[2024-01-25 18:08:20,411] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:20,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:20,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference
[2024-01-25 18:08:21,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:21,549] [INFO] Task started: Prodigal
[2024-01-25 18:08:21,549] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3d196d7-5540-4dda-aff7-4ba27c3022ed/GCF_020686985.1_ASM2068698v1_genomic.fna.gz | prodigal -d GCF_020686985.1_ASM2068698v1_genomic.fna/cds.fna -a GCF_020686985.1_ASM2068698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:28,812] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:28,812] [INFO] Task started: HMMsearch
[2024-01-25 18:08:28,812] [INFO] Running command: hmmsearch --tblout GCF_020686985.1_ASM2068698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/reference_markers.hmm GCF_020686985.1_ASM2068698v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:29,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:29,031] [INFO] Found 6/6 markers.
[2024-01-25 18:08:29,056] [INFO] Query marker FASTA was written to GCF_020686985.1_ASM2068698v1_genomic.fna/markers.fasta
[2024-01-25 18:08:29,057] [INFO] Task started: Blastn
[2024-01-25 18:08:29,057] [INFO] Running command: blastn -query GCF_020686985.1_ASM2068698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/reference_markers.fasta -out GCF_020686985.1_ASM2068698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:29,655] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:29,659] [INFO] Selected 29 target genomes.
[2024-01-25 18:08:29,660] [INFO] Target genome list was writen to GCF_020686985.1_ASM2068698v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:29,674] [INFO] Task started: fastANI
[2024-01-25 18:08:29,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d196d7-5540-4dda-aff7-4ba27c3022ed/GCF_020686985.1_ASM2068698v1_genomic.fna.gz --refList GCF_020686985.1_ASM2068698v1_genomic.fna/target_genomes.txt --output GCF_020686985.1_ASM2068698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:49,142] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:49,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:49,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:49,157] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:08:49,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:08:49,158] [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
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	81.4928	76	1051	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	81.2391	80	1051	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.0069	82	1051	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.907	77	1051	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	80.8251	99	1051	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	80.7268	190	1051	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	80.4712	80	1051	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	80.1907	102	1051	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	80.1814	101	1051	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.9193	78	1051	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.886	75	1051	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	79.8162	96	1051	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.6673	75	1051	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.6077	102	1051	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	79.5981	131	1051	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.5158	100	1051	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	79.4951	81	1051	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	79.0546	119	1051	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.7372	85	1051	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	78.4333	55	1051	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.2756	71	1051	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	78.2712	62	1051	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	77.4839	80	1051	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	77.4625	77	1051	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.4444	115	1051	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.8549	92	1051	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.8445	91	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:49,161] [INFO] DFAST Taxonomy check result was written to GCF_020686985.1_ASM2068698v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:49,162] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:49,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:49,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/checkm_data
[2024-01-25 18:08:49,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:49,208] [INFO] Task started: CheckM
[2024-01-25 18:08:49,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686985.1_ASM2068698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686985.1_ASM2068698v1_genomic.fna/checkm_input GCF_020686985.1_ASM2068698v1_genomic.fna/checkm_result
[2024-01-25 18:09:15,751] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:15,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:15,773] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:15,774] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:15,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686985.1_ASM2068698v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:15,774] [INFO] Task started: Blastn
[2024-01-25 18:09:15,774] [INFO] Running command: blastn -query GCF_020686985.1_ASM2068698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042ddc16-673f-419c-8b49-b25f8f987db9/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686985.1_ASM2068698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:16,861] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:16,864] [INFO] Selected 23 target genomes.
[2024-01-25 18:09:16,865] [INFO] Target genome list was writen to GCF_020686985.1_ASM2068698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:16,886] [INFO] Task started: fastANI
[2024-01-25 18:09:16,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3d196d7-5540-4dda-aff7-4ba27c3022ed/GCF_020686985.1_ASM2068698v1_genomic.fna.gz --refList GCF_020686985.1_ASM2068698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686985.1_ASM2068698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:30,924] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:30,936] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:30,936] [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
GCA_900555625.1	s__Ventrimonas sp900555625	98.7407	551	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.73	98.70	0.86	0.85	3	conclusive
GCF_003478505.1	s__Ventrimonas sp003478505	82.3428	293	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.07	97.61	0.91	0.78	6	-
GCF_003481985.1	s__Ventrimonas sp003506385	81.2388	307	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.83	98.43	0.90	0.84	6	-
GCF_003435375.1	s__Copromonas sp900066535	81.0148	171	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCF_003481825.1	s__Ventrimonas sp003481825	80.8276	277	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCF_003024715.1	s__Clostridium_Q fessum	80.7771	188	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.33	97.70	0.88	0.81	31	-
GCF_003480315.1	s__Ventrimonas sp003480315	80.352	292	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCA_900770535.1	s__Ventrimonas sp900770535	77.969	160	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.72	98.72	0.86	0.86	2	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	77.8782	108	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_004554205.1	s__Ventrimonas sp004554205	77.4566	132	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542035.1	s__UMGS1370 sp900542035	77.1417	71	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	99.54	99.09	0.95	0.91	3	-
GCA_910586205.1	s__Ventrimonas sp910586205	77.116	98	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	77.0517	59	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCA_910586255.1	s__Ventrimonas sp910586255	76.8489	112	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526995.1	s__Lacrimispora indolis	76.843	75	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.32	99.25	0.95	0.92	3	-
GCA_019114465.1	s__Lachnoclostridium_A avicola	76.8369	81	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.23	98.89	0.92	0.90	3	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	76.7203	54	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_910586315.1	s__Copromonas sp910586315	76.6813	57	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363835.1	s__Lacrimispora sp902363835	76.4939	74	1051	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_015057755.1	s__Copromonas sp015057755	76.3464	71	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367105.1	s__Lacrimispora sp002367105	76.3422	69	1051	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:30,938] [INFO] GTDB search result was written to GCF_020686985.1_ASM2068698v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:30,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:30,943] [INFO] DFAST_QC result json was written to GCF_020686985.1_ASM2068698v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:30,943] [INFO] DFAST_QC completed!
[2024-01-25 18:09:30,944] [INFO] Total running time: 0h1m11s