Updated and fixed bugs in pubmlst and ncbi downloads

[talnor]

Description

The features of this PR primarily concerns bioinformaticians

Summary of the changes made:

• Bug fix for ncbi reference download
• Updated pubmlst external reference download
• Added force_update flag for analyse command

If not self-evident, mention what prompted the change. The pubmlst website was updated and those mlst profiles that were only linked to pubmlst could therefore not be updated.

Primary function of PR

• [ ] Hotfix
• [X] Patch
• [ ] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

Test routine to verify the stability of the PR:

• _bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh fix_referencer_

• us

• _source activate S_microSALT_

• cg workflow microsalt config-case -t 244354

• _Remove the following references from the stage genomes directory: NC_016845.1 and NC_011751.1_

• microSALT analyse /home/proj/stage/microbial/queries/244354.json --input /home/proj/stage/microbial/fastq/ACC6369

• Verify that the removed references are redownloaded and indexed

• Verify that there are no unexpected errors when running

• cg workflow microsalt config-case ACC6369A41

• _microSALT analyse /home/proj/stage/microbial/queries/ACC6369A42.json --input /home/proj/stage/microbial/fastq/ACC6369/ACC6369A41 --force_update_

• Verify that the MLST profiles for E. coli are updated

• Verify that there are no unexpected errors when running

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR. References and MLST updated, see below for results. Also no errors from force flag.

Sign-offs

• [x] Code tested by @talnor
• [x] Approved to run at Clinical-Genomics by @sylvinite

[talnor]

Fixes issue #122

[talnor]

Reference download:

INFO - Downloaded reference NC_011751.1
INFO - Downloaded reference NC_016845.1

[21|278|284] 13d [hiseq.clinical@hasta:/home/proj/stage/microbial] [S_microSALT] $ ll references/genomes/NC_016845.1*
-rw-rw-r--+ 1 hiseq.clinical hasta-development 5410232 Nov 11 11:09 references/genomes/NC_016845.1.fasta
-rw-rw-r--+ 1 hiseq.clinical hasta-development      24 Nov 11 11:09 references/genomes/NC_016845.1.fasta.amb
-rw-rw-r--+ 1 hiseq.clinical hasta-development     115 Nov 11 11:09 references/genomes/NC_016845.1.fasta.ann
-rw-rw-r--+ 1 hiseq.clinical hasta-development 5334020 Nov 11 11:09 references/genomes/NC_016845.1.fasta.bwt
-rw-rw-r--+ 1 hiseq.clinical hasta-development      29 Nov 11 11:09 references/genomes/NC_016845.1.fasta.fai
-rw-rw-r--+ 1 hiseq.clinical hasta-development 1333487 Nov 11 11:09 references/genomes/NC_016845.1.fasta.pac
-rw-rw-r--+ 1 hiseq.clinical hasta-development 2667024 Nov 11 11:09 references/genomes/NC_016845.1.fasta.sa
[19|276|288] θ60° 13d [hiseq.clinical@hasta:/home/proj/stage/microbial] [S_microSALT] $ ll references/genomes/NC_011751.1*
-rw-rw-r--+ 1 hiseq.clinical hasta-development 5276461 Nov 11 11:09 references/genomes/NC_011751.1.fasta
-rw-rw-r--+ 1 hiseq.clinical hasta-development      12 Nov 11 11:09 references/genomes/NC_011751.1.fasta.amb
-rw-rw-r--+ 1 hiseq.clinical hasta-development      80 Nov 11 11:09 references/genomes/NC_011751.1.fasta.ann
-rw-rw-r--+ 1 hiseq.clinical hasta-development 5202176 Nov 11 11:09 references/genomes/NC_011751.1.fasta.bwt
-rw-rw-r--+ 1 hiseq.clinical hasta-development      29 Nov 11 11:09 references/genomes/NC_011751.1.fasta.fai
-rw-rw-r--+ 1 hiseq.clinical hasta-development 1300524 Nov 11 11:09 references/genomes/NC_011751.1.fasta.pac
-rw-rw-r--+ 1 hiseq.clinical hasta-development 2601096 Nov 11 11:09 references/genomes/NC_011751.1.fasta.sa

[talnor]

Update external MLST:

INFO - Downloading new MLST profiles for Escherichia coli#1

INFO - Re-indexed contents of /home/proj/stage/microbial/references/ST_loci/escherichia_coli

references/ST_loci/escherichia_coli:
total 11776
-rw-rw-r--+ 1 hiseq.clinical hasta-development  43130 Nov 11 16:20 adk.nhr
-rw-rw-r--+ 1 hiseq.clinical hasta-development  11384 Nov 11 16:20 adk.nin
-rw-rw-r--+ 1 hiseq.clinical hasta-development   3780 Nov 11 16:20 adk.nog
-rw-rw-r--+ 1 hiseq.clinical hasta-development  26072 Nov 11 16:20 adk.nsd
-rw-rw-r--+ 1 hiseq.clinical hasta-development    702 Nov 11 16:20 adk.nsi
-rw-rw-r--+ 1 hiseq.clinical hasta-development 126496 Nov 11 16:20 adk.nsq
-rw-rw-r--+ 1 hiseq.clinical hasta-development 511630 Nov 11 16:20 adk.tfa
-rw-rw-r--+ 1 hiseq.clinical hasta-development  70558 Nov 11 16:20 fumC.nhr
-rw-rw-r--+ 1 hiseq.clinical hasta-development  18032 Nov 11 16:20 fumC.nin
-rw-rw-r--+ 1 hiseq.clinical hasta-development   5996 Nov 11 16:20 fumC.nog
-rw-rw-r--+ 1 hiseq.clinical hasta-development  46454 Nov 11 16:20 fumC.nsd