[2024-01-24 11:12:27,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:27,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:27,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference
[2024-01-24 11:12:29,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,055] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgb46e7080-52b5-4384-bb56-926b7830fd61/GCF_008727865.1_ASM872786v1_genomic.fna.gz | prodigal -d GCF_008727865.1_ASM872786v1_genomic.fna/cds.fna -a GCF_008727865.1_ASM872786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:01,937] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:01,937] [INFO] Task started: HMMsearch
[2024-01-24 11:13:01,938] [INFO] Running command: hmmsearch --tblout GCF_008727865.1_ASM872786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/reference_markers.hmm GCF_008727865.1_ASM872786v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:02,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:02,227] [INFO] Found 6/6 markers.
[2024-01-24 11:13:02,268] [INFO] Query marker FASTA was written to GCF_008727865.1_ASM872786v1_genomic.fna/markers.fasta
[2024-01-24 11:13:02,269] [INFO] Task started: Blastn
[2024-01-24 11:13:02,269] [INFO] Running command: blastn -query GCF_008727865.1_ASM872786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/reference_markers.fasta -out GCF_008727865.1_ASM872786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:02,936] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:02,940] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:02,940] [INFO] Target genome list was writen to GCF_008727865.1_ASM872786v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:02,946] [INFO] Task started: fastANI
[2024-01-24 11:13:02,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46e7080-52b5-4384-bb56-926b7830fd61/GCF_008727865.1_ASM872786v1_genomic.fna.gz --refList GCF_008727865.1_ASM872786v1_genomic.fna/target_genomes.txt --output GCF_008727865.1_ASM872786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,658] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:20,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:20,672] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:20,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:20,672] [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 busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	100.0	1624	1624	95	conclusive
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	83.4302	1198	1624	95	below_threshold
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	83.3006	1200	1624	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	83.0556	1195	1624	95	below_threshold
Hymenobacter oligotrophus	strain=sh-6	GCA_003574965.1	2319843	2319843	type	True	81.0663	889	1624	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	80.3862	852	1624	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.1038	834	1624	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.0649	796	1624	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.8823	795	1624	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.8509	838	1624	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	79.5029	724	1624	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.4582	760	1624	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	79.2331	724	1624	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.3583	559	1624	95	below_threshold
Hymenobacter profundi	strain=M2	GCA_019334315.1	1982110	1982110	type	True	78.3563	551	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,677] [INFO] DFAST Taxonomy check result was written to GCF_008727865.1_ASM872786v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:20,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:20,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:20,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/checkm_data
[2024-01-24 11:13:20,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:20,731] [INFO] Task started: CheckM
[2024-01-24 11:13:20,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008727865.1_ASM872786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008727865.1_ASM872786v1_genomic.fna/checkm_input GCF_008727865.1_ASM872786v1_genomic.fna/checkm_result
[2024-01-24 11:14:41,008] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:41,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:41,029] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:41,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:41,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008727865.1_ASM872786v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:41,030] [INFO] Task started: Blastn
[2024-01-24 11:14:41,031] [INFO] Running command: blastn -query GCF_008727865.1_ASM872786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10f1aed8-fd30-48d8-ae8a-70b986627ece/dqc_reference/reference_markers_gtdb.fasta -out GCF_008727865.1_ASM872786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:42,005] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:42,009] [INFO] Selected 12 target genomes.
[2024-01-24 11:14:42,010] [INFO] Target genome list was writen to GCF_008727865.1_ASM872786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:42,044] [INFO] Task started: fastANI
[2024-01-24 11:14:42,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46e7080-52b5-4384-bb56-926b7830fd61/GCF_008727865.1_ASM872786v1_genomic.fna.gz --refList GCF_008727865.1_ASM872786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008727865.1_ASM872786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:56,135] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:56,148] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:56,148] [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_008727865.1	s__Solirubrum busanensis	100.0	1624	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003258365.1	s__Solirubrum edaphi	83.4249	1199	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771675.1	s__Solirubrum jeollabukense	83.3352	1194	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	83.0787	1192	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007105.1	s__Solirubrum sp002007105	82.5684	1129	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574965.1	s__Solirubrum oligotrophum	81.0739	888	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483135.1	s__Solirubrum puertoriconensis	80.4243	871	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	80.3884	851	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	80.1174	833	1624	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	79.7507	776	1624	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	79.2396	723	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589435.1	s__Hymenobacter defluvii	78.3675	567	1624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	96.38	96.38	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:56,150] [INFO] GTDB search result was written to GCF_008727865.1_ASM872786v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:56,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:56,154] [INFO] DFAST_QC result json was written to GCF_008727865.1_ASM872786v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:56,154] [INFO] DFAST_QC completed!
[2024-01-24 11:14:56,154] [INFO] Total running time: 0h2m28s