[2024-01-25 18:42:05,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference
[2024-01-25 18:42:06,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,815] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,815] [INFO] Running command: gunzip -c /var/lib/cwl/stgb73295c9-c994-49cf-92ec-5690ef5763da/GCF_013377905.1_ASM1337790v1_genomic.fna.gz | prodigal -d GCF_013377905.1_ASM1337790v1_genomic.fna/cds.fna -a GCF_013377905.1_ASM1337790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:25,778] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:25,778] [INFO] Task started: HMMsearch
[2024-01-25 18:42:25,778] [INFO] Running command: hmmsearch --tblout GCF_013377905.1_ASM1337790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/reference_markers.hmm GCF_013377905.1_ASM1337790v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:26,013] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:26,014] [INFO] Found 6/6 markers.
[2024-01-25 18:42:26,045] [INFO] Query marker FASTA was written to GCF_013377905.1_ASM1337790v1_genomic.fna/markers.fasta
[2024-01-25 18:42:26,045] [INFO] Task started: Blastn
[2024-01-25 18:42:26,045] [INFO] Running command: blastn -query GCF_013377905.1_ASM1337790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/reference_markers.fasta -out GCF_013377905.1_ASM1337790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:26,633] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:26,636] [INFO] Selected 13 target genomes.
[2024-01-25 18:42:26,636] [INFO] Target genome list was writen to GCF_013377905.1_ASM1337790v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:26,641] [INFO] Task started: fastANI
[2024-01-25 18:42:26,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgb73295c9-c994-49cf-92ec-5690ef5763da/GCF_013377905.1_ASM1337790v1_genomic.fna.gz --refList GCF_013377905.1_ASM1337790v1_genomic.fna/target_genomes.txt --output GCF_013377905.1_ASM1337790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:40,495] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:40,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:40,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:40,504] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:40,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:40,505] [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 terrestris	strain=P5252	GCA_013377905.1	2748310	2748310	type	True	100.0	1302	1312	95	conclusive
Hymenobacter lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	90.605	1138	1312	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	87.0197	1055	1312	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	86.7862	1044	1312	95	below_threshold
Hymenobacter psychrophilus	strain=CGMCC 1.8975	GCA_900107135.1	651662	651662	type	True	86.7817	1091	1312	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	83.6579	995	1312	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	82.8462	957	1312	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	80.7475	822	1312	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	80.1323	707	1312	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.7247	703	1312	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.2269	635	1312	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.1196	671	1312	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.9321	627	1312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:40,506] [INFO] DFAST Taxonomy check result was written to GCF_013377905.1_ASM1337790v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:40,507] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:40,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:40,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/checkm_data
[2024-01-25 18:42:40,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:40,555] [INFO] Task started: CheckM
[2024-01-25 18:42:40,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377905.1_ASM1337790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377905.1_ASM1337790v1_genomic.fna/checkm_input GCF_013377905.1_ASM1337790v1_genomic.fna/checkm_result
[2024-01-25 18:43:30,491] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:30,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:30,511] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:30,511] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:30,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377905.1_ASM1337790v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:30,513] [INFO] Task started: Blastn
[2024-01-25 18:43:30,513] [INFO] Running command: blastn -query GCF_013377905.1_ASM1337790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg172af318-9cfd-4e65-b72b-1e3a80ef6f3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377905.1_ASM1337790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:31,366] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:31,369] [INFO] Selected 11 target genomes.
[2024-01-25 18:43:31,369] [INFO] Target genome list was writen to GCF_013377905.1_ASM1337790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:31,377] [INFO] Task started: fastANI
[2024-01-25 18:43:31,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgb73295c9-c994-49cf-92ec-5690ef5763da/GCF_013377905.1_ASM1337790v1_genomic.fna.gz --refList GCF_013377905.1_ASM1337790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377905.1_ASM1337790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:43,296] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:43,304] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:43,304] [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_013377905.1	s__Hymenobacter terrestris	100.0	1302	1312	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_013377885.1	s__Hymenobacter lapidiphilus	90.605	1138	1312	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	89.2355	1097	1312	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	88.519	1027	1312	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	87.0197	1055	1312	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	86.7954	1043	1312	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	86.7828	1091	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204745.1	s__Hymenobacter amundsenii	83.6486	996	1312	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	82.8585	957	1312	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	80.403	761	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018145755.1	s__Hymenobacter sp018145755	80.1482	704	1312	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:43,305] [INFO] GTDB search result was written to GCF_013377905.1_ASM1337790v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:43,306] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:43,310] [INFO] DFAST_QC result json was written to GCF_013377905.1_ASM1337790v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:43,310] [INFO] DFAST_QC completed!
[2024-01-25 18:43:43,310] [INFO] Total running time: 0h1m38s