[2023-06-17 04:34:03,613] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:34:03,615] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:34:03,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference
[2023-06-17 04:34:05,190] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:34:05,192] [INFO] Task started: Prodigal
[2023-06-17 04:34:05,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg73e6dc93-cb5d-4625-9d38-154ad2f3632e/GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna.gz | prodigal -d GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/cds.fna -a GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:34:10,008] [INFO] Task succeeded: Prodigal
[2023-06-17 04:34:10,009] [INFO] Task started: HMMsearch
[2023-06-17 04:34:10,009] [INFO] Running command: hmmsearch --tblout GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/reference_markers.hmm GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:34:10,266] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:34:10,268] [INFO] Found 6/6 markers.
[2023-06-17 04:34:10,293] [INFO] Query marker FASTA was written to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/markers.fasta
[2023-06-17 04:34:10,294] [INFO] Task started: Blastn
[2023-06-17 04:34:10,294] [INFO] Running command: blastn -query GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/reference_markers.fasta -out GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:34:10,898] [INFO] Task succeeded: Blastn
[2023-06-17 04:34:10,903] [INFO] Selected 19 target genomes.
[2023-06-17 04:34:10,904] [INFO] Target genome list was writen to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/target_genomes.txt
[2023-06-17 04:34:10,908] [INFO] Task started: fastANI
[2023-06-17 04:34:10,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e6dc93-cb5d-4625-9d38-154ad2f3632e/GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna.gz --refList GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/target_genomes.txt --output GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:34:21,505] [INFO] Task succeeded: fastANI
[2023-06-17 04:34:21,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:34:21,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:34:21,516] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 04:34:21,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 04:34:21,517] [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
Lentihominibacter faecis	strain=BX16	GCA_014306095.1	2764712	2764712	type	True	97.9835	510	633	95	conclusive
Lentihominibacter hominis	strain=NSJ-24	GCA_014385065.1	2763645	2763645	type	True	76.7007	63	633	95	below_threshold
Zhenpiania hominis	strain=BX12	GCA_014333425.1	2763644	2763644	type	True	76.1539	65	633	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:34:21,519] [INFO] DFAST Taxonomy check result was written to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/tc_result.tsv
[2023-06-17 04:34:21,520] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:34:21,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:34:21,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/checkm_data
[2023-06-17 04:34:21,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:34:21,549] [INFO] Task started: CheckM
[2023-06-17 04:34:21,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/checkm_input GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/checkm_result
[2023-06-17 04:34:42,840] [INFO] Task succeeded: CheckM
[2023-06-17 04:34:42,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:34:42,864] [INFO] ===== Completeness check finished =====
[2023-06-17 04:34:42,865] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:34:42,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/markers.fasta)
[2023-06-17 04:34:42,866] [INFO] Task started: Blastn
[2023-06-17 04:34:42,866] [INFO] Running command: blastn -query GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg8374d1ea-fde2-4734-bf18-6a182b871483/dqc_reference/reference_markers_gtdb.fasta -out GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:34:43,741] [INFO] Task succeeded: Blastn
[2023-06-17 04:34:43,747] [INFO] Selected 19 target genomes.
[2023-06-17 04:34:43,747] [INFO] Target genome list was writen to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:34:43,755] [INFO] Task started: fastANI
[2023-06-17 04:34:43,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e6dc93-cb5d-4625-9d38-154ad2f3632e/GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna.gz --refList GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/target_genomes_gtdb.txt --output GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:34:50,884] [INFO] Task succeeded: fastANI
[2023-06-17 04:34:50,898] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:34:50,898] [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_014306095.1	s__Copromorpha sp900549125	98.0191	509	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	97.82	97.60	0.83	0.80	4	conclusive
GCA_902362435.1	s__Copromorpha sp900066305	78.4893	129	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.11	98.22	0.97	0.95	3	-
GCA_017416795.1	s__Copromorpha sp017416795	77.5526	84	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	95.76	95.76	0.88	0.88	2	-
GCA_905193765.1	s__Copromorpha sp905193765	77.5385	66	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542385.1	s__Copromorpha excrementavium	77.3138	70	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.28	99.27	0.88	0.84	3	-
GCF_014385065.1	s__Copromorpha sp900545775	76.7007	63	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.71	99.57	0.95	0.91	4	-
GCA_900543485.1	s__Copromorpha excrementipullorum	76.6846	74	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.13	99.09	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-17 04:34:50,901] [INFO] GTDB search result was written to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/result_gtdb.tsv
[2023-06-17 04:34:50,901] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:34:50,905] [INFO] DFAST_QC result json was written to GCA_905209145.1_ERR1600645-mag-bin.74_genomic.fna/dqc_result.json
[2023-06-17 04:34:50,905] [INFO] DFAST_QC completed!
[2023-06-17 04:34:50,906] [INFO] Total running time: 0h0m47s