[2024-01-24 13:21:11,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference
[2024-01-24 13:21:12,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,464] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a235710-995e-4462-9178-d302681bb81f/GCF_000425525.1_ASM42552v1_genomic.fna.gz | prodigal -d GCF_000425525.1_ASM42552v1_genomic.fna/cds.fna -a GCF_000425525.1_ASM42552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:22,723] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:22,724] [INFO] Task started: HMMsearch
[2024-01-24 13:21:22,724] [INFO] Running command: hmmsearch --tblout GCF_000425525.1_ASM42552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/reference_markers.hmm GCF_000425525.1_ASM42552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:22,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:22,994] [INFO] Found 6/6 markers.
[2024-01-24 13:21:23,037] [INFO] Query marker FASTA was written to GCF_000425525.1_ASM42552v1_genomic.fna/markers.fasta
[2024-01-24 13:21:23,038] [INFO] Task started: Blastn
[2024-01-24 13:21:23,038] [INFO] Running command: blastn -query GCF_000425525.1_ASM42552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/reference_markers.fasta -out GCF_000425525.1_ASM42552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:23,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:23,678] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:23,678] [INFO] Target genome list was writen to GCF_000425525.1_ASM42552v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:23,697] [INFO] Task started: fastANI
[2024-01-24 13:21:23,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a235710-995e-4462-9178-d302681bb81f/GCF_000425525.1_ASM42552v1_genomic.fna.gz --refList GCF_000425525.1_ASM42552v1_genomic.fna/target_genomes.txt --output GCF_000425525.1_ASM42552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:34,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:34,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:34,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:34,382] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:21:34,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:34,383] [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
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	100.0	1329	1334	95	conclusive
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	99.9992	1333	1334	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.716	67	1334	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	78.4452	65	1334	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	77.9776	68	1334	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	77.456	85	1334	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.3455	58	1334	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.337	57	1334	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.3326	75	1334	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.0796	76	1334	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.0312	83	1334	95	below_threshold
Blautia liquoris	strain=LZLJ-3	GCA_015159595.1	2779518	2779518	type	True	76.7834	54	1334	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.7615	53	1334	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	76.6435	51	1334	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	76.2318	60	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:34,384] [INFO] DFAST Taxonomy check result was written to GCF_000425525.1_ASM42552v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:34,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:34,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:34,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/checkm_data
[2024-01-24 13:21:34,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:34,427] [INFO] Task started: CheckM
[2024-01-24 13:21:34,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425525.1_ASM42552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425525.1_ASM42552v1_genomic.fna/checkm_input GCF_000425525.1_ASM42552v1_genomic.fna/checkm_result
[2024-01-24 13:22:12,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:12,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:12,034] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:12,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:12,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425525.1_ASM42552v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:12,035] [INFO] Task started: Blastn
[2024-01-24 13:22:12,035] [INFO] Running command: blastn -query GCF_000425525.1_ASM42552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg863685f3-d2dd-4379-9b47-096ec308f5ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425525.1_ASM42552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:13,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:13,277] [INFO] Selected 28 target genomes.
[2024-01-24 13:22:13,277] [INFO] Target genome list was writen to GCF_000425525.1_ASM42552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:13,312] [INFO] Task started: fastANI
[2024-01-24 13:22:13,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a235710-995e-4462-9178-d302681bb81f/GCF_000425525.1_ASM42552v1_genomic.fna.gz --refList GCF_000425525.1_ASM42552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425525.1_ASM42552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:28,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:28,932] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:28,933] [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_000425525.1	s__Ruminococcus_G gauvreauii	100.0	1329	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_900549995.1	s__UMGS1251 sp900549995	80.9118	70	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120315.1	s__Ruminococcus_G avistercoris	77.7751	176	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_G	95.0	99.47	98.95	0.89	0.84	3	-
GCF_004123145.1	s__Oliverpabstia faecicola	77.7479	112	1334	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_018374355.1	s__Oliverpabstia sp018374355	77.5874	101	1334	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_014337215.1	s__Scatomonas sp003481995	77.456	85	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.67	99.67	0.93	0.93	3	-
GCF_000403455.2	s__Sporofaciens sp000403455	77.3172	58	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCF_018919065.1	s__Blautia_A sp018919065	77.1162	58	1334	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	-
GCA_004562915.1	s__Oliverpabstia sp004562915	77.045	79	1334	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_900539175.1	s__Pelethocola sp900539175	77.0204	100	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	99.69	99.49	0.84	0.76	3	-
GCA_000432335.1	s__Oliverpabstia sp000432335	77.0197	85	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.29	99.14	0.86	0.81	5	-
GCA_004556655.1	s__Oliverpabstia sp004556655	77.0097	89	1334	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_004560705.1	s__Bariatricus sp004560705	76.9193	57	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCA_902363665.1	s__Choladousia sp902363665	76.7892	72	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCF_015159595.1	s__Pelethocola sp015159595	76.7205	50	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556565.1	s__Schaedlerella sp004556565	76.6614	52	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764225.1	s__Blautia_A sp900764225	76.5106	51	1334	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	-
GCA_019115005.1	s__Fusicatenibacter merdavium	76.2857	64	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	99.43	98.88	0.95	0.93	3	-
GCA_018711815.1	s__Egerieimonas intestinavium	76.1768	64	1334	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:28,937] [INFO] GTDB search result was written to GCF_000425525.1_ASM42552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:28,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:28,944] [INFO] DFAST_QC result json was written to GCF_000425525.1_ASM42552v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:28,944] [INFO] DFAST_QC completed!
[2024-01-24 13:22:28,945] [INFO] Total running time: 0h1m18s