[2024-01-24 14:30:16,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:16,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:16,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference
[2024-01-24 14:30:18,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,424] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf63d438-c1a2-4585-b8a0-28dc190d85db/GCF_014646975.1_ASM1464697v1_genomic.fna.gz | prodigal -d GCF_014646975.1_ASM1464697v1_genomic.fna/cds.fna -a GCF_014646975.1_ASM1464697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:29,634] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:29,635] [INFO] Task started: HMMsearch
[2024-01-24 14:30:29,635] [INFO] Running command: hmmsearch --tblout GCF_014646975.1_ASM1464697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/reference_markers.hmm GCF_014646975.1_ASM1464697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:29,950] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:29,951] [INFO] Found 6/6 markers.
[2024-01-24 14:30:29,999] [INFO] Query marker FASTA was written to GCF_014646975.1_ASM1464697v1_genomic.fna/markers.fasta
[2024-01-24 14:30:30,000] [INFO] Task started: Blastn
[2024-01-24 14:30:30,000] [INFO] Running command: blastn -query GCF_014646975.1_ASM1464697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/reference_markers.fasta -out GCF_014646975.1_ASM1464697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:30,674] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:30,678] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:30,679] [INFO] Target genome list was writen to GCF_014646975.1_ASM1464697v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:30,731] [INFO] Task started: fastANI
[2024-01-24 14:30:30,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf63d438-c1a2-4585-b8a0-28dc190d85db/GCF_014646975.1_ASM1464697v1_genomic.fna.gz --refList GCF_014646975.1_ASM1464697v1_genomic.fna/target_genomes.txt --output GCF_014646975.1_ASM1464697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:42,629] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:42,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:42,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:42,640] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:30:42,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:42,641] [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
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	100.0	1546	1547	95	conclusive
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	99.9956	1538	1547	95	conclusive
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	79.7626	451	1547	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	79.7425	456	1547	95	below_threshold
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	79.7115	450	1547	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	78.9771	410	1547	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	78.6284	417	1547	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	78.6255	339	1547	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.4688	234	1547	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	77.2757	109	1547	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	77.2742	106	1547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:42,642] [INFO] DFAST Taxonomy check result was written to GCF_014646975.1_ASM1464697v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:42,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:42,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:42,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/checkm_data
[2024-01-24 14:30:42,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:42,692] [INFO] Task started: CheckM
[2024-01-24 14:30:42,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646975.1_ASM1464697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646975.1_ASM1464697v1_genomic.fna/checkm_input GCF_014646975.1_ASM1464697v1_genomic.fna/checkm_result
[2024-01-24 14:31:21,285] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:21,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:21,308] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:21,308] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:21,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646975.1_ASM1464697v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:21,309] [INFO] Task started: Blastn
[2024-01-24 14:31:21,309] [INFO] Running command: blastn -query GCF_014646975.1_ASM1464697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d452aae-21a7-4d60-99e0-8744519b1f3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646975.1_ASM1464697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:22,201] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:22,205] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:22,205] [INFO] Target genome list was writen to GCF_014646975.1_ASM1464697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:22,217] [INFO] Task started: fastANI
[2024-01-24 14:31:22,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf63d438-c1a2-4585-b8a0-28dc190d85db/GCF_014646975.1_ASM1464697v1_genomic.fna.gz --refList GCF_014646975.1_ASM1464697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646975.1_ASM1464697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:35,206] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,216] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:35,217] [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_003858655.1	s__Amphritea balenae	99.9956	1538	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_016592435.1	s__Amphritea japonica	79.731	457	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018067325.1	s__Amphritea sp018067325	79.3992	302	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCA_016744155.1	s__Amphritea sp016744155	79.3092	442	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111095.1	s__Amphritea atlantica	78.9689	409	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223185.1	s__Amphritea sp018223185	78.8526	424	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_016924235.1	s__Amphritea sp016924235	78.7194	408	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_003957515.1	s__Amphritea opalescens	78.6255	338	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017051665.1	s__Amphritea spongicola	78.55	264	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860855.1	s__Amphritea atlantica_A	78.301	356	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	77.4645	85	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	77.3282	104	1547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,218] [INFO] GTDB search result was written to GCF_014646975.1_ASM1464697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:35,219] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:35,222] [INFO] DFAST_QC result json was written to GCF_014646975.1_ASM1464697v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:35,223] [INFO] DFAST_QC completed!
[2024-01-24 14:31:35,223] [INFO] Total running time: 0h1m18s