[2024-01-24 12:44:54,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:54,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:54,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference
[2024-01-24 12:44:55,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,416] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgda076e0f-a814-4655-a17a-4cc38fdf61a3/GCF_020447265.1_ASM2044726v1_genomic.fna.gz | prodigal -d GCF_020447265.1_ASM2044726v1_genomic.fna/cds.fna -a GCF_020447265.1_ASM2044726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:29,465] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:29,466] [INFO] Task started: HMMsearch
[2024-01-24 12:45:29,466] [INFO] Running command: hmmsearch --tblout GCF_020447265.1_ASM2044726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/reference_markers.hmm GCF_020447265.1_ASM2044726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:29,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:29,787] [INFO] Found 6/6 markers.
[2024-01-24 12:45:29,834] [INFO] Query marker FASTA was written to GCF_020447265.1_ASM2044726v1_genomic.fna/markers.fasta
[2024-01-24 12:45:29,834] [INFO] Task started: Blastn
[2024-01-24 12:45:29,834] [INFO] Running command: blastn -query GCF_020447265.1_ASM2044726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/reference_markers.fasta -out GCF_020447265.1_ASM2044726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:30,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:30,484] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:30,485] [INFO] Target genome list was writen to GCF_020447265.1_ASM2044726v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:30,490] [INFO] Task started: fastANI
[2024-01-24 12:45:30,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgda076e0f-a814-4655-a17a-4cc38fdf61a3/GCF_020447265.1_ASM2044726v1_genomic.fna.gz --refList GCF_020447265.1_ASM2044726v1_genomic.fna/target_genomes.txt --output GCF_020447265.1_ASM2044726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:43,971] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:43,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:43,982] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:43,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:43,982] [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 aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	85.8285	1403	1971	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	85.2172	1428	1971	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	84.2846	1385	1971	95	below_threshold
Hymenobacter elongatus	strain=JCM 17223	GCA_004745955.1	877208	877208	type	True	83.2327	1129	1971	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	82.6699	1119	1971	95	below_threshold
Hymenobacter daecheongensis	strain=DSM 21074	GCA_900141805.1	496053	496053	type	True	82.3531	1017	1971	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.8336	931	1971	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.4528	939	1971	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	80.1575	950	1971	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.0582	957	1971	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.5104	867	1971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,984] [INFO] DFAST Taxonomy check result was written to GCF_020447265.1_ASM2044726v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:43,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:43,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:43,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/checkm_data
[2024-01-24 12:45:43,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:44,049] [INFO] Task started: CheckM
[2024-01-24 12:45:44,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020447265.1_ASM2044726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020447265.1_ASM2044726v1_genomic.fna/checkm_input GCF_020447265.1_ASM2044726v1_genomic.fna/checkm_result
[2024-01-24 12:47:09,346] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:09,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:09,371] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:09,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:09,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020447265.1_ASM2044726v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:09,372] [INFO] Task started: Blastn
[2024-01-24 12:47:09,372] [INFO] Running command: blastn -query GCF_020447265.1_ASM2044726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8075c3f9-3848-4edc-8df6-1b9f90d6ade0/dqc_reference/reference_markers_gtdb.fasta -out GCF_020447265.1_ASM2044726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:10,201] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:10,205] [INFO] Selected 8 target genomes.
[2024-01-24 12:47:10,205] [INFO] Target genome list was writen to GCF_020447265.1_ASM2044726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:10,213] [INFO] Task started: fastANI
[2024-01-24 12:47:10,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgda076e0f-a814-4655-a17a-4cc38fdf61a3/GCF_020447265.1_ASM2044726v1_genomic.fna.gz --refList GCF_020447265.1_ASM2044726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020447265.1_ASM2044726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:20,156] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:20,164] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:20,165] [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_004765605.1	s__Hymenobacter aquaticus	85.8122	1405	1971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	85.2322	1426	1971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745645.1	s__Hymenobacter sp004745645	84.2934	1384	1971	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	83.2424	1128	1971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	82.6659	1119	1971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	82.3607	1016	1971	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	80.1597	950	1971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333615.1	s__Hymenobacter citatus	79.0338	729	1971	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 12:47:20,171] [INFO] GTDB search result was written to GCF_020447265.1_ASM2044726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:20,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:20,176] [INFO] DFAST_QC result json was written to GCF_020447265.1_ASM2044726v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:20,176] [INFO] DFAST_QC completed!
[2024-01-24 12:47:20,176] [INFO] Total running time: 0h2m26s