[2024-01-25 17:36:05,509] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:05,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:05,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference
[2024-01-25 17:36:06,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:06,679] [INFO] Task started: Prodigal
[2024-01-25 17:36:06,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f6ef0b9-1526-4168-969e-849ea4ab80e7/GCF_020447315.1_ASM2044731v1_genomic.fna.gz | prodigal -d GCF_020447315.1_ASM2044731v1_genomic.fna/cds.fna -a GCF_020447315.1_ASM2044731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:32,669] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:32,670] [INFO] Task started: HMMsearch
[2024-01-25 17:36:32,670] [INFO] Running command: hmmsearch --tblout GCF_020447315.1_ASM2044731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/reference_markers.hmm GCF_020447315.1_ASM2044731v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:32,948] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:32,949] [INFO] Found 6/6 markers.
[2024-01-25 17:36:32,993] [INFO] Query marker FASTA was written to GCF_020447315.1_ASM2044731v1_genomic.fna/markers.fasta
[2024-01-25 17:36:32,993] [INFO] Task started: Blastn
[2024-01-25 17:36:32,993] [INFO] Running command: blastn -query GCF_020447315.1_ASM2044731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/reference_markers.fasta -out GCF_020447315.1_ASM2044731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:33,653] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:33,656] [INFO] Selected 14 target genomes.
[2024-01-25 17:36:33,656] [INFO] Target genome list was writen to GCF_020447315.1_ASM2044731v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:33,665] [INFO] Task started: fastANI
[2024-01-25 17:36:33,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f6ef0b9-1526-4168-969e-849ea4ab80e7/GCF_020447315.1_ASM2044731v1_genomic.fna.gz --refList GCF_020447315.1_ASM2044731v1_genomic.fna/target_genomes.txt --output GCF_020447315.1_ASM2044731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:51,535] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:51,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:51,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:51,545] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:51,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:51,545] [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 aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	87.4446	1426	1833	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	85.9085	1405	1833	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	85.2521	1383	1833	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	83.2048	1143	1833	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	82.8077	1073	1833	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	82.2585	1012	1833	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.9623	963	1833	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.5862	943	1833	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	80.5399	905	1833	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	80.5271	920	1833	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.7384	876	1833	95	below_threshold
Hymenobacter citatus	strain=BT507	GCA_014333615.1	2763506	2763506	type	True	79.2598	749	1833	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.684	592	1833	95	below_threshold
Hymenobacter jejuensis	strain=17J68-5	GCA_006337165.1	2502781	2502781	type	True	78.5319	701	1833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:51,548] [INFO] DFAST Taxonomy check result was written to GCF_020447315.1_ASM2044731v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:51,549] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:51,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:51,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/checkm_data
[2024-01-25 17:36:51,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:51,625] [INFO] Task started: CheckM
[2024-01-25 17:36:51,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020447315.1_ASM2044731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020447315.1_ASM2044731v1_genomic.fna/checkm_input GCF_020447315.1_ASM2044731v1_genomic.fna/checkm_result
[2024-01-25 17:37:57,812] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:57,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:57,841] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:57,841] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:57,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020447315.1_ASM2044731v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:57,844] [INFO] Task started: Blastn
[2024-01-25 17:37:57,844] [INFO] Running command: blastn -query GCF_020447315.1_ASM2044731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3084c863-3913-4214-94e3-41bed335f48f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020447315.1_ASM2044731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:58,798] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:58,801] [INFO] Selected 13 target genomes.
[2024-01-25 17:37:58,801] [INFO] Target genome list was writen to GCF_020447315.1_ASM2044731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:58,804] [INFO] Task started: fastANI
[2024-01-25 17:37:58,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f6ef0b9-1526-4168-969e-849ea4ab80e7/GCF_020447315.1_ASM2044731v1_genomic.fna.gz --refList GCF_020447315.1_ASM2044731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020447315.1_ASM2044731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:14,063] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:14,072] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:38:14,073] [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_004765605.1	s__Hymenobacter aquaticus	87.4356	1427	1833	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	85.9003	1406	1833	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	85.2512	1383	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	83.2165	1141	1833	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	82.8254	1070	1833	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	82.2509	1013	1833	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	81.2819	991	1833	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	80.7245	940	1833	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	80.563	947	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576555.1	s__Hymenobacter swuensis	80.5533	903	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	80.5233	921	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333615.1	s__Hymenobacter citatus	79.2627	749	1833	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	78.5319	701	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.30	97.30	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:14,075] [INFO] GTDB search result was written to GCF_020447315.1_ASM2044731v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:14,076] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:14,080] [INFO] DFAST_QC result json was written to GCF_020447315.1_ASM2044731v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:14,080] [INFO] DFAST_QC completed!
[2024-01-25 17:38:14,080] [INFO] Total running time: 0h2m9s