[2024-01-24 12:05:26,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference
[2024-01-24 12:05:30,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,680] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,681] [INFO] Running command: gunzip -c /var/lib/cwl/stge07064ff-32f9-4d86-a5a6-43508a11ab94/GCF_019334315.1_ASM1933431v1_genomic.fna.gz | prodigal -d GCF_019334315.1_ASM1933431v1_genomic.fna/cds.fna -a GCF_019334315.1_ASM1933431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:59,143] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:59,144] [INFO] Task started: HMMsearch
[2024-01-24 12:05:59,144] [INFO] Running command: hmmsearch --tblout GCF_019334315.1_ASM1933431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/reference_markers.hmm GCF_019334315.1_ASM1933431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:59,464] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:59,466] [INFO] Found 6/6 markers.
[2024-01-24 12:05:59,511] [INFO] Query marker FASTA was written to GCF_019334315.1_ASM1933431v1_genomic.fna/markers.fasta
[2024-01-24 12:05:59,511] [INFO] Task started: Blastn
[2024-01-24 12:05:59,511] [INFO] Running command: blastn -query GCF_019334315.1_ASM1933431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/reference_markers.fasta -out GCF_019334315.1_ASM1933431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:00,122] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:00,125] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:00,125] [INFO] Target genome list was writen to GCF_019334315.1_ASM1933431v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:00,133] [INFO] Task started: fastANI
[2024-01-24 12:06:00,133] [INFO] Running command: fastANI --query /var/lib/cwl/stge07064ff-32f9-4d86-a5a6-43508a11ab94/GCF_019334315.1_ASM1933431v1_genomic.fna.gz --refList GCF_019334315.1_ASM1933431v1_genomic.fna/target_genomes.txt --output GCF_019334315.1_ASM1933431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:22,194] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:22,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:22,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:22,215] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:22,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:22,215] [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
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	100.0	1605	1640	95	conclusive
Hymenobacter citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	88.3673	1321	1640	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	79.157	629	1640	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	79.1305	702	1640	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	79.1003	658	1640	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.0245	697	1640	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.995	616	1640	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.9545	656	1640	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	78.9006	669	1640	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	78.8672	696	1640	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	78.7768	607	1640	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.613	621	1640	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	78.6001	676	1640	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	78.5272	548	1640	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.4972	589	1640	95	below_threshold
Hymenobacter crusticola	strain=MIMBbqt21	GCA_002154225.1	1770526	1770526	type	True	78.1152	567	1640	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	78.0372	565	1640	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	77.82	533	1640	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	77.618	392	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:22,217] [INFO] DFAST Taxonomy check result was written to GCF_019334315.1_ASM1933431v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:22,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:22,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:22,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/checkm_data
[2024-01-24 12:06:22,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:22,267] [INFO] Task started: CheckM
[2024-01-24 12:06:22,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019334315.1_ASM1933431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019334315.1_ASM1933431v1_genomic.fna/checkm_input GCF_019334315.1_ASM1933431v1_genomic.fna/checkm_result
[2024-01-24 12:07:36,826] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:36,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,850] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:36,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:36,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019334315.1_ASM1933431v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:36,851] [INFO] Task started: Blastn
[2024-01-24 12:07:36,851] [INFO] Running command: blastn -query GCF_019334315.1_ASM1933431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99a4aaf3-c9cd-4006-9037-4b4ba03d64af/dqc_reference/reference_markers_gtdb.fasta -out GCF_019334315.1_ASM1933431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:37,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:37,706] [INFO] Selected 22 target genomes.
[2024-01-24 12:07:37,707] [INFO] Target genome list was writen to GCF_019334315.1_ASM1933431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:37,729] [INFO] Task started: fastANI
[2024-01-24 12:07:37,730] [INFO] Running command: fastANI --query /var/lib/cwl/stge07064ff-32f9-4d86-a5a6-43508a11ab94/GCF_019334315.1_ASM1933431v1_genomic.fna.gz --refList GCF_019334315.1_ASM1933431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019334315.1_ASM1933431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:59,427] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:59,448] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:59,448] [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_017589435.1	s__Hymenobacter defluvii	96.6653	1407	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.38	96.38	0.86	0.86	2	conclusive
GCF_014333615.1	s__Hymenobacter citatus	88.3673	1321	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	79.4126	712	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760735.1	s__Hymenobacter sp018760735	79.1397	702	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313265.1	s__Hymenobacter sp017313265	79.0407	695	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.9883	617	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	78.9682	654	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	78.9537	609	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640315.1	s__Hymenobacter glacieicola	78.9017	670	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273015.1	s__Hymenobacter sp012273015	78.8855	587	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
GCF_000801315.1	s__Hymenobacter sp000801315	78.875	580	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	78.8679	697	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	78.7768	607	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280305.1	s__Hymenobacter sp001280305	78.6985	553	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	78.6028	675	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	78.5936	611	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275535.1	s__Hymenobacter artigasi	78.2957	577	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	78.2147	561	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734815.1	s__Hymenobacter rubidus	78.1938	549	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154225.1	s__Hymenobacter crusticola	78.102	569	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337165.1	s__Hymenobacter jejuensis	77.8281	532	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
GCF_008728635.1	s__Hymenobacter baengnokdamensis	77.7174	419	1640	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:59,451] [INFO] GTDB search result was written to GCF_019334315.1_ASM1933431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:59,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:59,456] [INFO] DFAST_QC result json was written to GCF_019334315.1_ASM1933431v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:59,456] [INFO] DFAST_QC completed!
[2024-01-24 12:07:59,457] [INFO] Total running time: 0h2m33s