[2024-01-25 18:55:35,542] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference
[2024-01-25 18:55:36,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,739] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d92c821-7a49-434f-961a-c8ad3239953e/GCF_002797975.1_ASM279797v1_genomic.fna.gz | prodigal -d GCF_002797975.1_ASM279797v1_genomic.fna/cds.fna -a GCF_002797975.1_ASM279797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:47,900] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:47,900] [INFO] Task started: HMMsearch
[2024-01-25 18:55:47,900] [INFO] Running command: hmmsearch --tblout GCF_002797975.1_ASM279797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/reference_markers.hmm GCF_002797975.1_ASM279797v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:48,206] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:48,209] [INFO] Found 6/6 markers.
[2024-01-25 18:55:48,263] [INFO] Query marker FASTA was written to GCF_002797975.1_ASM279797v1_genomic.fna/markers.fasta
[2024-01-25 18:55:48,264] [INFO] Task started: Blastn
[2024-01-25 18:55:48,264] [INFO] Running command: blastn -query GCF_002797975.1_ASM279797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/reference_markers.fasta -out GCF_002797975.1_ASM279797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:48,860] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:48,862] [INFO] Selected 16 target genomes.
[2024-01-25 18:55:48,863] [INFO] Target genome list was writen to GCF_002797975.1_ASM279797v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:48,875] [INFO] Task started: fastANI
[2024-01-25 18:55:48,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d92c821-7a49-434f-961a-c8ad3239953e/GCF_002797975.1_ASM279797v1_genomic.fna.gz --refList GCF_002797975.1_ASM279797v1_genomic.fna/target_genomes.txt --output GCF_002797975.1_ASM279797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:04,019] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:04,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:04,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:04,030] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:04,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:04,031] [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 celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	100.0	1757	1757	95	conclusive
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	93.927	1500	1757	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	93.9022	1496	1757	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	79.3061	513	1757	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	78.9177	55	1757	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.8728	302	1757	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.7294	458	1757	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	78.5459	58	1757	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	78.3348	260	1757	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	78.3202	301	1757	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.1514	59	1757	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.569	103	1757	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.593	58	1757	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	76.4065	52	1757	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.8661	57	1757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:04,032] [INFO] DFAST Taxonomy check result was written to GCF_002797975.1_ASM279797v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:04,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:04,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:04,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/checkm_data
[2024-01-25 18:56:04,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:04,086] [INFO] Task started: CheckM
[2024-01-25 18:56:04,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002797975.1_ASM279797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002797975.1_ASM279797v1_genomic.fna/checkm_input GCF_002797975.1_ASM279797v1_genomic.fna/checkm_result
[2024-01-25 18:56:40,365] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:40,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:40,383] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:40,383] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:40,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002797975.1_ASM279797v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:40,384] [INFO] Task started: Blastn
[2024-01-25 18:56:40,384] [INFO] Running command: blastn -query GCF_002797975.1_ASM279797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg456a75f8-9e34-4843-b00d-2c4cf488d391/dqc_reference/reference_markers_gtdb.fasta -out GCF_002797975.1_ASM279797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:41,378] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:41,380] [INFO] Selected 7 target genomes.
[2024-01-25 18:56:41,381] [INFO] Target genome list was writen to GCF_002797975.1_ASM279797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:41,387] [INFO] Task started: fastANI
[2024-01-25 18:56:41,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d92c821-7a49-434f-961a-c8ad3239953e/GCF_002797975.1_ASM279797v1_genomic.fna.gz --refList GCF_002797975.1_ASM279797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002797975.1_ASM279797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:50,484] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:50,490] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:50,490] [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_002797975.1	s__Lacrimispora celerecrescens	100.0	1757	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.58	99.58	0.96	0.96	2	conclusive
GCA_900105215.1	s__Lacrimispora sphenoides_A	93.9082	1524	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
GCF_900105615.1	s__Lacrimispora sphenoides	93.9022	1496	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	99.94	99.87	1.00	1.00	3	-
GCA_002367105.1	s__Lacrimispora sp002367105	93.7031	1405	1757	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_002365025.1	s__Lacrimispora sp002365025	93.341	1240	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.9912	N/A	N/A	N/A	N/A	1	-
GCF_000732605.1	s__Lacrimispora celerecrescens_B	91.1719	1363	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	96.56	95.54	0.85	0.79	5	-
GCA_002429965.1	s__Lacrimispora sp002429965	89.5567	1239	1757	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.06	99.06	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:50,491] [INFO] GTDB search result was written to GCF_002797975.1_ASM279797v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:50,492] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:50,495] [INFO] DFAST_QC result json was written to GCF_002797975.1_ASM279797v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:50,495] [INFO] DFAST_QC completed!
[2024-01-25 18:56:50,495] [INFO] Total running time: 0h1m15s