[2024-01-24 13:35:27,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference
[2024-01-24 13:35:28,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,868] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg0300ba21-4098-44c3-a6cb-3b14e5e84c1c/GCF_003231285.1_ASM323128v1_genomic.fna.gz | prodigal -d GCF_003231285.1_ASM323128v1_genomic.fna/cds.fna -a GCF_003231285.1_ASM323128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:57,567] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:57,567] [INFO] Task started: HMMsearch
[2024-01-24 13:35:57,568] [INFO] Running command: hmmsearch --tblout GCF_003231285.1_ASM323128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/reference_markers.hmm GCF_003231285.1_ASM323128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:57,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:57,878] [INFO] Found 6/6 markers.
[2024-01-24 13:35:57,925] [INFO] Query marker FASTA was written to GCF_003231285.1_ASM323128v1_genomic.fna/markers.fasta
[2024-01-24 13:35:57,925] [INFO] Task started: Blastn
[2024-01-24 13:35:57,925] [INFO] Running command: blastn -query GCF_003231285.1_ASM323128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/reference_markers.fasta -out GCF_003231285.1_ASM323128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:58,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:58,552] [INFO] Selected 17 target genomes.
[2024-01-24 13:35:58,552] [INFO] Target genome list was writen to GCF_003231285.1_ASM323128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:58,586] [INFO] Task started: fastANI
[2024-01-24 13:35:58,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg0300ba21-4098-44c3-a6cb-3b14e5e84c1c/GCF_003231285.1_ASM323128v1_genomic.fna.gz --refList GCF_003231285.1_ASM323128v1_genomic.fna/target_genomes.txt --output GCF_003231285.1_ASM323128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:16,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:16,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:16,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:16,615] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:16,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:16,615] [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 sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	100.0	1810	1811	95	conclusive
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	83.2305	1190	1811	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	81.1822	1005	1811	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	81.1571	1015	1811	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	80.9013	979	1811	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	80.8918	977	1811	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.6424	939	1811	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	80.3712	931	1811	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.2759	905	1811	95	below_threshold
Hymenobacter mucosus	strain=DSM 28041	GCA_900188255.1	1411120	1411120	type	True	80.155	875	1811	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.9518	816	1811	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.6534	855	1811	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.5221	827	1811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:16,617] [INFO] DFAST Taxonomy check result was written to GCF_003231285.1_ASM323128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:16,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:16,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:16,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/checkm_data
[2024-01-24 13:36:16,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:16,670] [INFO] Task started: CheckM
[2024-01-24 13:36:16,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003231285.1_ASM323128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003231285.1_ASM323128v1_genomic.fna/checkm_input GCF_003231285.1_ASM323128v1_genomic.fna/checkm_result
[2024-01-24 13:37:31,812] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:31,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:31,830] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:31,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:31,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003231285.1_ASM323128v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:31,832] [INFO] Task started: Blastn
[2024-01-24 13:37:31,832] [INFO] Running command: blastn -query GCF_003231285.1_ASM323128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042415d4-f6b5-444a-b7b7-2b22ed8b378c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003231285.1_ASM323128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:32,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:32,741] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:32,741] [INFO] Target genome list was writen to GCF_003231285.1_ASM323128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:32,780] [INFO] Task started: fastANI
[2024-01-24 13:37:32,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg0300ba21-4098-44c3-a6cb-3b14e5e84c1c/GCF_003231285.1_ASM323128v1_genomic.fna.gz --refList GCF_003231285.1_ASM323128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003231285.1_ASM323128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:52,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:52,263] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:52,264] [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_003231285.1	s__Hymenobacter sediminis	100.0	1810	1811	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_006352025.1	s__Hymenobacter sp006352025	86.7036	1340	1811	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	86.3095	1320	1811	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	83.2236	1191	1811	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	81.1795	1005	1811	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	80.8948	980	1811	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	80.881	978	1811	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	80.4797	874	1811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745865.1	s__Hymenobacter wooponensis	80.3692	932	1811	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	80.2554	909	1811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188255.1	s__Hymenobacter mucosus	80.1484	876	1811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	98.86	98.86	0.94	0.94	2	-
GCF_013137895.1	s__Hymenobacter sp013137895	80.1045	889	1811	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 13:37:52,266] [INFO] GTDB search result was written to GCF_003231285.1_ASM323128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:52,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:52,271] [INFO] DFAST_QC result json was written to GCF_003231285.1_ASM323128v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:52,271] [INFO] DFAST_QC completed!
[2024-01-24 13:37:52,271] [INFO] Total running time: 0h2m25s