[2024-01-24 14:22:01,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference
[2024-01-24 14:22:03,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,024] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg17e29777-3c8b-4cfe-9ee4-e0cc20d50d35/GCF_003024715.1_ASM302471v1_genomic.fna.gz | prodigal -d GCF_003024715.1_ASM302471v1_genomic.fna/cds.fna -a GCF_003024715.1_ASM302471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:11,304] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:11,305] [INFO] Task started: HMMsearch
[2024-01-24 14:22:11,305] [INFO] Running command: hmmsearch --tblout GCF_003024715.1_ASM302471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/reference_markers.hmm GCF_003024715.1_ASM302471v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:11,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:11,582] [INFO] Found 6/6 markers.
[2024-01-24 14:22:11,616] [INFO] Query marker FASTA was written to GCF_003024715.1_ASM302471v1_genomic.fna/markers.fasta
[2024-01-24 14:22:11,616] [INFO] Task started: Blastn
[2024-01-24 14:22:11,616] [INFO] Running command: blastn -query GCF_003024715.1_ASM302471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/reference_markers.fasta -out GCF_003024715.1_ASM302471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:12,331] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:12,335] [INFO] Selected 24 target genomes.
[2024-01-24 14:22:12,335] [INFO] Target genome list was writen to GCF_003024715.1_ASM302471v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:12,350] [INFO] Task started: fastANI
[2024-01-24 14:22:12,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e29777-3c8b-4cfe-9ee4-e0cc20d50d35/GCF_003024715.1_ASM302471v1_genomic.fna.gz --refList GCF_003024715.1_ASM302471v1_genomic.fna/target_genomes.txt --output GCF_003024715.1_ASM302471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:31,030] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:31,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:31,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:31,050] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:31,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:31,050] [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	100.0	1077	1078	95	conclusive
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	83.5542	78	1078	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	82.994	121	1078	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	82.4566	123	1078	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	82.3369	93	1078	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	82.2564	104	1078	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	81.9338	119	1078	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.8082	109	1078	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	80.8061	90	1078	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	80.3166	112	1078	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.9192	61	1078	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.7518	60	1078	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	79.3197	91	1078	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	79.2084	126	1078	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.9541	85	1078	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	78.2099	63	1078	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	77.9751	112	1078	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	77.9563	111	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:31,052] [INFO] DFAST Taxonomy check result was written to GCF_003024715.1_ASM302471v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:31,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:31,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:31,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/checkm_data
[2024-01-24 14:22:31,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:31,087] [INFO] Task started: CheckM
[2024-01-24 14:22:31,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024715.1_ASM302471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024715.1_ASM302471v1_genomic.fna/checkm_input GCF_003024715.1_ASM302471v1_genomic.fna/checkm_result
[2024-01-24 14:23:01,679] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:01,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:01,700] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:01,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:01,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024715.1_ASM302471v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:01,701] [INFO] Task started: Blastn
[2024-01-24 14:23:01,701] [INFO] Running command: blastn -query GCF_003024715.1_ASM302471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ff10cba-4d2a-4827-9ef7-16403c5aef1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024715.1_ASM302471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:02,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:02,802] [INFO] Selected 22 target genomes.
[2024-01-24 14:23:02,802] [INFO] Target genome list was writen to GCF_003024715.1_ASM302471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:02,837] [INFO] Task started: fastANI
[2024-01-24 14:23:02,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg17e29777-3c8b-4cfe-9ee4-e0cc20d50d35/GCF_003024715.1_ASM302471v1_genomic.fna.gz --refList GCF_003024715.1_ASM302471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024715.1_ASM302471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:16,158] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:16,174] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:16,174] [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	100.0	1077	1078	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
GCF_003478505.1	s__Ventrimonas sp003478505	83.1291	229	1078	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	81.841	229	1078	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	81.5136	206	1078	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_003480315.1	s__Ventrimonas sp003480315	80.7215	207	1078	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_018223375.1	s__Clostridium_Q sp000435655	78.8555	177	1078	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_016302185.1	s__Clostridium_Q sp016302185	78.335	196	1078	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_900553885.1	s__Mediterraneibacter sp900553885	78.2268	53	1078	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547735.1	s__Clostridium_Q sp900547735	78.1635	191	1078	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_018377235.1	s__Clostridium_Q sp018377235	78.13	141	1078	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_900626075.1	s__Clostridium_Q transplantifaecale	78.0385	196	1078	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_001304875.1	s__Ventrisoma faecale	77.9043	150	1078	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_000466485.1	s__Clostridium_Q symbiosum	77.8932	187	1078	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_900555625.1	s__Ventrimonas sp900555625	77.8653	103	1078	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.73	98.70	0.86	0.85	3	-
GCA_900770535.1	s__Ventrimonas sp900770535	77.7695	88	1078	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_009911305.1	s__Clostridium_Q sp009911305	77.4087	181	1078	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	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	77.2586	99	1078	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_004554205.1	s__Ventrimonas sp004554205	76.9223	90	1078	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_910588325.1	s__UBA3402 sp910588325	76.4118	64	1078	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:16,176] [INFO] GTDB search result was written to GCF_003024715.1_ASM302471v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:16,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:16,181] [INFO] DFAST_QC result json was written to GCF_003024715.1_ASM302471v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:16,181] [INFO] DFAST_QC completed!
[2024-01-24 14:23:16,182] [INFO] Total running time: 0h1m14s