[2024-01-24 13:17:11,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference
[2024-01-24 13:17:12,781] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,782] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgf630e055-f210-4773-a6a3-b953dfdb6ff6/GCF_002934545.1_ASM293454v1_genomic.fna.gz | prodigal -d GCF_002934545.1_ASM293454v1_genomic.fna/cds.fna -a GCF_002934545.1_ASM293454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:25,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:25,349] [INFO] Task started: HMMsearch
[2024-01-24 13:17:25,349] [INFO] Running command: hmmsearch --tblout GCF_002934545.1_ASM293454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/reference_markers.hmm GCF_002934545.1_ASM293454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:25,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:25,660] [INFO] Found 6/6 markers.
[2024-01-24 13:17:25,709] [INFO] Query marker FASTA was written to GCF_002934545.1_ASM293454v1_genomic.fna/markers.fasta
[2024-01-24 13:17:25,710] [INFO] Task started: Blastn
[2024-01-24 13:17:25,710] [INFO] Running command: blastn -query GCF_002934545.1_ASM293454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/reference_markers.fasta -out GCF_002934545.1_ASM293454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:26,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:26,345] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:26,346] [INFO] Target genome list was writen to GCF_002934545.1_ASM293454v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:26,396] [INFO] Task started: fastANI
[2024-01-24 13:17:26,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgf630e055-f210-4773-a6a3-b953dfdb6ff6/GCF_002934545.1_ASM293454v1_genomic.fna.gz --refList GCF_002934545.1_ASM293454v1_genomic.fna/target_genomes.txt --output GCF_002934545.1_ASM293454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:40,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:40,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:40,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:40,383] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:40,384] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:40,384] [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
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	80.0782	597	1859	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	79.3937	545	1859	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	79.3686	546	1859	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	79.3552	560	1859	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	79.2244	547	1859	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	78.2153	237	1859	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.9559	52	1859	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.5624	102	1859	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.5372	100	1859	95	below_threshold
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	76.4988	85	1859	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.496	102	1859	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.3917	59	1859	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	76.2931	54	1859	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	76.282	55	1859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:40,385] [INFO] DFAST Taxonomy check result was written to GCF_002934545.1_ASM293454v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:40,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:40,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:40,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/checkm_data
[2024-01-24 13:17:40,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:40,439] [INFO] Task started: CheckM
[2024-01-24 13:17:40,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934545.1_ASM293454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934545.1_ASM293454v1_genomic.fna/checkm_input GCF_002934545.1_ASM293454v1_genomic.fna/checkm_result
[2024-01-24 13:18:21,475] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:21,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:21,504] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:21,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:21,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934545.1_ASM293454v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:21,505] [INFO] Task started: Blastn
[2024-01-24 13:18:21,505] [INFO] Running command: blastn -query GCF_002934545.1_ASM293454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6877b0d7-2bc0-4dc0-90c0-c5b99ac22651/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934545.1_ASM293454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:22,581] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:22,586] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:22,586] [INFO] Target genome list was writen to GCF_002934545.1_ASM293454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:22,594] [INFO] Task started: fastANI
[2024-01-24 13:18:22,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgf630e055-f210-4773-a6a3-b953dfdb6ff6/GCF_002934545.1_ASM293454v1_genomic.fna.gz --refList GCF_002934545.1_ASM293454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934545.1_ASM293454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:31,518] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,535] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:31,536] [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_002934545.1	s__Lacrimispora xylanolytica	100.0	1856	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.92	98.92	0.97	0.97	2	conclusive
GCA_009712635.1	s__Lacrimispora sp009712635	94.6074	1618	1859	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_015057775.1	s__Lacrimispora sp015057775	94.2827	1152	1859	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_017084465.1	s__Lacrimispora xylanolytica_B	94.2073	1584	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.07	99.07	0.96	0.96	2	-
GCA_015057705.1	s__Lacrimispora sp015057705	94.1454	1289	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036995.1	s__Lacrimispora xylanolytica_A	93.9595	1411	1859	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_015057715.1	s__Lacrimispora sp015057715	93.7607	1364	1859	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,539] [INFO] GTDB search result was written to GCF_002934545.1_ASM293454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:31,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:31,546] [INFO] DFAST_QC result json was written to GCF_002934545.1_ASM293454v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:31,546] [INFO] DFAST_QC completed!
[2024-01-24 13:18:31,546] [INFO] Total running time: 0h1m20s