[2024-01-24 14:30:16,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference
[2024-01-24 14:30:18,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,333] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg220f2855-0798-4081-a42d-f895a19523bb/GCF_014287535.1_ASM1428753v1_genomic.fna.gz | prodigal -d GCF_014287535.1_ASM1428753v1_genomic.fna/cds.fna -a GCF_014287535.1_ASM1428753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:28,186] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:28,186] [INFO] Task started: HMMsearch
[2024-01-24 14:30:28,187] [INFO] Running command: hmmsearch --tblout GCF_014287535.1_ASM1428753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/reference_markers.hmm GCF_014287535.1_ASM1428753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:28,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:28,472] [INFO] Found 6/6 markers.
[2024-01-24 14:30:28,507] [INFO] Query marker FASTA was written to GCF_014287535.1_ASM1428753v1_genomic.fna/markers.fasta
[2024-01-24 14:30:28,507] [INFO] Task started: Blastn
[2024-01-24 14:30:28,508] [INFO] Running command: blastn -query GCF_014287535.1_ASM1428753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/reference_markers.fasta -out GCF_014287535.1_ASM1428753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:29,167] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:29,171] [INFO] Selected 20 target genomes.
[2024-01-24 14:30:29,172] [INFO] Target genome list was writen to GCF_014287535.1_ASM1428753v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:29,201] [INFO] Task started: fastANI
[2024-01-24 14:30:29,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg220f2855-0798-4081-a42d-f895a19523bb/GCF_014287535.1_ASM1428753v1_genomic.fna.gz --refList GCF_014287535.1_ASM1428753v1_genomic.fna/target_genomes.txt --output GCF_014287535.1_ASM1428753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:42,447] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:42,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:42,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:42,463] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:30:42,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:30:42,464] [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
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	82.2476	316	1269	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.6231	388	1269	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.5728	297	1269	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.5618	342	1269	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	81.408	165	1269	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	81.3917	122	1269	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.3538	294	1269	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	81.1963	373	1269	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.1106	361	1269	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	79.6761	88	1269	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.6047	285	1269	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	78.3885	93	1269	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.1049	67	1269	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.8505	65	1269	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	77.2148	112	1269	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.1939	114	1269	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.1418	113	1269	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.6887	69	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:42,466] [INFO] DFAST Taxonomy check result was written to GCF_014287535.1_ASM1428753v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:42,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:42,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:42,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/checkm_data
[2024-01-24 14:30:42,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:42,540] [INFO] Task started: CheckM
[2024-01-24 14:30:42,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287535.1_ASM1428753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287535.1_ASM1428753v1_genomic.fna/checkm_input GCF_014287535.1_ASM1428753v1_genomic.fna/checkm_result
[2024-01-24 14:31:18,363] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:18,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:18,386] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:18,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:18,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287535.1_ASM1428753v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:18,387] [INFO] Task started: Blastn
[2024-01-24 14:31:18,387] [INFO] Running command: blastn -query GCF_014287535.1_ASM1428753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60873b0f-c8b5-423a-a443-d8592f8cfce2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287535.1_ASM1428753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:19,541] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:19,545] [INFO] Selected 14 target genomes.
[2024-01-24 14:31:19,545] [INFO] Target genome list was writen to GCF_014287535.1_ASM1428753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:19,560] [INFO] Task started: fastANI
[2024-01-24 14:31:19,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg220f2855-0798-4081-a42d-f895a19523bb/GCF_014287535.1_ASM1428753v1_genomic.fna.gz --refList GCF_014287535.1_ASM1428753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287535.1_ASM1428753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:31,452] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:31,465] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:31,465] [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_003460605.1	s__Blautia_A sp900066145	98.7226	1120	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.04	98.72	0.92	0.85	9	conclusive
GCF_016908695.1	s__Blautia_A faecis	85.0238	789	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	-
GCA_905206915.1	s__Blautia_A sp905206915	84.6207	481	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763175.1	s__Blautia_A sp900763175	82.602	509	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477525.1	s__Blautia_A sp003477525	82.2444	402	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_003461245.1	s__Blautia_A sp000436615	81.735	378	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	-
GCF_013300825.1	s__Blautia_A wexlerae_B	81.6387	339	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_013304735.1	s__Blautia_A sp900066205	81.5081	387	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_013304825.1	s__Blautia_A schinkii	81.4766	351	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCA_000285855.2	s__Blautia_A sp000285855	81.3756	355	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.62	95.80	0.88	0.79	6	-
GCF_003461955.1	s__Blautia_A sp900066335	81.1893	349	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCF_004123145.1	s__Oliverpabstia faecicola	79.2415	178	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.72	97.58	0.88	0.80	5	-
GCA_900541985.1	s__Blautia_A sp900541985	78.9831	231	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCA_000702025.1	s__Blautia_A schinkii_A	78.5546	251	1269	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:31,470] [INFO] GTDB search result was written to GCF_014287535.1_ASM1428753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:31,471] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:31,479] [INFO] DFAST_QC result json was written to GCF_014287535.1_ASM1428753v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:31,479] [INFO] DFAST_QC completed!
[2024-01-24 14:31:31,479] [INFO] Total running time: 0h1m15s