[2024-01-24 12:22:48,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,748] [INFO] DQC Reference Directory: /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference
[2024-01-24 12:22:50,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:50,130] [INFO] Task started: Prodigal
[2024-01-24 12:22:50,131] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9b4ae3d-f47e-47fe-8acf-b907e241dc80/GCF_020686945.1_ASM2068694v1_genomic.fna.gz | prodigal -d GCF_020686945.1_ASM2068694v1_genomic.fna/cds.fna -a GCF_020686945.1_ASM2068694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:59,951] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:59,952] [INFO] Task started: HMMsearch
[2024-01-24 12:22:59,952] [INFO] Running command: hmmsearch --tblout GCF_020686945.1_ASM2068694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/reference_markers.hmm GCF_020686945.1_ASM2068694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:00,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:00,251] [INFO] Found 6/6 markers.
[2024-01-24 12:23:00,284] [INFO] Query marker FASTA was written to GCF_020686945.1_ASM2068694v1_genomic.fna/markers.fasta
[2024-01-24 12:23:00,285] [INFO] Task started: Blastn
[2024-01-24 12:23:00,285] [INFO] Running command: blastn -query GCF_020686945.1_ASM2068694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/reference_markers.fasta -out GCF_020686945.1_ASM2068694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:01,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:01,029] [INFO] Selected 28 target genomes.
[2024-01-24 12:23:01,029] [INFO] Target genome list was writen to GCF_020686945.1_ASM2068694v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:01,053] [INFO] Task started: fastANI
[2024-01-24 12:23:01,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b4ae3d-f47e-47fe-8acf-b907e241dc80/GCF_020686945.1_ASM2068694v1_genomic.fna.gz --refList GCF_020686945.1_ASM2068694v1_genomic.fna/target_genomes.txt --output GCF_020686945.1_ASM2068694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:17,922] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:17,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:17,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:17,944] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:17,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:17,944] [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	83.04	119	1248	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	81.6508	151	1248	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.311	141	1248	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	80.6865	75	1248	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.2849	127	1248	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	79.9419	79	1248	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.4258	77	1248	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	79.0115	151	1248	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.8066	90	1248	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.5551	92	1248	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	77.3975	88	1248	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.0342	56	1248	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.8529	73	1248	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.7769	69	1248	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.6105	80	1248	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.6083	75	1248	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.6057	73	1248	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.5981	82	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,946] [INFO] DFAST Taxonomy check result was written to GCF_020686945.1_ASM2068694v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:17,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:17,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:17,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/checkm_data
[2024-01-24 12:23:17,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:17,987] [INFO] Task started: CheckM
[2024-01-24 12:23:17,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686945.1_ASM2068694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686945.1_ASM2068694v1_genomic.fna/checkm_input GCF_020686945.1_ASM2068694v1_genomic.fna/checkm_result
[2024-01-24 12:23:51,147] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:51,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:51,170] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:51,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:51,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686945.1_ASM2068694v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:51,171] [INFO] Task started: Blastn
[2024-01-24 12:23:51,171] [INFO] Running command: blastn -query GCF_020686945.1_ASM2068694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga72ec973-2926-45bc-b17f-a7c53584aa63/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686945.1_ASM2068694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:52,372] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:52,376] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:52,376] [INFO] Target genome list was writen to GCF_020686945.1_ASM2068694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:52,389] [INFO] Task started: fastANI
[2024-01-24 12:23:52,389] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b4ae3d-f47e-47fe-8acf-b907e241dc80/GCF_020686945.1_ASM2068694v1_genomic.fna.gz --refList GCF_020686945.1_ASM2068694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686945.1_ASM2068694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:01,901] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:01,914] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:01,914] [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_018223435.1	s__Limivivens sp900543575	98.5345	1105	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	conclusive
GCF_003463065.1	s__Limivivens sp900066135	86.5506	833	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.47	97.63	0.91	0.79	5	-
GCF_013304735.1	s__Blautia_A sp900066205	83.2207	176	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCA_902362725.1	s__Merdisoma sp900066385	81.3387	182	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.97	97.93	0.91	0.83	3	-
GCF_900142165.1	s__Hespellia stercorisuis	80.6865	75	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hespellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001487165.1	s__Blautia_A massiliensis	80.0822	144	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	-
GCA_902363135.1	s__Choladousia sp902363135	79.7678	158	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_900551235.1	s__UMGS1375 sp900551235	79.1396	99	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004793585.1	s__CAG-56 sp004793585	78.5239	87	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	98.07	97.91	0.77	0.75	12	-
GCA_900544685.1	s__Marvinbryantia sp900544685	78.4107	97	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214955.1	s__Limivivens sp905214955	77.9366	164	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713105.1	s__Limivivens merdigallinarum	77.8973	163	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.32	98.32	0.87	0.87	2	-
GCA_900752065.1	s__CAG-56 sp900752065	77.1836	111	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.98	99.98	0.94	0.94	2	-
GCA_002361955.1	s__CAG-56 sp002361955	76.8867	118	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.90	99.85	0.92	0.90	5	-
GCA_019112735.1	s__Mediterraneibacter guildfordensis	76.7484	82	1248	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:01,917] [INFO] GTDB search result was written to GCF_020686945.1_ASM2068694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:01,917] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:01,924] [INFO] DFAST_QC result json was written to GCF_020686945.1_ASM2068694v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:01,924] [INFO] DFAST_QC completed!
[2024-01-24 12:24:01,925] [INFO] Total running time: 0h1m13s