[2023-06-16 19:18:16,930] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:18:16,932] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:18:16,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference
[2023-06-16 19:18:18,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:18:18,117] [INFO] Task started: Prodigal
[2023-06-16 19:18:18,117] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a9ed8cf-e91c-41ff-9924-2dcdf0ffde20/GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna.gz | prodigal -d GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/cds.fna -a GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:18:26,604] [INFO] Task succeeded: Prodigal
[2023-06-16 19:18:26,604] [INFO] Task started: HMMsearch
[2023-06-16 19:18:26,604] [INFO] Running command: hmmsearch --tblout GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/reference_markers.hmm GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:18:26,830] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:18:26,831] [INFO] Found 6/6 markers.
[2023-06-16 19:18:26,863] [INFO] Query marker FASTA was written to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/markers.fasta
[2023-06-16 19:18:26,863] [INFO] Task started: Blastn
[2023-06-16 19:18:26,863] [INFO] Running command: blastn -query GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/reference_markers.fasta -out GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:27,462] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:27,465] [INFO] Selected 26 target genomes.
[2023-06-16 19:18:27,466] [INFO] Target genome list was writen to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/target_genomes.txt
[2023-06-16 19:18:27,474] [INFO] Task started: fastANI
[2023-06-16 19:18:27,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9ed8cf-e91c-41ff-9924-2dcdf0ffde20/GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna.gz --refList GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/target_genomes.txt --output GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:18:42,876] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:42,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:18:42,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:18:42,895] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:18:42,896] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:18:42,896] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	83.1951	77	1088	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	81.8422	151	1088	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	81.7412	144	1088	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	81.3372	145	1088	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.0144	158	1088	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	80.6458	136	1088	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	80.2989	147	1088	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.2655	95	1088	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	80.2034	119	1088	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.8801	100	1088	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	79.2009	85	1088	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	77.6024	64	1088	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	77.4934	64	1088	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.3377	100	1088	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	77.3296	102	1088	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.2902	97	1088	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.2805	98	1088	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	77.2804	103	1088	95	below_threshold
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	77.2524	102	1088	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.237	95	1088	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	77.1392	58	1088	95	below_threshold
Blautia liquoris	strain=LZLJ-3	GCA_015159595.1	2779518	2779518	type	True	77.0727	54	1088	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:18:42,898] [INFO] DFAST Taxonomy check result was written to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/tc_result.tsv
[2023-06-16 19:18:42,899] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:18:42,899] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:18:42,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/checkm_data
[2023-06-16 19:18:42,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:18:42,935] [INFO] Task started: CheckM
[2023-06-16 19:18:42,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/checkm_input GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/checkm_result
[2023-06-16 19:19:12,538] [INFO] Task succeeded: CheckM
[2023-06-16 19:19:12,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:19:12,560] [INFO] ===== Completeness check finished =====
[2023-06-16 19:19:12,560] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:19:12,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/markers.fasta)
[2023-06-16 19:19:12,561] [INFO] Task started: Blastn
[2023-06-16 19:19:12,561] [INFO] Running command: blastn -query GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c370fd9-3aac-499c-929a-d93bca19dc23/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:19:13,428] [INFO] Task succeeded: Blastn
[2023-06-16 19:19:13,432] [INFO] Selected 20 target genomes.
[2023-06-16 19:19:13,432] [INFO] Target genome list was writen to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:19:13,455] [INFO] Task started: fastANI
[2023-06-16 19:19:13,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a9ed8cf-e91c-41ff-9924-2dcdf0ffde20/GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna.gz --refList GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/target_genomes_gtdb.txt --output GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:19:24,277] [INFO] Task succeeded: fastANI
[2023-06-16 19:19:24,291] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:19:24,291] [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_015557635.1	s__Fusicatenibacter saccharivorans	97.7983	935	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	conclusive
GCA_900772675.1	s__Fusicatenibacter sp900772675	90.1093	401	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003490145.1	s__CAG-95 sp900066375	82.1644	87	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.74	97.55	0.91	0.82	5	-
GCF_000210015.1	s__Blautia_A obeum_B	81.9946	164	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_900537995.1	s__Roseburia intestinalis	81.8417	151	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_009696065.1	s__Oliverpabstia intestinalis	79.0559	155	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCF_016899975.1	s__Fusicatenibacter sp900543115	78.8839	195	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	98.27	97.10	0.88	0.78	8	-
GCA_019119555.1	s__Fusicatenibacter intestinigallinarum	77.9838	136	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	99.96	99.96	0.92	0.92	2	-
GCA_017887445.1	s__Fusicatenibacter sp017887445	77.9555	174	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361775.1	s__Oliverpabstia sp002361775	77.9243	90	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_004556655.1	s__Oliverpabstia sp004556655	77.8368	103	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553305.1	s__CAG-95 sp900553305	77.6628	52	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_019115005.1	s__Fusicatenibacter merdavium	77.5393	141	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	99.43	98.88	0.95	0.93	3	-
GCA_019115765.1	s__Mediterraneibacter stercoripullorum	76.5072	62	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.91	99.91	0.91	0.91	2	-
GCA_018713585.1	s__Pullilachnospira stercoravium	76.4858	98	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
GCA_905214365.1	s__KLE1615 sp905214365	76.2315	66	1088	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:19:24,293] [INFO] GTDB search result was written to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/result_gtdb.tsv
[2023-06-16 19:19:24,294] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:19:24,298] [INFO] DFAST_QC result json was written to GCA_905201925.1_SRR413757-mag-bin.2_genomic.fna/dqc_result.json
[2023-06-16 19:19:24,298] [INFO] DFAST_QC completed!
[2023-06-16 19:19:24,298] [INFO] Total running time: 0h1m7s