Created
October 25, 2022 20:38
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$ ls exampleFiles | |
.gitkeep MW539688.1.fasta NC_016067.1.fasta test.fa | |
ilDeiPorc1.reads.fa MW539688.1.gb NC_016067.1.gb | |
$ time docker run --rm -w /data/ -v /home/jaruga/tmp/mitohifi/exampleFiles/:/data/ -t docker.io/biocontainers/mitohifi:2.2_cv1 mitohifi.py -c /data/test.fa -f /data/NC_016067.1.fasta -g /data/NC_016067.1.gb -t 4 -o 2 | |
2022-10-25 20:00:44 [INFO] Welcome to MitoHifi v2. Starting pipeline... | |
2022-10-25 20:00:44 [INFO] Length of related mitogenome is: 15659 bp | |
2022-10-25 20:00:44 [INFO] Number of genes on related mitogenome: 37 | |
2022-10-25 20:00:44 [INFO] Running MitoHifi pipeline in contigs mode... | |
2022-10-25 20:00:44 [INFO] 1. Fixing potentially conflicting FASTA headers | |
2022-10-25 20:00:44 [INFO] 2. Let's run the blast of the contigs versus the close-related mitogenome | |
2022-10-25 20:00:44 [INFO] 2.1. Creating BLAST database: | |
2022-10-25 20:00:44 [INFO] makeblastdb -in /data/NC_016067.1.fasta -dbtype nucl | |
2022-10-25 20:00:44 [INFO] Makeblastdb done. | |
2022-10-25 20:00:44 [INFO] 2.2. Running blast of contigs against close-related mitogenome: | |
2022-10-25 20:00:44 [INFO] blastn -query /data/test.fa -db /data/NC_016067.1.fasta -num_threads 4 -out contigs.blastn -outfmt 6 std qlen slen | |
2022-10-25 20:00:50 [INFO] Blast done. | |
2022-10-25 20:00:50 [INFO] 3. Filtering BLAST output to select target sequences | |
2022-10-25 20:00:50 [INFO] Filtering thresholds applied: | |
2022-10-25 20:00:50 [INFO] Minimum query percentage = 50 | |
2022-10-25 20:00:50 [INFO] Minimum query length = 80% subject length | |
2022-10-25 20:00:50 [INFO] Maximum query length = 5 times subject length | |
2022-10-25 20:00:51 [INFO] Filtering BLAST finished. A list of the filtered contigs was saved on ./contigs_filtering/contigs_ids.txt file | |
2022-10-25 20:00:51 [INFO] 4. Now we are going to circularize, annotate and rotate each filtered contig. Those are potential mitogenome(s). | |
2022-10-25 20:00:51 [INFO] Working with contig tig00007572_1 | |
2022-10-25 20:00:51 [INFO] Working with contig tig00007550_1 | |
2022-10-25 20:00:51 [INFO] Started tig00007550_1 circularization | |
2022-10-25 20:00:51 [INFO] Started tig00007572_1 circularization | |
2022-10-25 20:00:51 [INFO] tig00007572_1 circularization done. Circularization info saved on ./potential_contigs/tig00007572_1/tig00007572_1.circularisationCheck.txt | |
2022-10-25 20:00:51 [INFO] Started tig00007572_1 (MitoFinder) annotation | |
2022-10-25 20:00:51 [INFO] tig00007550_1 circularization done. Circularization info saved on ./potential_contigs/tig00007550_1/tig00007550_1.circularisationCheck.txt | |
2022-10-25 20:00:51 [INFO] Started tig00007550_1 (MitoFinder) annotation | |
2022-10-25 20:03:51 [INFO] tig00007550_1 annotation done. Annotation log saved on ./potential_contigs/tig00007550_1/tig00007550_1.annotation_MitoFinder.log | |
2022-10-25 20:03:52 [INFO] tig00007572_1 annotation done. Annotation log saved on ./potential_contigs/tig00007572_1/tig00007572_1.annotation_MitoFinder.log | |
2022-10-25 20:03:52 [INFO] Started tig00007572_1 rotation. | |
2022-10-25 20:03:52 [INFO] Started tig00007550_1 rotation. | |
2022-10-25 20:03:52 [INFO] Rotation of tig00007572_1 done. Rotated is at tig00007572_1.mitogenome.rotated.fa | |
2022-10-25 20:03:52 [INFO] Rotation of tig00007550_1 done. Rotated is at tig00007550_1.mitogenome.rotated.fa | |
Gene ND3 contains frameshift | |
Gene COX3 contains frameshift | |
Gene ATP6 contains frameshift | |
Gene COX2 contains frameshift | |
Gene COX1 contains frameshift | |
Gene ND2 contains frameshift | |
Gene ND1 contains frameshift | |
Gene CYTB contains frameshift | |
Gene ND6 contains frameshift | |
Gene ND4L contains frameshift | |
Gene ND4 contains frameshift | |
Gene ND5 contains frameshift | |
Gene ND1 contains frameshift | |
Gene CYTB contains frameshift | |
Gene ND6 contains frameshift | |
Gene ND4L contains frameshift | |
Gene ND4 contains frameshift | |
Gene ND5 contains frameshift | |
Gene ND3 contains frameshift | |
Gene COX3 contains frameshift | |
Gene ATP6 contains frameshift | |
Gene COX2 contains frameshift | |
Gene COX1 contains frameshift | |
Gene ND2 contains frameshift | |
2022-10-25 20:03:52 [INFO] 5. Now the rotated contigs will be aligned | |
2022-10-25 20:03:52 [INFO] List of contigs that will be aligned: ['tig00007572_1.mitogenome.rotated.fa', 'tig00007550_1.mitogenome.rotated.fa'] | |
2022-10-25 20:03:52 [INFO] MAFFT alignment will be called with: | |
mafft --quiet --clustalout --thread 4 all_mitogenomes.rotated.fa > all_mitogenomes.rotated.aligned.fa | |
2022-10-25 20:03:52 [INFO] Alignment done and saved at ./final_mitogenome_choice/all_mitogenomes.rotated.aligned.fa | |
2022-10-25 20:03:52 [INFO] 6. Now we will choose the most representative contig | |
/bin/MitoHiFi/getReprContig.py:96: UserWarning: Warning: representative contig contains frameshifts | |
warnings.warn("Warning: representative contig contains frameshifts") | |
2022-10-25 20:03:52 [INFO] Representative contig is tig00007550_1 that belongs to Cluster 0. This contig will be our final mitogenome. See all contigs and clusters in cdhit.out.clstr | |
2022-10-25 20:06:23 [INFO] 7. Calculating final stats for final mitogenome and other potential contigs. | |
Stats will be saved on contigs_stats.tsv file. | |
Gene ND3 contains frameshift | |
Gene COX3 contains frameshift | |
Gene ATP6 contains frameshift | |
Gene COX2 contains frameshift | |
Gene COX1 contains frameshift | |
Gene ND2 contains frameshift | |
Gene ND1 contains frameshift | |
Gene CYTB contains frameshift | |
Gene ND6 contains frameshift | |
Gene ND4L contains frameshift | |
Gene ND4 contains frameshift | |
Gene ND5 contains frameshift | |
2022-10-25 20:06:23 [INFO] Pipeline finished! | |
2022-10-25 20:06:23 [INFO] Run time: 338.59 seconds | |
real 5m41.835s | |
user 0m0.044s | |
sys 0m0.032s |
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