[2023-06-29 00:23:08,827] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:23:08,831] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:23:08,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference
[2023-06-29 00:23:10,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:23:10,531] [INFO] Task started: Prodigal
[2023-06-29 00:23:10,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg42286eac-5cf1-41fd-b8e9-134a5bbe2bd8/GCA_015152425.1_ASM1515242v1_genomic.fna.gz | prodigal -d GCA_015152425.1_ASM1515242v1_genomic.fna/cds.fna -a GCA_015152425.1_ASM1515242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:23:24,455] [INFO] Task succeeded: Prodigal
[2023-06-29 00:23:24,456] [INFO] Task started: HMMsearch
[2023-06-29 00:23:24,456] [INFO] Running command: hmmsearch --tblout GCA_015152425.1_ASM1515242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/reference_markers.hmm GCA_015152425.1_ASM1515242v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:23:24,830] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:23:24,832] [INFO] Found 6/6 markers.
[2023-06-29 00:23:24,886] [INFO] Query marker FASTA was written to GCA_015152425.1_ASM1515242v1_genomic.fna/markers.fasta
[2023-06-29 00:23:24,886] [INFO] Task started: Blastn
[2023-06-29 00:23:24,886] [INFO] Running command: blastn -query GCA_015152425.1_ASM1515242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/reference_markers.fasta -out GCA_015152425.1_ASM1515242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:25,552] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:25,556] [INFO] Selected 14 target genomes.
[2023-06-29 00:23:25,556] [INFO] Target genome list was writen to GCA_015152425.1_ASM1515242v1_genomic.fna/target_genomes.txt
[2023-06-29 00:23:25,557] [INFO] Task started: fastANI
[2023-06-29 00:23:25,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg42286eac-5cf1-41fd-b8e9-134a5bbe2bd8/GCA_015152425.1_ASM1515242v1_genomic.fna.gz --refList GCA_015152425.1_ASM1515242v1_genomic.fna/target_genomes.txt --output GCA_015152425.1_ASM1515242v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:23:39,552] [INFO] Task succeeded: fastANI
[2023-06-29 00:23:39,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:23:39,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:23:39,619] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:23:39,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:23:39,619] [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 sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	85.3124	1186	1825	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	85.3076	1188	1825	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	85.2712	1175	1825	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	78.9599	496	1825	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.2605	410	1825	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.7392	305	1825	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.5294	304	1825	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	75.8565	58	1825	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.587	59	1825	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	75.463	65	1825	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:23:39,622] [INFO] DFAST Taxonomy check result was written to GCA_015152425.1_ASM1515242v1_genomic.fna/tc_result.tsv
[2023-06-29 00:23:39,622] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:23:39,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:23:39,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/checkm_data
[2023-06-29 00:23:39,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:23:39,682] [INFO] Task started: CheckM
[2023-06-29 00:23:39,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015152425.1_ASM1515242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015152425.1_ASM1515242v1_genomic.fna/checkm_input GCA_015152425.1_ASM1515242v1_genomic.fna/checkm_result
[2023-06-29 00:24:23,790] [INFO] Task succeeded: CheckM
[2023-06-29 00:24:23,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:24:23,821] [INFO] ===== Completeness check finished =====
[2023-06-29 00:24:23,821] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:24:23,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015152425.1_ASM1515242v1_genomic.fna/markers.fasta)
[2023-06-29 00:24:23,822] [INFO] Task started: Blastn
[2023-06-29 00:24:23,822] [INFO] Running command: blastn -query GCA_015152425.1_ASM1515242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3ee0bb7-18c8-4461-b217-6b814d0366cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_015152425.1_ASM1515242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:24:24,845] [INFO] Task succeeded: Blastn
[2023-06-29 00:24:24,850] [INFO] Selected 12 target genomes.
[2023-06-29 00:24:24,850] [INFO] Target genome list was writen to GCA_015152425.1_ASM1515242v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:24:24,859] [INFO] Task started: fastANI
[2023-06-29 00:24:24,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg42286eac-5cf1-41fd-b8e9-134a5bbe2bd8/GCA_015152425.1_ASM1515242v1_genomic.fna.gz --refList GCA_015152425.1_ASM1515242v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015152425.1_ASM1515242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:24:39,255] [INFO] Task succeeded: fastANI
[2023-06-29 00:24:39,274] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:24:39,275] [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_000526995.1	s__Lacrimispora indolis	99.3929	1782	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.32	99.25	0.95	0.92	3	conclusive
GCA_902363835.1	s__Lacrimispora sp902363835	87.9831	1330	1825	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_002429965.1	s__Lacrimispora sp002429965	86.0364	1116	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.06	99.06	0.84	0.84	2	-
GCF_000144625.1	s__Lacrimispora saccharolytica	86.0064	1025	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001312405.1	s__Lacrimispora sp001312405	85.682	1056	1825	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_900105615.1	s__Lacrimispora sphenoides	85.3131	1187	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	99.94	99.87	1.00	1.00	3	-
GCF_002797975.1	s__Lacrimispora celerecrescens	85.2985	1189	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.58	99.58	0.96	0.96	2	-
GCA_900105215.1	s__Lacrimispora sphenoides_A	85.2095	1225	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
GCA_002365025.1	s__Lacrimispora sp002365025	85.1528	1023	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.9912	N/A	N/A	N/A	N/A	1	-
GCA_002367105.1	s__Lacrimispora sp002367105	85.1367	1151	1825	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_000732605.1	s__Lacrimispora celerecrescens_B	84.929	1116	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	96.56	95.54	0.85	0.79	5	-
GCF_900155545.1	s__Lacrimispora sp900155545	81.8763	811	1825	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:24:39,277] [INFO] GTDB search result was written to GCA_015152425.1_ASM1515242v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:24:39,278] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:24:39,283] [INFO] DFAST_QC result json was written to GCA_015152425.1_ASM1515242v1_genomic.fna/dqc_result.json
[2023-06-29 00:24:39,284] [INFO] DFAST_QC completed!
[2023-06-29 00:24:39,284] [INFO] Total running time: 0h1m30s