[2024-01-24 14:11:46,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,764] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference
[2024-01-24 14:11:47,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,952] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5164720-ce13-45ba-9095-558ed09b4ed7/GCF_024347275.1_ASM2434727v1_genomic.fna.gz | prodigal -d GCF_024347275.1_ASM2434727v1_genomic.fna/cds.fna -a GCF_024347275.1_ASM2434727v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:58,607] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:58,607] [INFO] Task started: HMMsearch
[2024-01-24 14:11:58,608] [INFO] Running command: hmmsearch --tblout GCF_024347275.1_ASM2434727v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/reference_markers.hmm GCF_024347275.1_ASM2434727v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:58,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:58,875] [INFO] Found 6/6 markers.
[2024-01-24 14:11:58,908] [INFO] Query marker FASTA was written to GCF_024347275.1_ASM2434727v1_genomic.fna/markers.fasta
[2024-01-24 14:11:58,908] [INFO] Task started: Blastn
[2024-01-24 14:11:58,908] [INFO] Running command: blastn -query GCF_024347275.1_ASM2434727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/reference_markers.fasta -out GCF_024347275.1_ASM2434727v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:59,556] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:59,559] [INFO] Selected 15 target genomes.
[2024-01-24 14:11:59,560] [INFO] Target genome list was writen to GCF_024347275.1_ASM2434727v1_genomic.fna/target_genomes.txt
[2024-01-24 14:11:59,583] [INFO] Task started: fastANI
[2024-01-24 14:11:59,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5164720-ce13-45ba-9095-558ed09b4ed7/GCF_024347275.1_ASM2434727v1_genomic.fna.gz --refList GCF_024347275.1_ASM2434727v1_genomic.fna/target_genomes.txt --output GCF_024347275.1_ASM2434727v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:11,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:11,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:11,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:11,382] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:12:11,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:11,382] [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 japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	100.0	1287	1292	95	conclusive
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	99.9925	1274	1292	95	conclusive
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	99.988	1252	1292	95	conclusive
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	79.9672	456	1292	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	79.9029	455	1292	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	79.2766	553	1292	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	79.133	538	1292	95	below_threshold
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	77.4839	99	1292	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.1747	84	1292	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	76.894	68	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:11,384] [INFO] DFAST Taxonomy check result was written to GCF_024347275.1_ASM2434727v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:11,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:11,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:11,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/checkm_data
[2024-01-24 14:12:11,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:11,426] [INFO] Task started: CheckM
[2024-01-24 14:12:11,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347275.1_ASM2434727v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347275.1_ASM2434727v1_genomic.fna/checkm_input GCF_024347275.1_ASM2434727v1_genomic.fna/checkm_result
[2024-01-24 14:12:50,522] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:50,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:50,545] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:50,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:50,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347275.1_ASM2434727v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:50,546] [INFO] Task started: Blastn
[2024-01-24 14:12:50,546] [INFO] Running command: blastn -query GCF_024347275.1_ASM2434727v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e1d537-acf9-4510-855d-1892b815d764/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347275.1_ASM2434727v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:51,423] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:51,428] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:51,429] [INFO] Target genome list was writen to GCF_024347275.1_ASM2434727v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:51,440] [INFO] Task started: fastANI
[2024-01-24 14:12:51,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5164720-ce13-45ba-9095-558ed09b4ed7/GCF_024347275.1_ASM2434727v1_genomic.fna.gz --refList GCF_024347275.1_ASM2434727v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347275.1_ASM2434727v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:59,907] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:59,916] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:59,917] [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_016592435.1	s__Amphritea japonica	99.9925	1274	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_016744155.1	s__Amphritea sp016744155	83.5079	970	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	83.3176	658	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_003858655.1	s__Amphritea balenae	79.9439	457	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018223185.1	s__Amphritea sp018223185	79.3665	529	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_900111095.1	s__Amphritea atlantica	79.2762	553	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	79.169	543	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_018860855.1	s__Amphritea atlantica_A	79.0217	392	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597735.1	s__Neptuniibacter pectenicola	77.4839	99	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:59,919] [INFO] GTDB search result was written to GCF_024347275.1_ASM2434727v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:59,920] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:59,924] [INFO] DFAST_QC result json was written to GCF_024347275.1_ASM2434727v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:59,924] [INFO] DFAST_QC completed!
[2024-01-24 14:12:59,924] [INFO] Total running time: 0h1m13s