcbfu21nu/round_2.fasta (5,127 bp)
#21 1.127   alignments: /tmp/tmpcbfu21nu/round_2.paf (102 alignments)
#21 1.221   output:     /tmp/tmpcbfu21nu/round_2_polished.fasta (5,119 bp)
#21 1.221 
#21 1.221 
#21 1.221 Assign read depths
#21 1.221     The reads are aligned to the contigs one final time to calculate read depth
#21 1.221 values.
#21 1.221 
#21 1.221 Aligning reads:
#21 1.267   reads:      long_reads_high_depth.fastq.gz (620 reads)
#21 1.267   contigs:    /tmp/tmpcbfu21nu/depths.fasta (5,119 bp)
#21 1.368   alignments: /tmp/tmpcbfu21nu/depths.paf (120 alignments)
#21 1.368   mean depth: 49.757x
#21 1.368 
#21 1.378 S	utg000001c	TGAGATATGGAATCCAGAGGGCTATTTCTCAGGTAATAATAGCGAAGTACAGCAGTTTACTTATCATGATGCTGAAGACAATTTGAAAACCAGCACGACACATCTCCTAACTCGCAGATTAAGGATGCTGTGGAATGCAACAGTACTCGTTATCGATCGCTATCTGAAAAATATGTGAAAATATCAAAAAATGGGCAGCAGGAACCTTACTGATAAATTCCCAAGGTAGAAATCACAATGTGAATGACTCAGGGCTGCTTTAGAGAATACAAAGGAATGTATTAAGATAAAGAAAATTCGCAACACAGAAACCGGTCGAGGCAATTTTTCGTGACCTGGAGCGGTTAGTATGAGAACTGGGCTAAAAGCATTTAGAATAAAGTTGCCACAAGTACTTAAGTGTACGGGACCAAAGTTTCTTTGGTATGATGTATCTGATATCCTAAAAATTAGGATACAGGGTGACTTGGAAGCCGCATTTTTACATTAGAAGAAAGAAAGGCTGTAGATGCAGAGTTTATTTGTTGTTTTTACTTTTTAGTGTGCTGTGCCTGGAATTACATTCCGTAACTGGGATTGCTATTGTTACAGCCATTCTATTCGTGCCTTTATTGGTAAGAAAAACTTATACTTATAAATGAGTGTTGGGTATTTAATTATTCTTTATGATATAAACAGTCTAGCAATCAAATGGGAATTGCTAGGACCAAACAAAGTAGATTGTATAGCAAATAGGTTTAATTTGCCACGGGGGCATAATTTGGTTTTTTTTTTCTGAAAACCTTTTTTGATGAACTTAAAAAATATGTGTTCAATAGCCATATTTTGAATATGGGCATAGAATAGTGCTTATCACTATTGCGTATGAGCATCTTATCTGACGCTAGGAAATAATTACCCTTCGTTGTTTTTTGTTATAAGGTATTATATATAAGTGCGCAGTATTAGGCCAAACAAAATATTTTTTATCGTGGTATCTTAAACTCATAAATTAAACCTCGTATATATTCTTTTCATTTTATTAAGGATCGAGTTAGAGAGAAAAGATTTTTTTGTGGGAATATCCTATAACCTCCTTGTTGGATGTCAAGGCTAACAATAACGTGATGGTTCAGGGAGGGACTGCTGGCTCCACATTCTTCTTCTAAATTGAGCGGGGTCTCTTGTTCAGAGAAAAGATCAAAGGACTCTTCTTGAGCATCCTCTTTTCTGCGCGAAATCTGCTGCCTGTCAACGAAAAAAAGCGCCTGGGAGCCGCTGGTTTGATCGAAGGTTAGTCAGTTGGGGAAGTGCTTAACGCTGGTAACTGGTTCAGAGAGCGCAAGATAACCAAATACTATCCTTCCAGTGTGCCGTAGTCCGGGCACTACTTCAAGAACTCTGTTGCCCATTTGCGCCATACGCTCGCCTAACCAGTTACAACCGGCTGCTCCAGTGGCGCTAGTCGTGTCTTACGGGGTGACTCAAAGACGATAGTTAACCGGATAAGGGCAGGCGGTCCGGGCGAAGGGGGGTTCGTGTACACCAGCCCAGCTGTGGAGCGAACGAGTACACCGAGCCAGATACCAAACGAAGCGTCAGCCTTTGGAAAGCGCCACGCGTTGCGAAGGGAGAAAGGGGACAGGTATCCGGTAAGCGGCGGTTCGGAACAGGTGAGCGACGAGGGAGCTTCCAGGGGAAAGCGCTGTAATCTTTATAGTCCGTCGGGTTTCGGCACCTCTGGCTTGGCGTCGATTTTGTGATGCCTCGTCAGGGGGGCGGAGCCTTCGAAAAACGCCTGCGGCGACTTGGCTTCTTCCGGTGCTTTGCTTTTTGCTCACATGTATCTTTGCCCGCTTTCATCCCCTGTTCGTGGATAACCTGTATTACCGCTTTTGAGTGAGCTGACACCGCTCGCCGCAGTCGAACGGTCCCGAGCGAGCGAGTAGGTGAGCGAGGATGGGAAAGAGCGCCCTTAGTGACCATTTCTCCTTCACGCTCTGTTGTGCCGTTCGGCATGGTGTCCCTGAGCGTTAATCTCTCGTGTAGTTCTACTTGCAAAGGCGGTCTGGATGCTGTTCTGGGAGTTCTCTCGCAGAGTCGTGCAGCTTCTCACAAATGGTAAGCCTGTTCGTCGCATCGAGGCGTCCAGTTTTCGAGCAGCGTCAGGCTTTGGGCTTTTATGAAATCCTGCCATGTTGTGAGTACGCTTGCTGCTGCTAGTTTGATCTTTTCGTTTTCCCGTTCTGTCTGTCCTCTGCGTTGTGTGATTATACGCGTCCACTGTTGACTGTTTTACCCGCCGGTATCCGCCGTCTGACGCTTGAGGGAATTTCTGCCTGACATACTGTCACTTGCCCAAAAAACTGCCGTGCCTTTGTCGGGTAATTCGAACTTGCGGCAGGGACAGGATGTGGTAATTGTTAACCGCGCAACATCCACGCTATAGATACCCCGGGTCAGGAGCTTTGCCCCACGCCACCATGTCCAGATACGGAGCCATGTTTTAACTGACAATACGAAGTGAAGTATACGCCAGGCGGGGCAATCAGTCGCCTGTTCGTCTGACGCCAGAAGAGACAGGAAATCAGAACAGGGCTGCTGAATGCGGCAAGCCGTTTCCGGTTTTTCTTACGGGGCGGCAGCTCTCGTAAGAAAAGTTAACTCACTGACTGATGATCGGGTACGAAAGAAGTTATGAGACTGGGGGGGCGTTACAGAAAAACTCTTTTATCGACCGGCAAGCTTGCGGGGATAGGGGAAGAATGCGGAGGGGCTGATTGGCTAATACGGAGATCACGTTGCCTGTTATCCAGGGCTTATGCAAATTAGCTTCCCGGAGAGAAACTTCCAAAAACAGCGGTATGAAACCGTAAGCTCCCAAAAGTGATCACCGTGTCGCTTTCAATGCATACCTAGCGCAGTGAGCGGATACCGATTCTGACGCATCCTTCCTTTTTTCGGGGGCTAAACCCTCTTTGTTTTGCGTATTTGCCGTCCAGAATTGCCGTTCAGCGCGTTTCAGCGGTGCGGTACATTTAAGGGATTATGGGGTACATCCACTTACTGTCTTGCCCTTCTAGCCAACAGATAAACCGCAGAATCGTGCTCAGCCCGCAGCCTTTGGATTTTTCGGGGGTAAGGGTCTTTGTGGCGGTAATCAGTACCCGGCATTATTTGGCCCCGAGTGAGTGTTAAAACATTCCGCTGGCCTGAGAAACTGTTGAATGGCGTTGTTGCACATCACCTCGGTGGATCTTTCCTGTCCGCATTATCTTTAGCTCCCATATCCCGAACTGCGAAAAAGGCACCATCTTCGTTCGTAGTGTCGGATTTTTGGCGGAAAAGTTGGGTCAAAAACCGTCATCAGACAGCCAATATACGTAATGCCGGGGATGTTGTTCCACCCTGGCCTTTGGGGTACAGGCTTGAGAGCTACTGTTGCTGTTCATATGGCGATAAGAACCAAGTTTGTTCCCGGTACGTCTCATGGTGTCTCCCTACCTTAAATATTTATTCTCGGTGGGTTATTATCGAAAGATTATCTTATCATCAGTTTCTGAGCGGGGCAGTGACCGAACAGCCTGGACAGAACCCCGTTTTTTTCCTGCTCCCAGAGCCTGCCTGAGCTGGGCTATCTCATTCTGTAGCTGGTTCGTTTGGCTTCCTGGGCCGGCGCTCCGTATCCTGGGCTGTTTATCCTCAAGCATCAGGTCAGGCATTGTTTCAGGCTCATTTCAGTTCCGGAGAATTGGTTCTGGTCTGATATCATGAGTTTTTCTGAGTTCCTTGAGTTTGCCTTTCTGTGTCTCTCCGCTTTATTTTCGCCGTATGCCGGATCAGTTCCTGGTTTTCAAATCCCGTCTCCGTCCTGGGCTGGTACGGTTCACTAACAGACTAGCGCTATCACGGTTAAAACTGTGAACGCGTCTTCCATATTTTCATGCGTCCCGGAGTGGTGGCATGACATAAAGATACAAGGTCCATAAGGTTCTCATTCTCAGGGTTTCAGTTAAAACATAATTGAGGTCTGAGAAACGTAATGTTTGTCCGGTTTTTTTGGGGCACGGGTTCGAATAGCACGTGATTGTGGGGGGCTGTTTTTTTGATCTGTTTCACGAAATGACATCCAGAGGTGTAGTGGAAATGCAGCGCGTAATTTAAACTTATATAAAAACAGTGATTATATATACAGTATATTGTTTTTAACTATTTGTTTTTAATGTCAAAGAGGCATTATATAATGGAAACAGCTGTAGCCGTACAATAAAATGAGGTTCCTTTGAGATAAGGGGGCAGGTAATCATTCTCTTTTTGAATTGTAAATGCCAGACGGGAGTGCTCTGGCGGTGGGTGTGGAACATGGAGGTAGCAAAAGTGAAAGTCTGCAGCATCTTGCCACGCTAAATGGTCTACGTGCTTCAAATGAAGAGAACGCAGGCAGAACCAGGCTGCCCGAAGGCAAAAAGTCCGCAAGCACAGGCTAGCAAAAAGCAAACGGATGCGTTGACTCAACACGAAAAGGTATATTGTGGAATGAAGCGCTTCGCCATTATTCACGTCCATCCGAGGGTTATTGACCTGGCCATGACCAATAATTGAGCATGCAGGCAGAAAGCAGGGGGTTCGCCCTTGCAAAAGCAGAAGAAAAAGCGCCCGTAAGAGCGGAAGTCTGCGGAAAAGTCTTTTCAGGAAAGCAGAACAATACTAAAGAGATAGAGAAAGGAGCAGGCTGAGAACAAAAAGCCAATTGAACTGAGCTGAGGGATGTAAGGAAACGCCGGCAGCATTGGTGTGAGGCCCCGGGCTGGTGGAGGGGCACAAAAAAATCTTGCTGGGTGACACAAATAATGAGCTGGCGAAAGTGGATGAAGAGATTAATACGCCGCCATACCCGTAAGCTCCATATTCATGCCCCTGATGCGAAAGCGAATAGTATCCGGAAAACGAAATGAGTTGGATCAGGATCTGCTAAATATAAAGAACGGATGAAAGGGTTACAACTTTACTTCCTAGGGCGTATGAATCCGCCTTAGAGTCGCCTTTTTTTGAGCCCAGACTCGGGCGAGAGCTGGTGATGAATGGAGGAAAAACAAAAGAGGTAACAAGCATCAGAAACGCGTCTTAACCCGATTAGCTC	dp:f:49.757
#21 1.378 L	utg000001c	+	utg000001c	+	0M
#21 1.378 L	utg000001c	-	utg000001c	-	0M
#21 DONE 2.3s

erinyoung

I have no changes to recommend. I'll get this merged and deployed.

erinyoung · 2026-03-13T16:22:51Z

You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/23060171280

cwoodside1278 added 4 commits March 11, 2026 19:10

Create README.md for 0.2.1

0f1823a

Create Dockerfile for 0.2.1

e0fa605

Update README.md to include 0.2.1

619a2a2

Update Dockerfile

3f34a85

added pip install --break-system-packages v${MINIPOLISH_VER}.tar.gz && \

dockerfile- updating how the tools are tested

584862c

The very last line is the new code to test and try without a wrapper script

erinyoung approved these changes Mar 13, 2026

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erinyoung merged commit b35ed3b into StaPH-B:master Mar 13, 2026
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cwoodside1278 deleted the minipolish-0.2.1 branch March 27, 2026 15:56

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Update Minipolish to 0.2.1#1592

Update Minipolish to 0.2.1#1592
erinyoung merged 5 commits intoStaPH-B:masterfrom
cwoodside1278:minipolish-0.2.1

cwoodside1278 commented Mar 11, 2026

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cwoodside1278 commented Mar 11, 2026

Description

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Test build

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cwoodside1278 commented Mar 12, 2026 •

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