[2023-06-29 16:46:57,801] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:46:57,803] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:46:57,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference
[2023-06-29 16:46:59,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:46:59,128] [INFO] Task started: Prodigal
[2023-06-29 16:46:59,128] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6ada137-e445-4d02-b794-b89f79b07e59/GCA_023708865.1_ASM2370886v1_genomic.fna.gz | prodigal -d GCA_023708865.1_ASM2370886v1_genomic.fna/cds.fna -a GCA_023708865.1_ASM2370886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:47:07,488] [INFO] Task succeeded: Prodigal
[2023-06-29 16:47:07,489] [INFO] Task started: HMMsearch
[2023-06-29 16:47:07,489] [INFO] Running command: hmmsearch --tblout GCA_023708865.1_ASM2370886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/reference_markers.hmm GCA_023708865.1_ASM2370886v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:47:07,807] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:47:07,809] [INFO] Found 6/6 markers.
[2023-06-29 16:47:07,851] [INFO] Query marker FASTA was written to GCA_023708865.1_ASM2370886v1_genomic.fna/markers.fasta
[2023-06-29 16:47:07,851] [INFO] Task started: Blastn
[2023-06-29 16:47:07,852] [INFO] Running command: blastn -query GCA_023708865.1_ASM2370886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/reference_markers.fasta -out GCA_023708865.1_ASM2370886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:08,559] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:08,568] [INFO] Selected 24 target genomes.
[2023-06-29 16:47:08,569] [INFO] Target genome list was writen to GCA_023708865.1_ASM2370886v1_genomic.fna/target_genomes.txt
[2023-06-29 16:47:08,571] [INFO] Task started: fastANI
[2023-06-29 16:47:08,571] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ada137-e445-4d02-b794-b89f79b07e59/GCA_023708865.1_ASM2370886v1_genomic.fna.gz --refList GCA_023708865.1_ASM2370886v1_genomic.fna/target_genomes.txt --output GCA_023708865.1_ASM2370886v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:24,761] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:24,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:24,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:24,775] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 16:47:24,775] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 16:47:24,776] [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
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	98.372	737	1057	95	conclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.3447	54	1057	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.2398	61	1057	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.0857	64	1057	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.048	57	1057	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.0308	75	1057	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.937	67	1057	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.9232	100	1057	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.9165	66	1057	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.8996	93	1057	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	76.846	100	1057	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	76.846	100	1057	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.7852	84	1057	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.7768	107	1057	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.6797	103	1057	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:47:24,778] [INFO] DFAST Taxonomy check result was written to GCA_023708865.1_ASM2370886v1_genomic.fna/tc_result.tsv
[2023-06-29 16:47:24,778] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:24,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:24,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/checkm_data
[2023-06-29 16:47:24,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:24,816] [INFO] Task started: CheckM
[2023-06-29 16:47:24,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708865.1_ASM2370886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708865.1_ASM2370886v1_genomic.fna/checkm_input GCA_023708865.1_ASM2370886v1_genomic.fna/checkm_result
[2023-06-29 16:47:55,114] [INFO] Task succeeded: CheckM
[2023-06-29 16:47:55,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:47:55,141] [INFO] ===== Completeness check finished =====
[2023-06-29 16:47:55,141] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:47:55,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708865.1_ASM2370886v1_genomic.fna/markers.fasta)
[2023-06-29 16:47:55,142] [INFO] Task started: Blastn
[2023-06-29 16:47:55,142] [INFO] Running command: blastn -query GCA_023708865.1_ASM2370886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97678d9-4d1f-45e2-8bff-aee5130c3e27/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708865.1_ASM2370886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:56,228] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:56,234] [INFO] Selected 22 target genomes.
[2023-06-29 16:47:56,234] [INFO] Target genome list was writen to GCA_023708865.1_ASM2370886v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:47:56,238] [INFO] Task started: fastANI
[2023-06-29 16:47:56,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ada137-e445-4d02-b794-b89f79b07e59/GCA_023708865.1_ASM2370886v1_genomic.fna.gz --refList GCA_023708865.1_ASM2370886v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708865.1_ASM2370886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:48:08,940] [INFO] Task succeeded: fastANI
[2023-06-29 16:48:08,960] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:48:08,960] [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_003024715.1	s__Clostridium_Q fessum	98.372	737	1057	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	conclusive
GCA_016302185.1	s__Clostridium_Q sp016302185	78.449	184	1057	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_018223375.1	s__Clostridium_Q sp000435655	78.2699	142	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCA_900555625.1	s__Ventrimonas sp900555625	78.2515	85	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.73	98.70	0.86	0.85	3	-
GCF_003481825.1	s__Ventrimonas sp003481825	78.0933	142	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCA_900547735.1	s__Clostridium_Q sp900547735	78.0674	179	1057	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_900538475.1	s__Ventrimonas sp900538475	78.0135	91	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	77.9312	173	1057	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	-
GCF_003480315.1	s__Ventrimonas sp003480315	77.9233	155	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCF_000466485.1	s__Clostridium_Q symbiosum	77.8451	170	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCA_018377235.1	s__Clostridium_Q sp018377235	77.8319	130	1057	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	-
GCF_003478505.1	s__Ventrimonas sp003478505	77.7946	144	1057	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_003435375.1	s__Copromonas sp900066535	77.7505	166	1057	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_004554205.1	s__Ventrimonas sp004554205	77.6614	88	1057	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_900770535.1	s__Ventrimonas sp900770535	77.6428	88	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.72	98.72	0.86	0.86	2	-
GCA_900540335.1	s__Ventrimonas sp900540335	77.619	91	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_001304875.1	s__Ventrisoma faecale	77.1848	134	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma	95.0	98.23	97.74	0.91	0.86	4	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	76.988	96	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCA_009911305.1	s__Clostridium_Q sp009911305	76.8084	174	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.99	98.99	0.91	0.91	2	-
GCA_910585435.1	s__UBA3402 sp910585435	76.5147	70	1057	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:48:08,962] [INFO] GTDB search result was written to GCA_023708865.1_ASM2370886v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:48:08,962] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:48:08,967] [INFO] DFAST_QC result json was written to GCA_023708865.1_ASM2370886v1_genomic.fna/dqc_result.json
[2023-06-29 16:48:08,967] [INFO] DFAST_QC completed!
[2023-06-29 16:48:08,967] [INFO] Total running time: 0h1m11s