Closed Kincekara closed 2 weeks ago
It looks like the tests worked.
#12 [test 3/3] RUN el_gato.py --assembly GCF_900119765.1_2532STDY5467631_genomic.fna --out test/ && cat test/run.log
#12 0.726 GCF_900119765.1_2532STDY5467631_genomic 62 8 10 3 15 18 1 6
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Running el_gato version 1.20.0
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Starting preprocessing
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] User supplied the assembly file, adopting the alignment/in silico pcr route
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] New output directory created
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking if all the prerequisite programs are installed
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking for program minimap2
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] minimap2 version is 2.24-r1122
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking for program samtools
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] samtools version is samtools 1.13
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking for program makeblastdb
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] makeblastdb version is makeblastdb: 2.12.0+
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking for program blastn
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] blastn version is blastn: 2.12.0+
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking for program isPcr
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] isPcr version is 33x2
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] All prerequisite programs are accessible
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Checking if all the required input files exist
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Input files are present
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Ensuring thread counts are correct
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Thread count has been validated
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] All reference files have been discovered
#12 0.736 [10/01/2024 07:27:19 PM | test/ ] Parameters input:
#12 0.736 Read 1 None
#12 0.736 Read 2 None
#12 0.736 caaggcgatttgactttagacgttggttacatgtggtttaactacttcaa
#12 0.736 cgctatgcacaatactggcgtatttaatggatttgaaaCTGATTTCGCAG
#12 0.736 CTTCTG
#12 0.736
#12 0.736
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Finished running mompS2 primer2
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Found the sequence: >NZ_LT632614.1:3483454-3484167:1+606 mompS_2 606bp TTGACCATGAGTGGGATTGG CAGAAGCTGCGAAATCAG
#12 0.736 TTGACCATGAGTGGGATTGGggcttcaaattagaaggttcttatcacttc
#12 0.736 aatactggtaatgacatcaatgtgaactggtatcattttgataatgacag
#12 0.736 cgatcactgggctgattttgctaactggcacaactacaacaacaagtggg
#12 0.736 atgctgttaatgctgaattaggtcaattcgtagatttcagcgctaacaag
#12 0.736 aaaatgcgtttccacggcggtgttcaatacgctcgcattgaagctgatgt
#12 0.736 gaaccgttatttcaataactttgcctttaacgggttcaactctaagttca
#12 0.736 atggctttggtcctcgcactggtttagacatgaactatgtatttggcaat
#12 0.736 ggctttggtgtttatgctaaaggagctgctgctattctggttggtaccag
#12 0.736 cgatttctacgatggaatcaacttcattaatggctctaaaaatgccatcg
#12 0.736 ttcctgagttagaagctaagcttggtgctgattacacttacgcaatggct
#12 0.736 caaggcgatttgactttagacgttggttacatgtggtttaactacttcaa
#12 0.736 cgctatgcacaatactggcgtatttaatggatttgaaaCTGATTTCGCAG
#12 0.736 CTTCTG
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Looking for
#12 0.736 >NZ_LT632614.1:3483454-3484167:1+606 mompS_2 606bp TTGACCATGAGTGGGATTGG CAGAAGCTGCGAAATCAG
#12 0.736 TTGACCATGAGTGGGATTGGggcttcaaattagaaggttcttatcacttc
#12 0.736 aatactggtaatgacatcaatgtgaactggtatcattttgataatgacag
#12 0.736 cgatcactgggctgattttgctaactggcacaactacaacaacaagtggg
#12 0.736 atgctgttaatgctgaattaggtcaattcgtagatttcagcgctaacaag
#12 0.736 aaaatgcgtttccacggcggtgttcaatacgctcgcattgaagctgatgt
#12 0.736 gaaccgttatttcaataactttgcctttaacgggttcaactctaagttca
#12 0.736 atggctttggtcctcgcactggtttagacatgaactatgtatttggcaat
#12 0.736 ggctttggtgtttatgctaaaggagctgctgctattctggttggtaccag
#12 0.736 cgatttctacgatggaatcaacttcattaatggctctaaaaatgccatcg
#12 0.736 ttcctgagttagaagctaagcttggtgctgattacacttacgcaatggct
#12 0.736 caaggcgatttgactttagacgttggttacatgtggtttaactacttcaa
#12 0.736 cgctatgcacaatactggcgtatttaatggatttgaaaCTGATTTCGCAG
#12 0.736 CTTCTG
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Running command: blastn -query - -db /usr/local/bin/db/all_loci.fasta -outfmt '6 std qlen slen sseqid' -max_target_seqs 50000 | awk -F'\t' '{OFS=FS}{gsub(/_.+/, "", $15)}1' | sort -k15,15 -k12,12gr | sort -u -k15,15
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Running blastn/mompS
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Command log for blastn/mompS:
#12 0.736 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen sseqid
#12 0.736 NZ_LT632614.1:3483454-3484167:1+606 mompS_18 100.000 352 0 0 94 445 1 352 0.0 651 606 352 mompS
#12 0.736
#12 0.736
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Finished running blastn/mompS
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] mompS alleles identified: 18
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Running command: blastn -query GCF_900119765.1_2532STDY5467631_genomic.fna -db /usr/local/bin/db/all_loci.fasta -outfmt '6 std qlen slen' -max_target_seqs 50000
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Running blast
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Finished running blast
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Command log for blast:
#12 0.736 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen
#12 0.736 NZ_LT632614.1 flaA_8 100.000 182 0 0 1498635 1498816 182 1 2.16e-90 337 3530817 182
#12 0.736 NZ_LT632614.1 pilE_10 100.000 333 0 0 721006 721338 333 1 2.48e-174 616 3530817 333
#12 0.736 NZ_LT632614.1 asd_3 100.000 473 0 0 2650534 2651006 473 1 0.0 874 3530817 473
#12 0.736 NZ_LT632614.1 mip_15 100.000 402 0 0 941537 941938 1 402 0.0 743 3530817 402
#12 0.736 NZ_LT632614.1 proA_1 100.000 405 0 0 568377 568781 1 405 0.0 749 3530817 405
#12 0.736 NZ_LT632614.1 neuA_neuAH_6 100.000 354 0 0 898051 898404 1 354 0.0 654 3530817 354
#12 0.736
#12 0.736
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Finished running blast
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Finished analysis
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] Output =
#12 0.736 GCF_900119765.1_2532STDY5467631_genomic 62 8 10 3 15 18 1 6
#12 0.736
#12 0.736 [10/01/2024 07:27:20 PM | test/ ] The program took 0s
#12 DONE 0.7s
Thank you for putting this together!
You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/11147021617
No major changes.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15
)spades/3.12.0/Dockerfile
)shigatyper/2.0.1/test.sh
)spades/3.12.0/README.md
)