[2024-01-25 18:45:20,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:20,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:20,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference
[2024-01-25 18:45:21,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:21,844] [INFO] Task started: Prodigal
[2024-01-25 18:45:21,844] [INFO] Running command: gunzip -c /var/lib/cwl/stgd268febf-9b86-4a02-9698-003876c0fc9f/GCF_002101635.1_ASM210163v1_genomic.fna.gz | prodigal -d GCF_002101635.1_ASM210163v1_genomic.fna/cds.fna -a GCF_002101635.1_ASM210163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:45,113] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:45,114] [INFO] Task started: HMMsearch
[2024-01-25 18:45:45,114] [INFO] Running command: hmmsearch --tblout GCF_002101635.1_ASM210163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/reference_markers.hmm GCF_002101635.1_ASM210163v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:45,382] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:45,383] [INFO] Found 6/6 markers.
[2024-01-25 18:45:45,433] [INFO] Query marker FASTA was written to GCF_002101635.1_ASM210163v1_genomic.fna/markers.fasta
[2024-01-25 18:45:45,433] [INFO] Task started: Blastn
[2024-01-25 18:45:45,433] [INFO] Running command: blastn -query GCF_002101635.1_ASM210163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/reference_markers.fasta -out GCF_002101635.1_ASM210163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:46,573] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:46,576] [INFO] Selected 9 target genomes.
[2024-01-25 18:45:46,577] [INFO] Target genome list was writen to GCF_002101635.1_ASM210163v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:46,582] [INFO] Task started: fastANI
[2024-01-25 18:45:46,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgd268febf-9b86-4a02-9698-003876c0fc9f/GCF_002101635.1_ASM210163v1_genomic.fna.gz --refList GCF_002101635.1_ASM210163v1_genomic.fna/target_genomes.txt --output GCF_002101635.1_ASM210163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:00,492] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:00,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:00,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:00,499] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:46:00,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:00,499] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	100.0	2040	2041	95	conclusive
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	99.9989	2041	2041	95	conclusive
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	90.3372	1693	2041	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	89.4396	1749	2041	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	89.4184	1759	2041	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	88.6188	1582	2041	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	88.3043	1594	2041	95	below_threshold
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	88.2148	1411	2041	95	below_threshold
Mycobacterium numidiamassiliense	strain=AB215	GCA_900157365.1	1841861	1841861	type	True	83.4817	1359	2041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:00,502] [INFO] DFAST Taxonomy check result was written to GCF_002101635.1_ASM210163v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:00,503] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:00,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:00,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/checkm_data
[2024-01-25 18:46:00,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:00,561] [INFO] Task started: CheckM
[2024-01-25 18:46:00,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101635.1_ASM210163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101635.1_ASM210163v1_genomic.fna/checkm_input GCF_002101635.1_ASM210163v1_genomic.fna/checkm_result
[2024-01-25 18:47:06,695] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:06,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:06,716] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:06,716] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:06,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101635.1_ASM210163v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:06,717] [INFO] Task started: Blastn
[2024-01-25 18:47:06,718] [INFO] Running command: blastn -query GCF_002101635.1_ASM210163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26ef1ab6-4595-4337-ab78-330380169527/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101635.1_ASM210163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:08,438] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:08,441] [INFO] Selected 11 target genomes.
[2024-01-25 18:47:08,441] [INFO] Target genome list was writen to GCF_002101635.1_ASM210163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:08,449] [INFO] Task started: fastANI
[2024-01-25 18:47:08,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgd268febf-9b86-4a02-9698-003876c0fc9f/GCF_002101635.1_ASM210163v1_genomic.fna.gz --refList GCF_002101635.1_ASM210163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101635.1_ASM210163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:24,776] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:24,784] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:24,784] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_010730355.1	s__Mycobacterium florentinum	99.9989	2041	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010731715.1	s__Mycobacterium stomatepiae	90.326	1695	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000689255.1	s__Mycobacterium triplex	89.4442	1748	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001373395.1	s__Mycobacterium lentiflavum	88.6839	1665	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176255.2	s__Mycobacterium ahvazicum	88.2884	1598	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526915.1	s__Mycobacterium genavense	88.2148	1411	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665235.1	s__Mycobacterium sp001665235	85.1737	1486	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157365.1	s__Mycobacterium numidiamassiliense	83.4883	1357	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	82.6811	1202	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_001667275.1	s__Mycobacterium sp001667275	82.6639	1254	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_001907675.1	s__Mycobacterium paraffinicum	82.4672	1213	2041	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:24,786] [INFO] GTDB search result was written to GCF_002101635.1_ASM210163v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:24,786] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:24,864] [INFO] DFAST_QC result json was written to GCF_002101635.1_ASM210163v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:24,864] [INFO] DFAST_QC completed!
[2024-01-25 18:47:24,864] [INFO] Total running time: 0h2m4s