[2024-01-24 11:43:35,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:35,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:35,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference
[2024-01-24 11:43:36,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,265] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,265] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0519b55-2513-4221-9613-f843a2a24ad3/GCF_022370755.2_ASM2237075v2_genomic.fna.gz | prodigal -d GCF_022370755.2_ASM2237075v2_genomic.fna/cds.fna -a GCF_022370755.2_ASM2237075v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:03,844] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:03,845] [INFO] Task started: HMMsearch
[2024-01-24 11:44:03,845] [INFO] Running command: hmmsearch --tblout GCF_022370755.2_ASM2237075v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/reference_markers.hmm GCF_022370755.2_ASM2237075v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:04,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:04,188] [INFO] Found 6/6 markers.
[2024-01-24 11:44:04,248] [INFO] Query marker FASTA was written to GCF_022370755.2_ASM2237075v2_genomic.fna/markers.fasta
[2024-01-24 11:44:04,249] [INFO] Task started: Blastn
[2024-01-24 11:44:04,249] [INFO] Running command: blastn -query GCF_022370755.2_ASM2237075v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/reference_markers.fasta -out GCF_022370755.2_ASM2237075v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,441] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,446] [INFO] Selected 24 target genomes.
[2024-01-24 11:44:05,446] [INFO] Target genome list was writen to GCF_022370755.2_ASM2237075v2_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,456] [INFO] Task started: fastANI
[2024-01-24 11:44:05,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0519b55-2513-4221-9613-f843a2a24ad3/GCF_022370755.2_ASM2237075v2_genomic.fna.gz --refList GCF_022370755.2_ASM2237075v2_genomic.fna/target_genomes.txt --output GCF_022370755.2_ASM2237075v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:37,095] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:37,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:37,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:37,118] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:37,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:37,119] [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	82.6024	1418	2247	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	81.8057	1210	2247	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	81.7582	1341	2247	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	81.7425	1369	2247	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	81.6151	1225	2247	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	81.5904	1212	2247	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	81.5826	1246	2247	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	81.436	1264	2247	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	81.3572	1171	2247	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	81.2622	1074	2247	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	81.2121	1154	2247	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	81.16	1165	2247	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	81.1537	1202	2247	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	81.1032	1174	2247	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	81.0042	1207	2247	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.5578	1083	2247	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.513	1075	2247	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	80.1407	966	2247	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	80.1366	966	2247	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.0402	942	2247	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5306	845	2247	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.512	823	2247	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4044	842	2247	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.1992	834	2247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:37,120] [INFO] DFAST Taxonomy check result was written to GCF_022370755.2_ASM2237075v2_genomic.fna/tc_result.tsv
[2024-01-24 11:44:37,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:37,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:37,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/checkm_data
[2024-01-24 11:44:37,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:37,191] [INFO] Task started: CheckM
[2024-01-24 11:44:37,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022370755.2_ASM2237075v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022370755.2_ASM2237075v2_genomic.fna/checkm_input GCF_022370755.2_ASM2237075v2_genomic.fna/checkm_result
[2024-01-24 11:46:40,859] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:40,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:40,885] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:40,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:40,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022370755.2_ASM2237075v2_genomic.fna/markers.fasta)
[2024-01-24 11:46:40,886] [INFO] Task started: Blastn
[2024-01-24 11:46:40,887] [INFO] Running command: blastn -query GCF_022370755.2_ASM2237075v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80abc0ec-b3aa-488e-988f-7603dc6aa01a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022370755.2_ASM2237075v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:42,731] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:42,735] [INFO] Selected 16 target genomes.
[2024-01-24 11:46:42,736] [INFO] Target genome list was writen to GCF_022370755.2_ASM2237075v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:42,767] [INFO] Task started: fastANI
[2024-01-24 11:46:42,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0519b55-2513-4221-9613-f843a2a24ad3/GCF_022370755.2_ASM2237075v2_genomic.fna.gz --refList GCF_022370755.2_ASM2237075v2_genomic.fna/target_genomes_gtdb.txt --output GCF_022370755.2_ASM2237075v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:06,248] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:06,265] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:06,265] [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_002798385.1	s__Mycobacterium goodii	99.1098	1976	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	conclusive
GCF_001187505.1	s__Mycobacterium goodii_B	88.7015	1830	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457595.1	s__Mycobacterium smegmatis	88.6134	1862	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002101965.1	s__Mycobacterium wolinskyi	82.6135	1416	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.70	97.70	0.86	0.86	2	-
GCF_900078665.2	s__Mycobacterium houstonense	81.7924	1212	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	81.7506	1369	2247	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	81.5851	1215	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001942045.1	s__Mycobacterium porcinum_A	81.5549	1177	2247	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	81.5096	1238	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	81.2188	1145	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_000295855.1	s__Mycobacterium fortuitum	81.1436	1168	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	81.0229	1223	2247	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	80.8195	1215	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.3802	896	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101555.1	s__Mycobacterium canariasense	80.129	968	2247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010729895.1	s__Mycobacterium confluentis	79.9654	937	2247	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 11:47:06,267] [INFO] GTDB search result was written to GCF_022370755.2_ASM2237075v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:06,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:06,272] [INFO] DFAST_QC result json was written to GCF_022370755.2_ASM2237075v2_genomic.fna/dqc_result.json
[2024-01-24 11:47:06,272] [INFO] DFAST_QC completed!
[2024-01-24 11:47:06,272] [INFO] Total running time: 0h3m31s