[2024-01-24 13:58:25,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference
[2024-01-24 13:58:26,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,846] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,847] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf4a316f-5749-4bf2-b3e0-cc4310cac98f/GCF_014288005.1_ASM1428800v1_genomic.fna.gz | prodigal -d GCF_014288005.1_ASM1428800v1_genomic.fna/cds.fna -a GCF_014288005.1_ASM1428800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:44,919] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:44,919] [INFO] Task started: HMMsearch
[2024-01-24 13:58:44,919] [INFO] Running command: hmmsearch --tblout GCF_014288005.1_ASM1428800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/reference_markers.hmm GCF_014288005.1_ASM1428800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:45,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:45,289] [INFO] Found 6/6 markers.
[2024-01-24 13:58:45,348] [INFO] Query marker FASTA was written to GCF_014288005.1_ASM1428800v1_genomic.fna/markers.fasta
[2024-01-24 13:58:45,349] [INFO] Task started: Blastn
[2024-01-24 13:58:45,349] [INFO] Running command: blastn -query GCF_014288005.1_ASM1428800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/reference_markers.fasta -out GCF_014288005.1_ASM1428800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:46,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:46,013] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:46,014] [INFO] Target genome list was writen to GCF_014288005.1_ASM1428800v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:46,025] [INFO] Task started: fastANI
[2024-01-24 13:58:46,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4a316f-5749-4bf2-b3e0-cc4310cac98f/GCF_014288005.1_ASM1428800v1_genomic.fna.gz --refList GCF_014288005.1_ASM1428800v1_genomic.fna/target_genomes.txt --output GCF_014288005.1_ASM1428800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:02,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:02,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:02,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:02,621] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:02,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:02,622] [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
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	95.4801	1829	2351	95	conclusive
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	87.3156	1546	2351	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	87.0882	1381	2351	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.6891	197	2351	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.6228	202	2351	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.1906	300	2351	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.1536	294	2351	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.1318	214	2351	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	78.0475	244	2351	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	77.2971	108	2351	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.1576	224	2351	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.1368	112	2351	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.0227	229	2351	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	76.8116	66	2351	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.5089	90	2351	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.0839	89	2351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,623] [INFO] DFAST Taxonomy check result was written to GCF_014288005.1_ASM1428800v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:02,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:02,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:02,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/checkm_data
[2024-01-24 13:59:02,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:02,690] [INFO] Task started: CheckM
[2024-01-24 13:59:02,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288005.1_ASM1428800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288005.1_ASM1428800v1_genomic.fna/checkm_input GCF_014288005.1_ASM1428800v1_genomic.fna/checkm_result
[2024-01-24 13:59:55,919] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:55,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:55,944] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:55,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:55,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288005.1_ASM1428800v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:55,945] [INFO] Task started: Blastn
[2024-01-24 13:59:55,946] [INFO] Running command: blastn -query GCF_014288005.1_ASM1428800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbab1aa1d-df9b-40c0-9784-91b6165de8d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288005.1_ASM1428800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:57,068] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:57,073] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:57,073] [INFO] Target genome list was writen to GCF_014288005.1_ASM1428800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:57,110] [INFO] Task started: fastANI
[2024-01-24 13:59:57,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4a316f-5749-4bf2-b3e0-cc4310cac98f/GCF_014288005.1_ASM1428800v1_genomic.fna.gz --refList GCF_014288005.1_ASM1428800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288005.1_ASM1428800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:14,835] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:14,856] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:14,856] [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_003201875.1	s__Hungatella effluvii	95.4801	1829	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	95.81	95.49	0.78	0.75	20	conclusive
GCF_005845265.1	s__Hungatella sp005845265	86.9212	1478	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	98.89	98.68	0.87	0.80	12	-
GCF_000424325.1	s__Enterocloster clostridioformis_A	78.512	198	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCF_900155545.1	s__Lacrimispora sp900155545	78.4294	348	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526995.1	s__Lacrimispora indolis	78.3436	323	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.32	99.25	0.95	0.92	3	-
GCF_013036995.1	s__Lacrimispora xylanolytica_A	78.3074	238	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732605.1	s__Lacrimispora celerecrescens_B	78.2793	282	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	96.56	95.54	0.85	0.79	5	-
GCF_900113155.1	s__Enterocloster clostridioformis	78.1694	210	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCA_900105215.1	s__Lacrimispora sphenoides_A	78.0928	301	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
GCA_902363835.1	s__Lacrimispora sp902363835	78.0445	324	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367105.1	s__Lacrimispora sp002367105	78.0418	276	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363735.1	s__Lacrimispora sp902363735	77.995	223	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215155.1	s__Lacrimispora sp905215155	77.8712	245	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003435375.1	s__Copromonas sp900066535	77.5407	118	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCA_019114305.1	s__Hungatella pullicola	77.2209	177	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	99.96	99.96	0.96	0.96	2	-
GCF_003480435.1	s__Copromonas sp900066055	77.1608	110	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.09	96.90	0.88	0.80	7	-
GCF_000158075.1	s__Enterocloster asparagiformis	77.0436	225	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_000155435.1	s__Enterocloster sp000155435	77.0226	214	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCA_900547735.1	s__Clostridium_Q sp900547735	76.9785	156	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556515.1	s__Copromonas sp017556515	76.6705	57	2351	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:14,858] [INFO] GTDB search result was written to GCF_014288005.1_ASM1428800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:14,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:14,863] [INFO] DFAST_QC result json was written to GCF_014288005.1_ASM1428800v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:14,864] [INFO] DFAST_QC completed!
[2024-01-24 14:00:14,864] [INFO] Total running time: 0h1m49s