[2024-01-24 15:18:38,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference
[2024-01-24 15:18:40,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,152] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c029f05-be3a-448d-8573-a5d42841a9a4/GCF_003944705.1_ASM394470v1_genomic.fna.gz | prodigal -d GCF_003944705.1_ASM394470v1_genomic.fna/cds.fna -a GCF_003944705.1_ASM394470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:11,731] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:11,731] [INFO] Task started: HMMsearch
[2024-01-24 15:19:11,731] [INFO] Running command: hmmsearch --tblout GCF_003944705.1_ASM394470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/reference_markers.hmm GCF_003944705.1_ASM394470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:12,041] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:12,042] [INFO] Found 6/6 markers.
[2024-01-24 15:19:12,087] [INFO] Query marker FASTA was written to GCF_003944705.1_ASM394470v1_genomic.fna/markers.fasta
[2024-01-24 15:19:12,087] [INFO] Task started: Blastn
[2024-01-24 15:19:12,087] [INFO] Running command: blastn -query GCF_003944705.1_ASM394470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/reference_markers.fasta -out GCF_003944705.1_ASM394470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:12,786] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:12,790] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:12,790] [INFO] Target genome list was writen to GCF_003944705.1_ASM394470v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:12,796] [INFO] Task started: fastANI
[2024-01-24 15:19:12,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c029f05-be3a-448d-8573-a5d42841a9a4/GCF_003944705.1_ASM394470v1_genomic.fna.gz --refList GCF_003944705.1_ASM394470v1_genomic.fna/target_genomes.txt --output GCF_003944705.1_ASM394470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:31,626] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:31,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:31,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:31,640] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:31,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:31,640] [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 metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	100.0	1717	1719	95	conclusive
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	85.8262	1320	1719	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	84.2216	1236	1719	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	83.776	1258	1719	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	82.9886	1105	1719	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	81.8506	1054	1719	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	81.6254	923	1719	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	81.1678	945	1719	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	81.0969	870	1719	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.9924	927	1719	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	80.4332	967	1719	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.1938	879	1719	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.1228	872	1719	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.9649	699	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,642] [INFO] DFAST Taxonomy check result was written to GCF_003944705.1_ASM394470v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:31,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:31,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:31,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/checkm_data
[2024-01-24 15:19:31,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:31,697] [INFO] Task started: CheckM
[2024-01-24 15:19:31,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003944705.1_ASM394470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003944705.1_ASM394470v1_genomic.fna/checkm_input GCF_003944705.1_ASM394470v1_genomic.fna/checkm_result
[2024-01-24 15:20:47,789] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:47,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:47,810] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:47,811] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:47,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003944705.1_ASM394470v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:47,812] [INFO] Task started: Blastn
[2024-01-24 15:20:47,812] [INFO] Running command: blastn -query GCF_003944705.1_ASM394470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc48076f0-eecd-4298-a047-6937f03e0ee3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003944705.1_ASM394470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:48,788] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:48,793] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:48,793] [INFO] Target genome list was writen to GCF_003944705.1_ASM394470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:48,801] [INFO] Task started: fastANI
[2024-01-24 15:20:48,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c029f05-be3a-448d-8573-a5d42841a9a4/GCF_003944705.1_ASM394470v1_genomic.fna.gz --refList GCF_003944705.1_ASM394470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003944705.1_ASM394470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:00,835] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:00,846] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:00,847] [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_003944705.1	s__Hymenobacter metallilatus	100.0	1717	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003944715.1	s__Hymenobacter rigui	85.8195	1321	1719	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	84.2281	1234	1719	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	83.7759	1258	1719	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	82.8091	1002	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199535.1	s__Hymenobacter latericoloratus	82.585	1117	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006352025.1	s__Hymenobacter sp006352025	82.0043	1087	1719	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	81.6865	1027	1719	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	81.6154	924	1719	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	81.0277	855	1719	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:00,848] [INFO] GTDB search result was written to GCF_003944705.1_ASM394470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:00,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:00,852] [INFO] DFAST_QC result json was written to GCF_003944705.1_ASM394470v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:00,852] [INFO] DFAST_QC completed!
[2024-01-24 15:21:00,852] [INFO] Total running time: 0h2m22s