[2024-01-25 20:22:50,615] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference
[2024-01-25 20:22:51,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,765] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,765] [INFO] Running command: gunzip -c /var/lib/cwl/stgfea9257f-0a88-4265-8bad-4167498af6ec/GCF_013377885.1_ASM1337788v1_genomic.fna.gz | prodigal -d GCF_013377885.1_ASM1337788v1_genomic.fna/cds.fna -a GCF_013377885.1_ASM1337788v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:13,090] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:13,090] [INFO] Task started: HMMsearch
[2024-01-25 20:23:13,090] [INFO] Running command: hmmsearch --tblout GCF_013377885.1_ASM1337788v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/reference_markers.hmm GCF_013377885.1_ASM1337788v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:13,445] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:13,446] [INFO] Found 6/6 markers.
[2024-01-25 20:23:13,485] [INFO] Query marker FASTA was written to GCF_013377885.1_ASM1337788v1_genomic.fna/markers.fasta
[2024-01-25 20:23:13,485] [INFO] Task started: Blastn
[2024-01-25 20:23:13,485] [INFO] Running command: blastn -query GCF_013377885.1_ASM1337788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/reference_markers.fasta -out GCF_013377885.1_ASM1337788v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:14,106] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:14,110] [INFO] Selected 22 target genomes.
[2024-01-25 20:23:14,111] [INFO] Target genome list was writen to GCF_013377885.1_ASM1337788v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:14,120] [INFO] Task started: fastANI
[2024-01-25 20:23:14,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea9257f-0a88-4265-8bad-4167498af6ec/GCF_013377885.1_ASM1337788v1_genomic.fna.gz --refList GCF_013377885.1_ASM1337788v1_genomic.fna/target_genomes.txt --output GCF_013377885.1_ASM1337788v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:37,691] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:37,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:37,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:37,702] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:37,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:37,703] [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 lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	100.0	1478	1483	95	conclusive
Hymenobacter terrestris	strain=P5252	GCA_013377905.1	2748310	2748310	type	True	90.5481	1143	1483	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	87.2402	1124	1483	95	below_threshold
Hymenobacter psychrophilus	strain=CGMCC 1.8975	GCA_900107135.1	651662	651662	type	True	87.1911	1191	1483	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	87.1721	1108	1483	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	83.9831	1098	1483	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	83.0393	1035	1483	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	81.3353	942	1483	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.0056	763	1483	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	79.9886	831	1483	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.4174	723	1483	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.371	710	1483	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	79.1412	773	1483	95	below_threshold
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	79.0907	787	1483	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.0771	679	1483	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	78.7994	673	1483	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.1746	516	1483	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.7616	71	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:37,708] [INFO] DFAST Taxonomy check result was written to GCF_013377885.1_ASM1337788v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:37,713] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:37,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:37,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/checkm_data
[2024-01-25 20:23:37,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:37,758] [INFO] Task started: CheckM
[2024-01-25 20:23:37,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377885.1_ASM1337788v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377885.1_ASM1337788v1_genomic.fna/checkm_input GCF_013377885.1_ASM1337788v1_genomic.fna/checkm_result
[2024-01-25 20:24:33,523] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:33,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:33,624] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:33,624] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:33,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377885.1_ASM1337788v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:33,625] [INFO] Task started: Blastn
[2024-01-25 20:24:33,625] [INFO] Running command: blastn -query GCF_013377885.1_ASM1337788v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0b2cf0-8b27-4ba4-833d-f8f782bc2569/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377885.1_ASM1337788v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:34,564] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:34,567] [INFO] Selected 13 target genomes.
[2024-01-25 20:24:34,567] [INFO] Target genome list was writen to GCF_013377885.1_ASM1337788v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:34,588] [INFO] Task started: fastANI
[2024-01-25 20:24:34,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea9257f-0a88-4265-8bad-4167498af6ec/GCF_013377885.1_ASM1337788v1_genomic.fna.gz --refList GCF_013377885.1_ASM1337788v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377885.1_ASM1337788v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:47,962] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:47,968] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:47,969] [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_013377885.1	s__Hymenobacter lapidiphilus	100.0	1478	1483	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_013377905.1	s__Hymenobacter terrestris	90.5655	1141	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003417065.2	s__Hymenobacter sp003417065	89.7731	1167	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613725.1	s__Hymenobacter sp018613725	89.3711	1102	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111515.1	s__Hymenobacter actinosclerus	87.2372	1125	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382225.1	s__Hymenobacter aerophilus	87.1721	1108	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107135.1	s__Hymenobacter psychrophilus	87.1628	1195	1483	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	83.7747	1051	1483	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	79.1216	707	1483	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:47,970] [INFO] GTDB search result was written to GCF_013377885.1_ASM1337788v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:47,971] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:47,973] [INFO] DFAST_QC result json was written to GCF_013377885.1_ASM1337788v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:47,973] [INFO] DFAST_QC completed!
[2024-01-25 20:24:47,974] [INFO] Total running time: 0h1m57s