[2023-06-05 01:05:17,312] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:05:17,315] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:05:17,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference
[2023-06-05 01:05:18,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:05:18,695] [INFO] Task started: Prodigal
[2023-06-05 01:05:18,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgf77f6bb6-7142-4bd2-b009-7e4b5cec1c30/GCA_934560985.1_ERR7738598_bin.164_genomic.fna.gz | prodigal -d GCA_934560985.1_ERR7738598_bin.164_genomic.fna/cds.fna -a GCA_934560985.1_ERR7738598_bin.164_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:05:26,393] [INFO] Task succeeded: Prodigal
[2023-06-05 01:05:26,394] [INFO] Task started: HMMsearch
[2023-06-05 01:05:26,394] [INFO] Running command: hmmsearch --tblout GCA_934560985.1_ERR7738598_bin.164_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/reference_markers.hmm GCA_934560985.1_ERR7738598_bin.164_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:05:26,641] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:05:26,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf77f6bb6-7142-4bd2-b009-7e4b5cec1c30/GCA_934560985.1_ERR7738598_bin.164_genomic.fna.gz]
[2023-06-05 01:05:26,676] [INFO] Query marker FASTA was written to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/markers.fasta
[2023-06-05 01:05:26,676] [INFO] Task started: Blastn
[2023-06-05 01:05:26,677] [INFO] Running command: blastn -query GCA_934560985.1_ERR7738598_bin.164_genomic.fna/markers.fasta -db /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/reference_markers.fasta -out GCA_934560985.1_ERR7738598_bin.164_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:05:27,257] [INFO] Task succeeded: Blastn
[2023-06-05 01:05:27,261] [INFO] Selected 14 target genomes.
[2023-06-05 01:05:27,262] [INFO] Target genome list was writen to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/target_genomes.txt
[2023-06-05 01:05:27,263] [INFO] Task started: fastANI
[2023-06-05 01:05:27,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77f6bb6-7142-4bd2-b009-7e4b5cec1c30/GCA_934560985.1_ERR7738598_bin.164_genomic.fna.gz --refList GCA_934560985.1_ERR7738598_bin.164_genomic.fna/target_genomes.txt --output GCA_934560985.1_ERR7738598_bin.164_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:05:34,272] [INFO] Task succeeded: fastANI
[2023-06-05 01:05:34,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:05:34,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:05:34,278] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:05:34,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:05:34,278] [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=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.6365	55	828	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.6133	59	828	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.5173	60	828	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.3154	54	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:05:34,310] [INFO] DFAST Taxonomy check result was written to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/tc_result.tsv
[2023-06-05 01:05:34,311] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:05:34,312] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:05:34,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/checkm_data
[2023-06-05 01:05:34,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:05:34,351] [INFO] Task started: CheckM
[2023-06-05 01:05:34,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934560985.1_ERR7738598_bin.164_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934560985.1_ERR7738598_bin.164_genomic.fna/checkm_input GCA_934560985.1_ERR7738598_bin.164_genomic.fna/checkm_result
[2023-06-05 01:06:02,692] [INFO] Task succeeded: CheckM
[2023-06-05 01:06:02,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:06:02,715] [INFO] ===== Completeness check finished =====
[2023-06-05 01:06:02,715] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:06:02,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934560985.1_ERR7738598_bin.164_genomic.fna/markers.fasta)
[2023-06-05 01:06:02,716] [INFO] Task started: Blastn
[2023-06-05 01:06:02,716] [INFO] Running command: blastn -query GCA_934560985.1_ERR7738598_bin.164_genomic.fna/markers.fasta -db /var/lib/cwl/stg4baff3c5-edf0-4597-9dea-6bab849342f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934560985.1_ERR7738598_bin.164_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:06:03,554] [INFO] Task succeeded: Blastn
[2023-06-05 01:06:03,559] [INFO] Selected 10 target genomes.
[2023-06-05 01:06:03,560] [INFO] Target genome list was writen to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:06:03,566] [INFO] Task started: fastANI
[2023-06-05 01:06:03,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgf77f6bb6-7142-4bd2-b009-7e4b5cec1c30/GCA_934560985.1_ERR7738598_bin.164_genomic.fna.gz --refList GCA_934560985.1_ERR7738598_bin.164_genomic.fna/target_genomes_gtdb.txt --output GCA_934560985.1_ERR7738598_bin.164_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:06:08,376] [INFO] Task succeeded: fastANI
[2023-06-05 01:06:08,387] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:06:08,388] [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_900757695.1	s__HGM13006 sp900757695	96.5554	561	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	98.45	98.45	0.78	0.78	2	conclusive
GCA_900756575.1	s__HGM13006 sp900756575	82.1614	461	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	98.02	98.02	0.80	0.80	2	-
GCA_905202605.1	s__HGM13006 sp905202605	82.0378	420	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201305.1	s__HGM13006 sp905201305	81.7456	364	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778525.1	s__HGM13006 sp902778525	78.3795	196	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	98.52	98.52	0.77	0.77	2	-
GCA_017469795.1	s__HGM13006 sp017469795	78.3545	221	828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__HGM13006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:06:08,389] [INFO] GTDB search result was written to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/result_gtdb.tsv
[2023-06-05 01:06:08,390] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:06:08,393] [INFO] DFAST_QC result json was written to GCA_934560985.1_ERR7738598_bin.164_genomic.fna/dqc_result.json
[2023-06-05 01:06:08,393] [INFO] DFAST_QC completed!
[2023-06-05 01:06:08,393] [INFO] Total running time: 0h0m51s