[2024-01-24 12:36:58,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference
[2024-01-24 12:36:59,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,980] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,980] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbbf3074-3f76-4cb2-84c4-fe230f112a97/GCF_014640435.1_ASM1464043v1_genomic.fna.gz | prodigal -d GCF_014640435.1_ASM1464043v1_genomic.fna/cds.fna -a GCF_014640435.1_ASM1464043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:30,353] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:30,354] [INFO] Task started: HMMsearch
[2024-01-24 12:37:30,354] [INFO] Running command: hmmsearch --tblout GCF_014640435.1_ASM1464043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/reference_markers.hmm GCF_014640435.1_ASM1464043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:30,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:30,659] [INFO] Found 6/6 markers.
[2024-01-24 12:37:30,704] [INFO] Query marker FASTA was written to GCF_014640435.1_ASM1464043v1_genomic.fna/markers.fasta
[2024-01-24 12:37:30,704] [INFO] Task started: Blastn
[2024-01-24 12:37:30,705] [INFO] Running command: blastn -query GCF_014640435.1_ASM1464043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/reference_markers.fasta -out GCF_014640435.1_ASM1464043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:31,426] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:31,429] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:31,430] [INFO] Target genome list was writen to GCF_014640435.1_ASM1464043v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:31,445] [INFO] Task started: fastANI
[2024-01-24 12:37:31,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbbf3074-3f76-4cb2-84c4-fe230f112a97/GCF_014640435.1_ASM1464043v1_genomic.fna.gz --refList GCF_014640435.1_ASM1464043v1_genomic.fna/target_genomes.txt --output GCF_014640435.1_ASM1464043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:47,067] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:47,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:47,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:47,079] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:47,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:47,079] [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 frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	100.0	1526	1535	95	conclusive
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.1024	1111	1535	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	83.9261	1133	1535	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	83.4422	1072	1535	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	83.0408	1001	1535	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	82.9357	970	1535	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	82.897	1042	1535	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.3384	1021	1535	95	below_threshold
Hymenobacter terrenus	strain=MIMtkLc17	GCA_000972495.1	1629124	1629124	type	True	81.3703	918	1535	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	80.9537	882	1535	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	79.1877	692	1535	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.7419	619	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:47,081] [INFO] DFAST Taxonomy check result was written to GCF_014640435.1_ASM1464043v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:47,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:47,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:47,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/checkm_data
[2024-01-24 12:37:47,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:47,136] [INFO] Task started: CheckM
[2024-01-24 12:37:47,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640435.1_ASM1464043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640435.1_ASM1464043v1_genomic.fna/checkm_input GCF_014640435.1_ASM1464043v1_genomic.fna/checkm_result
[2024-01-24 12:39:01,775] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:01,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:01,800] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:01,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:01,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640435.1_ASM1464043v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:01,802] [INFO] Task started: Blastn
[2024-01-24 12:39:01,802] [INFO] Running command: blastn -query GCF_014640435.1_ASM1464043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg905517d8-b5d8-49d6-8980-f8b699c35cf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640435.1_ASM1464043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:02,679] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:02,683] [INFO] Selected 13 target genomes.
[2024-01-24 12:39:02,683] [INFO] Target genome list was writen to GCF_014640435.1_ASM1464043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:02,693] [INFO] Task started: fastANI
[2024-01-24 12:39:02,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbbf3074-3f76-4cb2-84c4-fe230f112a97/GCF_014640435.1_ASM1464043v1_genomic.fna.gz --refList GCF_014640435.1_ASM1464043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640435.1_ASM1464043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:18,622] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:18,637] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:18,637] [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_014640435.1	s__Hymenobacter frigidus	100.0	1526	1535	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_012275535.1	s__Hymenobacter artigasi	83.9314	1131	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018967845.1	s__Hymenobacter sp018967845	83.7567	1118	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	-
GCF_015694525.1	s__Hymenobacter ruricola	83.4783	1055	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	83.337	1061	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_001816145.1	s__Hymenobacter lapidarius	83.033	1004	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	82.9457	969	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	82.8794	1046	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	82.699	1024	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	82.3285	1022	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115775.1	s__Hymenobacter arizonensis	81.9782	1033	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571495.1	s__Hymenobacter negativus	81.8179	1000	1535	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972495.1	s__Hymenobacter terrenus	81.3778	917	1535	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 12:39:18,639] [INFO] GTDB search result was written to GCF_014640435.1_ASM1464043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:18,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:18,644] [INFO] DFAST_QC result json was written to GCF_014640435.1_ASM1464043v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:18,644] [INFO] DFAST_QC completed!
[2024-01-24 12:39:18,644] [INFO] Total running time: 0h2m20s