[2024-01-24 14:12:45,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference
[2024-01-24 14:12:47,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,221] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg03525127-6ef0-4d51-9719-b2b8c2bc105a/GCF_009696065.1_ASM969606v1_genomic.fna.gz | prodigal -d GCF_009696065.1_ASM969606v1_genomic.fna/cds.fna -a GCF_009696065.1_ASM969606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:55,209] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:55,210] [INFO] Task started: HMMsearch
[2024-01-24 14:12:55,210] [INFO] Running command: hmmsearch --tblout GCF_009696065.1_ASM969606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/reference_markers.hmm GCF_009696065.1_ASM969606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:55,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:55,463] [INFO] Found 6/6 markers.
[2024-01-24 14:12:55,491] [INFO] Query marker FASTA was written to GCF_009696065.1_ASM969606v1_genomic.fna/markers.fasta
[2024-01-24 14:12:55,492] [INFO] Task started: Blastn
[2024-01-24 14:12:55,492] [INFO] Running command: blastn -query GCF_009696065.1_ASM969606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/reference_markers.fasta -out GCF_009696065.1_ASM969606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:56,131] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:56,135] [INFO] Selected 27 target genomes.
[2024-01-24 14:12:56,135] [INFO] Target genome list was writen to GCF_009696065.1_ASM969606v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:56,155] [INFO] Task started: fastANI
[2024-01-24 14:12:56,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg03525127-6ef0-4d51-9719-b2b8c2bc105a/GCF_009696065.1_ASM969606v1_genomic.fna.gz --refList GCF_009696065.1_ASM969606v1_genomic.fna/target_genomes.txt --output GCF_009696065.1_ASM969606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:10,840] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:10,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:10,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:10,865] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:10,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:10,865] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.6691	155	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	79.5256	96	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	79.3962	97	1034	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	79.3493	99	1034	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	79.2922	148	1034	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.9416	193	1034	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.6985	170	1034	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.6899	179	1034	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.6421	160	1034	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.6386	178	1034	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.6018	128	1034	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.4972	113	1034	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	78.3097	124	1034	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.2973	164	1034	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	78.2336	126	1034	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.1536	108	1034	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.0303	120	1034	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.775	61	1034	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.6649	129	1034	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.6283	92	1034	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.5429	128	1034	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	77.5401	121	1034	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.5202	118	1034	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	77.4784	61	1034	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.4656	86	1034	95	below_threshold
Novisyntrophococcus fermenticellae	strain=JN500902	GCA_018866245.1	2068655	2068655	type	True	77.2305	78	1034	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.1353	72	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,867] [INFO] DFAST Taxonomy check result was written to GCF_009696065.1_ASM969606v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:10,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:10,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:10,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/checkm_data
[2024-01-24 14:13:10,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:10,901] [INFO] Task started: CheckM
[2024-01-24 14:13:10,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696065.1_ASM969606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696065.1_ASM969606v1_genomic.fna/checkm_input GCF_009696065.1_ASM969606v1_genomic.fna/checkm_result
[2024-01-24 14:13:40,106] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:40,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:40,133] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:40,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:40,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696065.1_ASM969606v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:40,134] [INFO] Task started: Blastn
[2024-01-24 14:13:40,134] [INFO] Running command: blastn -query GCF_009696065.1_ASM969606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a1b43d7-5cd5-47b5-a0aa-e0d1c1a4da99/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696065.1_ASM969606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:41,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:41,227] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:41,227] [INFO] Target genome list was writen to GCF_009696065.1_ASM969606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:41,241] [INFO] Task started: fastANI
[2024-01-24 14:13:41,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg03525127-6ef0-4d51-9719-b2b8c2bc105a/GCF_009696065.1_ASM969606v1_genomic.fna.gz --refList GCF_009696065.1_ASM969606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696065.1_ASM969606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:49,569] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:49,586] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:49,587] [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_009696065.1	s__Oliverpabstia intestinalis	100.0	1033	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	conclusive
GCF_004123145.1	s__Oliverpabstia faecicola	91.4571	806	1034	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_004562915.1	s__Oliverpabstia sp004562915	80.1841	252	1034	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_002361775.1	s__Oliverpabstia sp002361775	79.7775	250	1034	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	79.6019	248	1034	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_018374355.1	s__Oliverpabstia sp018374355	79.1943	231	1034	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_000432335.1	s__Oliverpabstia sp000432335	78.9046	231	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.29	99.14	0.86	0.81	5	-
GCF_003477525.1	s__Blautia_A sp003477525	78.7639	189	1034	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_018919065.1	s__Blautia_A sp018919065	78.3859	158	1034	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_013300725.1	s__Bariatricus comes_A	78.3069	134	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCF_000174195.1	s__Roseburia inulinivorans	77.6225	90	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_900765975.1	s__Schaedlerella sp900765975	77.3925	62	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_900551715.1	s__Blautia_A sp900551715	77.3319	112	1034	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 14:13:49,588] [INFO] GTDB search result was written to GCF_009696065.1_ASM969606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:49,589] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:49,593] [INFO] DFAST_QC result json was written to GCF_009696065.1_ASM969606v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:49,593] [INFO] DFAST_QC completed!
[2024-01-24 14:13:49,593] [INFO] Total running time: 0h1m4s