[2023-06-28 06:59:05,090] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:59:05,092] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:59:05,092] [INFO] DQC Reference Directory: /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference
[2023-06-28 06:59:06,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:59:06,278] [INFO] Task started: Prodigal
[2023-06-28 06:59:06,278] [INFO] Running command: gunzip -c /var/lib/cwl/stga2fa0d50-3873-4bb7-93ca-0fade4803c57/GCA_944385885.1_E02_bin5_genomic.fna.gz | prodigal -d GCA_944385885.1_E02_bin5_genomic.fna/cds.fna -a GCA_944385885.1_E02_bin5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:59:10,957] [INFO] Task succeeded: Prodigal
[2023-06-28 06:59:10,958] [INFO] Task started: HMMsearch
[2023-06-28 06:59:10,958] [INFO] Running command: hmmsearch --tblout GCA_944385885.1_E02_bin5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/reference_markers.hmm GCA_944385885.1_E02_bin5_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:59:11,163] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:59:11,164] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga2fa0d50-3873-4bb7-93ca-0fade4803c57/GCA_944385885.1_E02_bin5_genomic.fna.gz]
[2023-06-28 06:59:11,190] [INFO] Query marker FASTA was written to GCA_944385885.1_E02_bin5_genomic.fna/markers.fasta
[2023-06-28 06:59:11,190] [INFO] Task started: Blastn
[2023-06-28 06:59:11,190] [INFO] Running command: blastn -query GCA_944385885.1_E02_bin5_genomic.fna/markers.fasta -db /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/reference_markers.fasta -out GCA_944385885.1_E02_bin5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:59:11,844] [INFO] Task succeeded: Blastn
[2023-06-28 06:59:11,849] [INFO] Selected 20 target genomes.
[2023-06-28 06:59:11,849] [INFO] Target genome list was writen to GCA_944385885.1_E02_bin5_genomic.fna/target_genomes.txt
[2023-06-28 06:59:11,852] [INFO] Task started: fastANI
[2023-06-28 06:59:11,852] [INFO] Running command: fastANI --query /var/lib/cwl/stga2fa0d50-3873-4bb7-93ca-0fade4803c57/GCA_944385885.1_E02_bin5_genomic.fna.gz --refList GCA_944385885.1_E02_bin5_genomic.fna/target_genomes.txt --output GCA_944385885.1_E02_bin5_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:59:21,501] [INFO] Task succeeded: fastANI
[2023-06-28 06:59:21,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:59:21,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:59:21,512] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:59:21,513] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:59:21,513] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.2307	79	531	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.1753	80	531	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.025	64	531	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.9403	60	531	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.9403	60	531	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.6488	68	531	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	76.4649	50	531	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.3691	56	531	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.203	62	531	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:59:21,515] [INFO] DFAST Taxonomy check result was written to GCA_944385885.1_E02_bin5_genomic.fna/tc_result.tsv
[2023-06-28 06:59:21,516] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:59:21,516] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:59:21,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/checkm_data
[2023-06-28 06:59:21,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:59:21,543] [INFO] Task started: CheckM
[2023-06-28 06:59:21,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385885.1_E02_bin5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385885.1_E02_bin5_genomic.fna/checkm_input GCA_944385885.1_E02_bin5_genomic.fna/checkm_result
[2023-06-28 06:59:41,571] [INFO] Task succeeded: CheckM
[2023-06-28 06:59:41,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:59:41,603] [INFO] ===== Completeness check finished =====
[2023-06-28 06:59:41,603] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:59:41,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385885.1_E02_bin5_genomic.fna/markers.fasta)
[2023-06-28 06:59:41,604] [INFO] Task started: Blastn
[2023-06-28 06:59:41,604] [INFO] Running command: blastn -query GCA_944385885.1_E02_bin5_genomic.fna/markers.fasta -db /var/lib/cwl/stg7187a696-0ed4-4ed9-b6d5-b38daeaa680b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385885.1_E02_bin5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:59:42,694] [INFO] Task succeeded: Blastn
[2023-06-28 06:59:42,699] [INFO] Selected 22 target genomes.
[2023-06-28 06:59:42,699] [INFO] Target genome list was writen to GCA_944385885.1_E02_bin5_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:59:42,712] [INFO] Task started: fastANI
[2023-06-28 06:59:42,712] [INFO] Running command: fastANI --query /var/lib/cwl/stga2fa0d50-3873-4bb7-93ca-0fade4803c57/GCA_944385885.1_E02_bin5_genomic.fna.gz --refList GCA_944385885.1_E02_bin5_genomic.fna/target_genomes_gtdb.txt --output GCA_944385885.1_E02_bin5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:59:51,112] [INFO] Task succeeded: fastANI
[2023-06-28 06:59:51,129] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:59:51,129] [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_017540645.1	s__UBA738 sp017540645	78.7674	157	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	97.89	97.89	0.90	0.90	2	-
GCA_017411265.1	s__UBA738 sp017411265	78.7626	166	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455685.1	s__UBA738 sp017455685	77.8739	115	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768805.1	s__UBA738 sp902768805	77.868	69	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	97.59	96.33	0.82	0.75	3	-
GCA_017541825.1	s__UBA738 sp017541825	77.86	130	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557735.1	s__UBA738 sp004557735	77.832	107	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	96.30	95.55	0.89	0.83	10	-
GCA_017545165.1	s__Limivicinus sp017545165	77.5622	60	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765595.1	s__Limivicinus sp002350825	77.2706	68	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_002404605.1	s__UBA738 sp002404605	77.2333	87	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	99.68	99.62	0.91	0.89	3	-
GCA_902778275.1	s__Limivicinus sp902778275	77.1647	79	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003522945.1	s__UBA738 sp003522945	77.046	70	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738	95.0	97.42	97.25	0.82	0.69	7	-
GCA_017427645.1	s__CAG-83 sp017427645	77.0109	57	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286665.1	s__UBA1774 sp016286665	76.9912	58	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1774	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551945.1	s__Evtepia sp004551945	76.8747	73	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	98.68	98.58	0.91	0.88	5	-
GCF_002159265.1	s__Flavonifractor sp002159265	76.7496	79	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795345.1	s__UBA1774 sp902795345	76.7298	65	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1774	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296565.1	s__Evtepia sp016296565	76.6262	60	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Evtepia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579435.1	s__Dysosmobacter sp910579435	76.3577	72	531	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:59:51,131] [INFO] GTDB search result was written to GCA_944385885.1_E02_bin5_genomic.fna/result_gtdb.tsv
[2023-06-28 06:59:51,131] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:59:51,135] [INFO] DFAST_QC result json was written to GCA_944385885.1_E02_bin5_genomic.fna/dqc_result.json
[2023-06-28 06:59:51,135] [INFO] DFAST_QC completed!
[2023-06-28 06:59:51,135] [INFO] Total running time: 0h0m46s