[2023-06-19 01:23:58,824] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:23:58,847] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:23:58,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference
[2023-06-19 01:24:00,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:24:00,486] [INFO] Task started: Prodigal
[2023-06-19 01:24:00,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg11250523-c05a-48e5-9f51-24a3d4afcb5b/GCA_018969455.1_ASM1896945v1_genomic.fna.gz | prodigal -d GCA_018969455.1_ASM1896945v1_genomic.fna/cds.fna -a GCA_018969455.1_ASM1896945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:24:26,257] [INFO] Task succeeded: Prodigal
[2023-06-19 01:24:26,257] [INFO] Task started: HMMsearch
[2023-06-19 01:24:26,257] [INFO] Running command: hmmsearch --tblout GCA_018969455.1_ASM1896945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/reference_markers.hmm GCA_018969455.1_ASM1896945v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:24:26,516] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:24:26,517] [INFO] Found 6/6 markers.
[2023-06-19 01:24:26,624] [INFO] Query marker FASTA was written to GCA_018969455.1_ASM1896945v1_genomic.fna/markers.fasta
[2023-06-19 01:24:26,625] [INFO] Task started: Blastn
[2023-06-19 01:24:26,625] [INFO] Running command: blastn -query GCA_018969455.1_ASM1896945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/reference_markers.fasta -out GCA_018969455.1_ASM1896945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:24:27,191] [INFO] Task succeeded: Blastn
[2023-06-19 01:24:27,195] [INFO] Selected 27 target genomes.
[2023-06-19 01:24:27,195] [INFO] Target genome list was writen to GCA_018969455.1_ASM1896945v1_genomic.fna/target_genomes.txt
[2023-06-19 01:24:27,203] [INFO] Task started: fastANI
[2023-06-19 01:24:27,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg11250523-c05a-48e5-9f51-24a3d4afcb5b/GCA_018969455.1_ASM1896945v1_genomic.fna.gz --refList GCA_018969455.1_ASM1896945v1_genomic.fna/target_genomes.txt --output GCA_018969455.1_ASM1896945v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:24:50,152] [INFO] Task succeeded: fastANI
[2023-06-19 01:24:50,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:24:50,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:24:50,164] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:24:50,164] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 01:24:50,165] [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
--------------------------------------------------------------------------------
[2023-06-19 01:24:50,167] [INFO] DFAST Taxonomy check result was written to GCA_018969455.1_ASM1896945v1_genomic.fna/tc_result.tsv
[2023-06-19 01:24:50,168] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:24:50,168] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:24:50,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/checkm_data
[2023-06-19 01:24:50,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:24:50,218] [INFO] Task started: CheckM
[2023-06-19 01:24:50,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969455.1_ASM1896945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969455.1_ASM1896945v1_genomic.fna/checkm_input GCA_018969455.1_ASM1896945v1_genomic.fna/checkm_result
[2023-06-19 01:26:01,010] [INFO] Task succeeded: CheckM
[2023-06-19 01:26:01,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:26:01,047] [INFO] ===== Completeness check finished =====
[2023-06-19 01:26:01,047] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:26:01,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969455.1_ASM1896945v1_genomic.fna/markers.fasta)
[2023-06-19 01:26:01,048] [INFO] Task started: Blastn
[2023-06-19 01:26:01,048] [INFO] Running command: blastn -query GCA_018969455.1_ASM1896945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb3f3ebf-41e8-4ad9-97ef-ec027568575c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969455.1_ASM1896945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:26:01,801] [INFO] Task succeeded: Blastn
[2023-06-19 01:26:01,806] [INFO] Selected 24 target genomes.
[2023-06-19 01:26:01,807] [INFO] Target genome list was writen to GCA_018969455.1_ASM1896945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:26:01,856] [INFO] Task started: fastANI
[2023-06-19 01:26:01,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg11250523-c05a-48e5-9f51-24a3d4afcb5b/GCA_018969455.1_ASM1896945v1_genomic.fna.gz --refList GCA_018969455.1_ASM1896945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969455.1_ASM1896945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:26:21,353] [INFO] Task succeeded: fastANI
[2023-06-19 01:26:21,376] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:26:21,376] [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_018969455.1	s__M3007 sp018969455	100.0	1100	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903905445.1	s__M3007 sp903905445	78.5354	360	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.58	99.54	0.86	0.85	3	-
GCA_016719605.1	s__M3007 sp016719605	76.5487	74	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787465.1	s__M3007 sp016787465	76.3877	70	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711435.1	s__M3007 sp016711435	76.3737	118	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787415.1	s__M3007 sp016787415	76.3644	107	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303475.1	s__M3007 sp017303475	76.3542	79	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708875.1	s__M3007 sp016708875	76.3204	61	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719895.1	s__M3007 sp016719895	76.2755	89	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.47	99.47	0.95	0.95	2	-
GCA_903933805.1	s__M3007 sp903933805	76.1944	51	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	99.57	99.51	0.91	0.90	6	-
GCA_016712415.1	s__M3007 sp016712415	76.1121	90	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303875.1	s__M3007 sp017303875	76.1023	111	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787345.1	s__M3007 sp016787345	76.0029	106	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713985.1	s__M3007 sp016713985	75.9563	109	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298845.1	s__M3007 sp013298845	75.7656	73	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787285.1	s__M3007 sp016787285	75.7125	75	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226345.1	s__M3007 sp006226345	75.4916	54	1113	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:26:21,379] [INFO] GTDB search result was written to GCA_018969455.1_ASM1896945v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:26:21,379] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:26:21,385] [INFO] DFAST_QC result json was written to GCA_018969455.1_ASM1896945v1_genomic.fna/dqc_result.json
[2023-06-19 01:26:21,386] [INFO] DFAST_QC completed!
[2023-06-19 01:26:21,386] [INFO] Total running time: 0h2m23s