[2024-01-24 13:01:24,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference
[2024-01-24 13:01:25,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,479] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg0683f51b-d8a0-4814-a577-73d8d85416fa/GCF_001457595.1_NCTC8159_genomic.fna.gz | prodigal -d GCF_001457595.1_NCTC8159_genomic.fna/cds.fna -a GCF_001457595.1_NCTC8159_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:48,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:48,858] [INFO] Task started: HMMsearch
[2024-01-24 13:01:48,858] [INFO] Running command: hmmsearch --tblout GCF_001457595.1_NCTC8159_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/reference_markers.hmm GCF_001457595.1_NCTC8159_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:49,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:49,226] [INFO] Found 6/6 markers.
[2024-01-24 13:01:49,286] [INFO] Query marker FASTA was written to GCF_001457595.1_NCTC8159_genomic.fna/markers.fasta
[2024-01-24 13:01:49,286] [INFO] Task started: Blastn
[2024-01-24 13:01:49,286] [INFO] Running command: blastn -query GCF_001457595.1_NCTC8159_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/reference_markers.fasta -out GCF_001457595.1_NCTC8159_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:50,549] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:50,553] [INFO] Selected 24 target genomes.
[2024-01-24 13:01:50,553] [INFO] Target genome list was writen to GCF_001457595.1_NCTC8159_genomic.fna/target_genomes.txt
[2024-01-24 13:01:50,562] [INFO] Task started: fastANI
[2024-01-24 13:01:50,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg0683f51b-d8a0-4814-a577-73d8d85416fa/GCF_001457595.1_NCTC8159_genomic.fna.gz --refList GCF_001457595.1_NCTC8159_genomic.fna/target_genomes.txt --output GCF_001457595.1_NCTC8159_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:22,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:22,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:22,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:22,300] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:02:22,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:02:22,300] [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
Mycolicibacterium wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	82.4818	1418	2327	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	82.1461	1368	2327	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	82.1362	1367	2327	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	82.008	1268	2327	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	81.9826	1256	2327	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	81.8501	1270	2327	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	81.8394	1278	2327	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	81.771	1254	2327	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	81.6739	1302	2327	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	81.6571	1212	2327	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	81.5527	1200	2327	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	81.5211	1214	2327	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	81.507	1128	2327	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	81.493	1205	2327	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	81.4331	1218	2327	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.9507	1123	2327	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.9095	1101	2327	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.465	1065	2327	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	80.3757	1008	2327	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	80.3407	1012	2327	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.8608	859	2327	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.7601	917	2327	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6263	916	2327	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.6026	865	2327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:22,301] [INFO] DFAST Taxonomy check result was written to GCF_001457595.1_NCTC8159_genomic.fna/tc_result.tsv
[2024-01-24 13:02:22,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:22,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:22,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/checkm_data
[2024-01-24 13:02:22,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:22,365] [INFO] Task started: CheckM
[2024-01-24 13:02:22,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001457595.1_NCTC8159_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001457595.1_NCTC8159_genomic.fna/checkm_input GCF_001457595.1_NCTC8159_genomic.fna/checkm_result
[2024-01-24 13:04:08,451] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:08,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:08,474] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:08,475] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:08,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001457595.1_NCTC8159_genomic.fna/markers.fasta)
[2024-01-24 13:04:08,476] [INFO] Task started: Blastn
[2024-01-24 13:04:08,476] [INFO] Running command: blastn -query GCF_001457595.1_NCTC8159_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d3f2b31-965e-426d-97bd-c8ffade44945/dqc_reference/reference_markers_gtdb.fasta -out GCF_001457595.1_NCTC8159_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:10,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:10,348] [INFO] Selected 15 target genomes.
[2024-01-24 13:04:10,348] [INFO] Target genome list was writen to GCF_001457595.1_NCTC8159_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:10,359] [INFO] Task started: fastANI
[2024-01-24 13:04:10,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg0683f51b-d8a0-4814-a577-73d8d85416fa/GCF_001457595.1_NCTC8159_genomic.fna.gz --refList GCF_001457595.1_NCTC8159_genomic.fna/target_genomes_gtdb.txt --output GCF_001457595.1_NCTC8159_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:36,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:36,338] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:36,338] [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_001457595.1	s__Mycobacterium smegmatis	100.0	2326	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	conclusive
GCF_001187505.1	s__Mycobacterium goodii_B	88.7864	1839	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	88.4208	1772	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002101965.1	s__Mycobacterium wolinskyi	82.4666	1421	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.70	97.70	0.86	0.86	2	-
GCF_010727475.1	s__Mycobacterium mageritense	82.1034	1377	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_010731295.1	s__Mycobacterium boenickei	82.0087	1266	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_900078665.2	s__Mycobacterium houstonense	81.9929	1255	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942045.1	s__Mycobacterium porcinum_A	81.9103	1196	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	81.7793	1288	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001583415.1	s__Mycobacterium phlei	81.7301	1169	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	81.4682	1248	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	81.4197	1221	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665685.1	s__Mycobacterium sp001665685	81.2152	1200	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	81.2025	1147	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729895.1	s__Mycobacterium confluentis	80.4451	1024	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:36,340] [INFO] GTDB search result was written to GCF_001457595.1_NCTC8159_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:36,340] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:36,345] [INFO] DFAST_QC result json was written to GCF_001457595.1_NCTC8159_genomic.fna/dqc_result.json
[2024-01-24 13:04:36,346] [INFO] DFAST_QC completed!
[2024-01-24 13:04:36,346] [INFO] Total running time: 0h3m12s