[2024-01-24 12:37:37,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference
[2024-01-24 12:37:41,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,020] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eabe8c9-f783-451a-8b84-05d14d66f9ef/GCF_014638675.1_ASM1463867v1_genomic.fna.gz | prodigal -d GCF_014638675.1_ASM1463867v1_genomic.fna/cds.fna -a GCF_014638675.1_ASM1463867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:38:07,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:38:07,659] [INFO] Task started: HMMsearch
[2024-01-24 12:38:07,659] [INFO] Running command: hmmsearch --tblout GCF_014638675.1_ASM1463867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/reference_markers.hmm GCF_014638675.1_ASM1463867v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:07,945] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:07,946] [INFO] Found 6/6 markers.
[2024-01-24 12:38:07,995] [INFO] Query marker FASTA was written to GCF_014638675.1_ASM1463867v1_genomic.fna/markers.fasta
[2024-01-24 12:38:07,996] [INFO] Task started: Blastn
[2024-01-24 12:38:07,996] [INFO] Running command: blastn -query GCF_014638675.1_ASM1463867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/reference_markers.fasta -out GCF_014638675.1_ASM1463867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:08,579] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:08,584] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:08,584] [INFO] Target genome list was writen to GCF_014638675.1_ASM1463867v1_genomic.fna/target_genomes.txt
[2024-01-24 12:38:08,597] [INFO] Task started: fastANI
[2024-01-24 12:38:08,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eabe8c9-f783-451a-8b84-05d14d66f9ef/GCF_014638675.1_ASM1463867v1_genomic.fna.gz --refList GCF_014638675.1_ASM1463867v1_genomic.fna/target_genomes.txt --output GCF_014638675.1_ASM1463867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:23,964] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:23,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:23,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:23,977] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:23,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:23,977] [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 qilianensis	strain=CGMCC 1.12720	GCA_014638675.1	1385715	1385715	type	True	100.0	1664	1666	95	conclusive
Hymenobacter qilianensis	strain=JCM 19763	GCA_014489555.1	1385715	1385715	type	True	99.9523	1663	1666	95	conclusive
Hymenobacter radiodurans	strain=17J36-26	GCA_004355185.1	2496028	2496028	type	True	86.1266	1370	1666	95	below_threshold
Hymenobacter roseosalivarius	strain=DSM 11622	GCA_900176135.1	89967	89967	type	True	84.6471	1169	1666	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	78.6565	620	1666	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.4628	664	1666	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	78.4335	579	1666	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.3403	610	1666	95	below_threshold
Hymenobacter cavernae	strain=CGMCC 1.15197	GCA_014641455.1	2044852	2044852	type	True	78.223	584	1666	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.1955	564	1666	95	below_threshold
Hymenobacter norwichensis	strain=DSM 15439	GCA_000420705.1	223903	223903	type	True	78.0531	543	1666	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	77.8263	487	1666	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	77.7481	434	1666	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	77.1129	362	1666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,979] [INFO] DFAST Taxonomy check result was written to GCF_014638675.1_ASM1463867v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:23,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:23,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:23,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/checkm_data
[2024-01-24 12:38:23,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:24,034] [INFO] Task started: CheckM
[2024-01-24 12:38:24,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638675.1_ASM1463867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638675.1_ASM1463867v1_genomic.fna/checkm_input GCF_014638675.1_ASM1463867v1_genomic.fna/checkm_result
[2024-01-24 12:39:35,467] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:35,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:35,499] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:35,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:35,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638675.1_ASM1463867v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:35,501] [INFO] Task started: Blastn
[2024-01-24 12:39:35,501] [INFO] Running command: blastn -query GCF_014638675.1_ASM1463867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c1f1957-9151-4cc6-8998-e10bc7332d7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638675.1_ASM1463867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:36,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:36,383] [INFO] Selected 11 target genomes.
[2024-01-24 12:39:36,383] [INFO] Target genome list was writen to GCF_014638675.1_ASM1463867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:36,396] [INFO] Task started: fastANI
[2024-01-24 12:39:36,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eabe8c9-f783-451a-8b84-05d14d66f9ef/GCF_014638675.1_ASM1463867v1_genomic.fna.gz --refList GCF_014638675.1_ASM1463867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638675.1_ASM1463867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:48,161] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:48,173] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:48,173] [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_014489555.1	s__Hymenobacter qilianensis	99.9523	1663	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCF_014333585.1	s__Hymenobacter sp014333585	89.4258	1396	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355185.1	s__Hymenobacter radiodurans	86.1266	1370	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.17	96.17	0.96	0.96	2	-
GCF_900176135.1	s__Hymenobacter roseosalivarius	84.6384	1170	1666	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	78.6792	615	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	78.4574	665	1666	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	78.4526	698	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634355.1	s__Hymenobacter sp003634355	78.2021	504	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801315.1	s__Hymenobacter sp000801315	78.1912	573	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420705.1	s__Hymenobacter norwichensis	78.0806	540	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	77.7555	433	1666	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 12:39:48,176] [INFO] GTDB search result was written to GCF_014638675.1_ASM1463867v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:48,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:48,183] [INFO] DFAST_QC result json was written to GCF_014638675.1_ASM1463867v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:48,184] [INFO] DFAST_QC completed!
[2024-01-24 12:39:48,184] [INFO] Total running time: 0h2m10s