[2024-01-24 13:45:57,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:57,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:57,113] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference
[2024-01-24 13:45:58,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:58,368] [INFO] Task started: Prodigal
[2024-01-24 13:45:58,368] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e1ce8e2-badd-4939-a733-2e05ec4aa7da/GCF_008271285.1_ASM827128v1_genomic.fna.gz | prodigal -d GCF_008271285.1_ASM827128v1_genomic.fna/cds.fna -a GCF_008271285.1_ASM827128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:26,256] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:26,257] [INFO] Task started: HMMsearch
[2024-01-24 13:46:26,257] [INFO] Running command: hmmsearch --tblout GCF_008271285.1_ASM827128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/reference_markers.hmm GCF_008271285.1_ASM827128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:26,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:26,559] [INFO] Found 6/6 markers.
[2024-01-24 13:46:26,599] [INFO] Query marker FASTA was written to GCF_008271285.1_ASM827128v1_genomic.fna/markers.fasta
[2024-01-24 13:46:26,599] [INFO] Task started: Blastn
[2024-01-24 13:46:26,599] [INFO] Running command: blastn -query GCF_008271285.1_ASM827128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/reference_markers.fasta -out GCF_008271285.1_ASM827128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:27,246] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:27,250] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:27,251] [INFO] Target genome list was writen to GCF_008271285.1_ASM827128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:27,279] [INFO] Task started: fastANI
[2024-01-24 13:46:27,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1ce8e2-badd-4939-a733-2e05ec4aa7da/GCF_008271285.1_ASM827128v1_genomic.fna.gz --refList GCF_008271285.1_ASM827128v1_genomic.fna/target_genomes.txt --output GCF_008271285.1_ASM827128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:45,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:45,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:45,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:45,601] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:45,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:45,601] [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 guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	85.9318	1240	1606	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	81.5433	864	1606	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	81.3476	877	1606	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	81.2892	830	1606	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	81.2835	891	1606	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	81.208	879	1606	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	81.1255	853	1606	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	81.1108	829	1606	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	80.7376	785	1606	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	80.7278	810	1606	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	80.6423	891	1606	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	80.6156	760	1606	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.3984	844	1606	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.992	763	1606	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	79.8637	685	1606	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	79.7299	722	1606	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.2046	693	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:45,603] [INFO] DFAST Taxonomy check result was written to GCF_008271285.1_ASM827128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:45,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:45,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:45,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/checkm_data
[2024-01-24 13:46:45,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:45,653] [INFO] Task started: CheckM
[2024-01-24 13:46:45,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008271285.1_ASM827128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008271285.1_ASM827128v1_genomic.fna/checkm_input GCF_008271285.1_ASM827128v1_genomic.fna/checkm_result
[2024-01-24 13:47:57,906] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:57,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:57,927] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:57,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:57,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008271285.1_ASM827128v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:57,928] [INFO] Task started: Blastn
[2024-01-24 13:47:57,928] [INFO] Running command: blastn -query GCF_008271285.1_ASM827128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc0f703-23e8-4ede-9230-3e430444b07d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008271285.1_ASM827128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:58,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:58,775] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:58,775] [INFO] Target genome list was writen to GCF_008271285.1_ASM827128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:58,860] [INFO] Task started: fastANI
[2024-01-24 13:47:58,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1ce8e2-badd-4939-a733-2e05ec4aa7da/GCF_008271285.1_ASM827128v1_genomic.fna.gz --refList GCF_008271285.1_ASM827128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008271285.1_ASM827128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:17,395] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:17,409] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:17,409] [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_012273015.1	s__Hymenobacter sp012273015	97.5365	1429	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	conclusive
GCF_015773195.1	s__Hymenobacter sp015773195	85.9166	1242	1606	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	81.6424	886	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944765.1	s__Hymenobacter perfusus	81.522	867	1606	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	81.3269	880	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	81.2846	830	1606	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	81.2759	892	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	81.1929	881	1606	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	81.1565	849	1606	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	81.1108	829	1606	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	80.7676	909	1606	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	80.7612	831	1606	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	80.7123	812	1606	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	80.626	894	1606	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	80.6218	782	1606	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	80.6183	759	1606	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	80.5332	782	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013137895.1	s__Hymenobacter sp013137895	79.3692	669	1606	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 13:48:17,411] [INFO] GTDB search result was written to GCF_008271285.1_ASM827128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:17,411] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:17,415] [INFO] DFAST_QC result json was written to GCF_008271285.1_ASM827128v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:17,415] [INFO] DFAST_QC completed!
[2024-01-24 13:48:17,416] [INFO] Total running time: 0h2m20s