[2024-01-24 14:28:02,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,983] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference
[2024-01-24 14:28:04,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,229] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,230] [INFO] Running command: gunzip -c /var/lib/cwl/stgc434adba-8850-4e15-985a-a261d8a74c6b/GCF_000689255.1_BN973_1_genomic.fna.gz | prodigal -d GCF_000689255.1_BN973_1_genomic.fna/cds.fna -a GCF_000689255.1_BN973_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:26,674] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:26,675] [INFO] Task started: HMMsearch
[2024-01-24 14:28:26,675] [INFO] Running command: hmmsearch --tblout GCF_000689255.1_BN973_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/reference_markers.hmm GCF_000689255.1_BN973_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:27,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:27,137] [INFO] Found 6/6 markers.
[2024-01-24 14:28:27,212] [INFO] Query marker FASTA was written to GCF_000689255.1_BN973_1_genomic.fna/markers.fasta
[2024-01-24 14:28:27,213] [INFO] Task started: Blastn
[2024-01-24 14:28:27,213] [INFO] Running command: blastn -query GCF_000689255.1_BN973_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/reference_markers.fasta -out GCF_000689255.1_BN973_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:28,541] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:28,554] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:28,555] [INFO] Target genome list was writen to GCF_000689255.1_BN973_1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:28,566] [INFO] Task started: fastANI
[2024-01-24 14:28:28,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgc434adba-8850-4e15-985a-a261d8a74c6b/GCF_000689255.1_BN973_1_genomic.fna.gz --refList GCF_000689255.1_BN973_1_genomic.fna/target_genomes.txt --output GCF_000689255.1_BN973_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:51,790] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:51,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:51,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:51,808] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:51,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:51,809] [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 triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	100.0	2125	2125	95	conclusive
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	99.9795	2093	2125	95	conclusive
Mycobacterium genavense	strain=ATCC 51234	GCA_000526915.1	36812	36812	type	True	93.8759	1497	2125	95	below_threshold
Mycobacterium florentinum	strain=JCM 14740	GCA_010730355.1	292462	292462	type	True	89.5075	1752	2125	95	below_threshold
Mycobacterium florentinum	strain=DSM 44852	GCA_002101635.1	292462	292462	type	True	89.4174	1763	2125	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	89.0981	1636	2125	95	below_threshold
Mycobacterium lentiflavum	strain=ATCC 51985	GCA_022374895.2	141349	141349	type	True	88.6593	1597	2125	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	88.1326	1604	2125	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	84.2757	1385	2125	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	83.4377	1191	2125	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	83.4205	1289	2125	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	83.3821	1299	2125	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	83.3305	1221	2125	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	78.8578	614	2125	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	78.8416	771	2125	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	78.8121	610	2125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:51,812] [INFO] DFAST Taxonomy check result was written to GCF_000689255.1_BN973_1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:51,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:51,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:51,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/checkm_data
[2024-01-24 14:28:51,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:51,873] [INFO] Task started: CheckM
[2024-01-24 14:28:51,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000689255.1_BN973_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000689255.1_BN973_1_genomic.fna/checkm_input GCF_000689255.1_BN973_1_genomic.fna/checkm_result
[2024-01-24 14:29:55,627] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:55,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:55,651] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:55,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:55,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000689255.1_BN973_1_genomic.fna/markers.fasta)
[2024-01-24 14:29:55,652] [INFO] Task started: Blastn
[2024-01-24 14:29:55,652] [INFO] Running command: blastn -query GCF_000689255.1_BN973_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf770c20-7e83-4e8d-b6cf-1489bb41af01/dqc_reference/reference_markers_gtdb.fasta -out GCF_000689255.1_BN973_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:57,299] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:57,303] [INFO] Selected 16 target genomes.
[2024-01-24 14:29:57,303] [INFO] Target genome list was writen to GCF_000689255.1_BN973_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:57,333] [INFO] Task started: fastANI
[2024-01-24 14:29:57,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgc434adba-8850-4e15-985a-a261d8a74c6b/GCF_000689255.1_BN973_1_genomic.fna.gz --refList GCF_000689255.1_BN973_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000689255.1_BN973_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:20,614] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:20,634] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:20,635] [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_000689255.1	s__Mycobacterium triplex	100.0	2125	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000526915.1	s__Mycobacterium genavense	93.8629	1498	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730355.1	s__Mycobacterium florentinum	89.4989	1753	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900176255.2	s__Mycobacterium ahvazicum	89.1136	1634	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001373395.1	s__Mycobacterium lentiflavum	88.4218	1675	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731715.1	s__Mycobacterium stomatepiae	88.1295	1606	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112775.1	s__Mycobacterium montefiorense	86.8319	1533	2125	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	85.1649	1454	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102355.1	s__Mycobacterium sherrisii	84.2882	1383	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	-
GCF_900157375.1	s__Mycobacterium rhizamassiliense	84.2362	1403	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727605.1	s__Mycobacterium simiae	83.8405	1396	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
GCF_003284935.1	s__Mycobacterium arosiense_A	83.6582	1221	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356315.1	s__Mycobacterium shigaense	83.3811	1298	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.82	1.00	1.00	3	-
GCF_001907675.1	s__Mycobacterium paraffinicum	83.3203	1348	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086125.1	s__Mycobacterium arosiense	83.3202	1222	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	78.86	683	2125	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:20,637] [INFO] GTDB search result was written to GCF_000689255.1_BN973_1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:20,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:20,644] [INFO] DFAST_QC result json was written to GCF_000689255.1_BN973_1_genomic.fna/dqc_result.json
[2024-01-24 14:30:20,644] [INFO] DFAST_QC completed!
[2024-01-24 14:30:20,644] [INFO] Total running time: 0h2m18s