[2024-01-24 11:02:49,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:49,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:49,226] [INFO] DQC Reference Directory: /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference
[2024-01-24 11:02:50,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:50,423] [INFO] Task started: Prodigal
[2024-01-24 11:02:50,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ac69c5e-f28c-43a3-a823-64c94d6576d1/GCF_025821985.1_ASM2582198v1_genomic.fna.gz | prodigal -d GCF_025821985.1_ASM2582198v1_genomic.fna/cds.fna -a GCF_025821985.1_ASM2582198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:03:08,109] [INFO] Task succeeded: Prodigal
[2024-01-24 11:03:08,110] [INFO] Task started: HMMsearch
[2024-01-24 11:03:08,110] [INFO] Running command: hmmsearch --tblout GCF_025821985.1_ASM2582198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/reference_markers.hmm GCF_025821985.1_ASM2582198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:03:08,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:03:08,409] [INFO] Found 6/6 markers.
[2024-01-24 11:03:08,462] [INFO] Query marker FASTA was written to GCF_025821985.1_ASM2582198v1_genomic.fna/markers.fasta
[2024-01-24 11:03:08,462] [INFO] Task started: Blastn
[2024-01-24 11:03:08,462] [INFO] Running command: blastn -query GCF_025821985.1_ASM2582198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/reference_markers.fasta -out GCF_025821985.1_ASM2582198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:09,684] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:09,688] [INFO] Selected 30 target genomes.
[2024-01-24 11:03:09,688] [INFO] Target genome list was writen to GCF_025821985.1_ASM2582198v1_genomic.fna/target_genomes.txt
[2024-01-24 11:03:09,712] [INFO] Task started: fastANI
[2024-01-24 11:03:09,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac69c5e-f28c-43a3-a823-64c94d6576d1/GCF_025821985.1_ASM2582198v1_genomic.fna.gz --refList GCF_025821985.1_ASM2582198v1_genomic.fna/target_genomes.txt --output GCF_025821985.1_ASM2582198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:44,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:44,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:44,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:44,937] [INFO] Found 30 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:03:44,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:44,937] [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 avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	98.7639	1533	1925	95	conclusive
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	98.7304	1394	1925	95	conclusive
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.455	1427	1925	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.4331	1429	1925	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000172115.1	1767	1767	suspected-type	True	87.3249	1271	1925	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.3086	1432	1925	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	87.2719	1398	1925	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	87.2606	1445	1925	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	87.1133	1419	1925	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	87.0905	1381	1925	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	87.0886	1429	1925	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	87.0624	1367	1925	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	86.6123	1442	1925	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	86.1807	1322	1925	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	83.6574	1250	1925	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	83.3417	1084	1925	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	82.3883	998	1925	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	81.1067	964	1925	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	80.9815	955	1925	95	below_threshold
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	80.6062	922	1925	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	80.602	909	1925	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	80.5518	909	1925	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	80.3608	856	1925	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	80.3323	823	1925	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.2346	795	1925	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.1813	814	1925	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	79.9545	767	1925	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.4834	759	1925	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	79.468	750	1925	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	79.3997	813	1925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:44,939] [INFO] DFAST Taxonomy check result was written to GCF_025821985.1_ASM2582198v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:44,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:44,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:44,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/checkm_data
[2024-01-24 11:03:44,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:44,998] [INFO] Task started: CheckM
[2024-01-24 11:03:44,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821985.1_ASM2582198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821985.1_ASM2582198v1_genomic.fna/checkm_input GCF_025821985.1_ASM2582198v1_genomic.fna/checkm_result
[2024-01-24 11:04:41,944] [INFO] Task succeeded: CheckM
[2024-01-24 11:04:41,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:04:41,968] [INFO] ===== Completeness check finished =====
[2024-01-24 11:04:41,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:04:41,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821985.1_ASM2582198v1_genomic.fna/markers.fasta)
[2024-01-24 11:04:41,969] [INFO] Task started: Blastn
[2024-01-24 11:04:41,969] [INFO] Running command: blastn -query GCF_025821985.1_ASM2582198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79e1083a-6e48-4c3a-9fa9-c95d7d1ad8a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821985.1_ASM2582198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:43,744] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:43,749] [INFO] Selected 30 target genomes.
[2024-01-24 11:04:43,749] [INFO] Target genome list was writen to GCF_025821985.1_ASM2582198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:04:43,783] [INFO] Task started: fastANI
[2024-01-24 11:04:43,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ac69c5e-f28c-43a3-a823-64c94d6576d1/GCF_025821985.1_ASM2582198v1_genomic.fna.gz --refList GCF_025821985.1_ASM2582198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821985.1_ASM2582198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:21,320] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:21,346] [INFO] Found 30 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:05:21,346] [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_009741445.1	s__Mycobacterium avium	98.7618	1533	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	inconclusive
GCA_002291465.1	s__Mycobacterium lepraemurium	96.9321	1297	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000277125.1	s__Mycobacterium intracellulare	87.4419	1428	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_002105755.1	s__Mycobacterium colombiense	87.1009	1421	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_010731675.1	s__Mycobacterium marseillense	87.0815	1382	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_001672755.1	s__Mycobacterium colombiense_C	86.8978	1374	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665835.1	s__Mycobacterium colombiense_A	86.8831	1375	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	86.8779	1320	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	86.7787	1330	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298145.1	s__Mycobacterium sp004298145	86.6847	1347	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284975.1	s__Mycobacterium europaeum_A	86.6271	1294	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.84	95.70	0.84	0.79	6	-
GCF_001667145.1	s__Mycobacterium sp001667145	85.7541	1305	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	84.6685	1312	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	84.5687	1301	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_001667735.1	s__Mycobacterium sp001667735	84.4436	1256	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.16	0.95	0.92	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	84.2807	1254	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_001665295.1	s__Mycobacterium sp001665295	83.9966	1199	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	83.9844	1237	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730575.1	s__Mycobacterium parmense	83.6224	1268	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	83.327	1085	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002102185.1	s__Mycobacterium fragae	80.9677	956	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592155.1	s__Mycobacterium heckeshornense	80.535	908	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_900603025.1	s__Mycobacterium hassiacum	80.3883	860	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_008709575.1	s__Mycobacterium sp008709575	80.3336	709	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.292	776	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	80.148	868	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	79.974	868	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	79.6202	826	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001907655.1	s__Mycobacterium diernhoferi	79.5455	789	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_003284965.1	s__Mycobacterium sp003284965	79.5187	752	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:21,348] [INFO] GTDB search result was written to GCF_025821985.1_ASM2582198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:21,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:21,359] [INFO] DFAST_QC result json was written to GCF_025821985.1_ASM2582198v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:21,359] [INFO] DFAST_QC completed!
[2024-01-24 11:05:21,359] [INFO] Total running time: 0h2m32s