[2024-01-24 14:55:07,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference
[2024-01-24 14:55:09,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,555] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg9144f1a7-ffad-4596-b740-8c605c7008bf/GCF_013137895.1_ASM1313789v1_genomic.fna.gz | prodigal -d GCF_013137895.1_ASM1313789v1_genomic.fna/cds.fna -a GCF_013137895.1_ASM1313789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:35,075] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:35,076] [INFO] Task started: HMMsearch
[2024-01-24 14:55:35,076] [INFO] Running command: hmmsearch --tblout GCF_013137895.1_ASM1313789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/reference_markers.hmm GCF_013137895.1_ASM1313789v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:35,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:35,395] [INFO] Found 6/6 markers.
[2024-01-24 14:55:35,437] [INFO] Query marker FASTA was written to GCF_013137895.1_ASM1313789v1_genomic.fna/markers.fasta
[2024-01-24 14:55:35,438] [INFO] Task started: Blastn
[2024-01-24 14:55:35,438] [INFO] Running command: blastn -query GCF_013137895.1_ASM1313789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/reference_markers.fasta -out GCF_013137895.1_ASM1313789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:36,145] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:36,148] [INFO] Selected 19 target genomes.
[2024-01-24 14:55:36,149] [INFO] Target genome list was writen to GCF_013137895.1_ASM1313789v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:36,159] [INFO] Task started: fastANI
[2024-01-24 14:55:36,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg9144f1a7-ffad-4596-b740-8c605c7008bf/GCF_013137895.1_ASM1313789v1_genomic.fna.gz --refList GCF_013137895.1_ASM1313789v1_genomic.fna/target_genomes.txt --output GCF_013137895.1_ASM1313789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:56,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:56,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:56,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:56,655] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:56,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:56,656] [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 wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	84.3927	1308	1626	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	83.695	1276	1626	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	82.3086	1132	1626	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	80.506	905	1626	95	below_threshold
Hymenobacter sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	80.1703	870	1626	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	80.0739	820	1626	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	79.9901	860	1626	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	79.7387	841	1626	95	below_threshold
Hymenobacter duratus	strain=BT646	GCA_014698995.1	2771356	2771356	type	True	79.4745	707	1626	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.3835	722	1626	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.326	693	1626	95	below_threshold
Hymenobacter mucosus	strain=DSM 28041	GCA_900188255.1	1411120	1411120	type	True	79.2562	787	1626	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.9327	727	1626	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.0863	530	1626	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	77.6532	512	1626	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	77.3172	365	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:56,659] [INFO] DFAST Taxonomy check result was written to GCF_013137895.1_ASM1313789v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:56,659] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:56,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:56,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/checkm_data
[2024-01-24 14:55:56,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:56,714] [INFO] Task started: CheckM
[2024-01-24 14:55:56,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013137895.1_ASM1313789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013137895.1_ASM1313789v1_genomic.fna/checkm_input GCF_013137895.1_ASM1313789v1_genomic.fna/checkm_result
[2024-01-24 14:57:05,167] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:05,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:05,187] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:05,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:05,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013137895.1_ASM1313789v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:05,188] [INFO] Task started: Blastn
[2024-01-24 14:57:05,188] [INFO] Running command: blastn -query GCF_013137895.1_ASM1313789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425c946f-d752-4862-924a-9e590c01ffe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_013137895.1_ASM1313789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:06,066] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:06,069] [INFO] Selected 15 target genomes.
[2024-01-24 14:57:06,069] [INFO] Target genome list was writen to GCF_013137895.1_ASM1313789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:06,080] [INFO] Task started: fastANI
[2024-01-24 14:57:06,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg9144f1a7-ffad-4596-b740-8c605c7008bf/GCF_013137895.1_ASM1313789v1_genomic.fna.gz --refList GCF_013137895.1_ASM1313789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013137895.1_ASM1313789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:22,436] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:22,454] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:22,455] [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_013137895.1	s__Hymenobacter sp013137895	100.0	1626	1626	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_004745865.1	s__Hymenobacter wooponensis	84.415	1304	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745825.1	s__Hymenobacter sp004745825	83.7045	1275	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187375.1	s__Hymenobacter gelipurpurascens	82.3107	1132	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352025.1	s__Hymenobacter sp006352025	80.6266	932	1626	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	80.6256	924	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640315.1	s__Hymenobacter glacieicola	80.4954	907	1626	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	80.0536	823	1626	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	79.9837	861	1626	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	79.9414	804	1626	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	79.7494	598	1626	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	79.5614	722	1626	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	79.4706	708	1626	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	79.2191	733	1626	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	78.5923	585	1626	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 14:57:22,456] [INFO] GTDB search result was written to GCF_013137895.1_ASM1313789v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:22,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:22,460] [INFO] DFAST_QC result json was written to GCF_013137895.1_ASM1313789v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:22,460] [INFO] DFAST_QC completed!
[2024-01-24 14:57:22,460] [INFO] Total running time: 0h2m15s