adding masurca version 4.1.4

[erinyoung]

There's a new version of masurca!

But it doesn't work with Docker.

This is the command and output:

$ masurca -t 2 -i short_reads_1.fastq.gz,short_reads_2.fastq.gz -r long_reads_low_depth.fastq.gz
Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
creating script file for the actions...done.
execute assemble.sh to run assembly
[Tue Jul  1 18:13:52 UTC 2025] Processing pe library reads
[Tue Jul  1 18:13:53 UTC 2025] Average PE read length 125
[Tue Jul  1 18:13:53 UTC 2025] Using kmer size of 83 for the graph
[Tue Jul  1 18:13:53 UTC 2025] MIN_Q_CHAR: 33
[Tue Jul  1 18:13:53 UTC 2025] Creating mer database for Quorum
[Tue Jul  1 18:13:58 UTC 2025] Error correct PE
[Tue Jul  1 18:14:11 UTC 2025] Estimating genome size
[Tue Jul  1 18:14:15 UTC 2025] Estimated genome size: 187640
[Tue Jul  1 18:14:15 UTC 2025] Creating k-unitigs with k=83
[Tue Jul  1 18:14:18 UTC 2025] Computing super reads from PE 
[Tue Jul  1 18:14:19 UTC 2025] Using CABOG from /MaSuRCA-4.1.3/bin/../CA8/Linux-amd64/bin
[Tue Jul  1 18:14:19 UTC 2025] Running mega-reads correction/assembly
[Tue Jul  1 18:14:19 UTC 2025] Using mer size 17 for mapping, B=15, d=0.02
[Tue Jul  1 18:14:19 UTC 2025] Estimated Genome Size 187640
[Tue Jul  1 18:14:19 UTC 2025] Estimated Ploidy 1
[Tue Jul  1 18:14:19 UTC 2025] Using 2 threads
[Tue Jul  1 18:14:19 UTC 2025] Output prefix mr.83.17.15.0.02
[Tue Jul  1 18:14:19 UTC 2025] Creating k-unitigs for k=19
[Tue Jul  1 18:14:20 UTC 2025] Pre-correcting long reads
[Tue Jul  1 18:14:22 UTC 2025] Pre-corrected reads are in longest_reads.25x.fa
[Tue Jul  1 18:14:22 UTC 2025] Computing mega-reads
[Tue Jul  1 18:14:22 UTC 2025] Running locally in 1 batch
[Tue Jul  1 18:14:22 UTC 2025] mega-reads pass 1 failed
[Tue Jul  1 18:14:22 UTC 2025] mega-reads exited before assembly

And the error:

$ cat create_mega-reads.err
set_mempolicy: Operation not permitted
setting interleave mask: Operation not permitted

This draft PR is just here as a placeholder. The prior PR placeholder (#908) was too out-of-date to use, so I created a new branch with the files.

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

One of these days...