[2024-01-24 13:24:12,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference
[2024-01-24 13:24:13,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,410] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg70641573-8aab-45d2-9b1c-9a5f30f877a1/GCF_017051665.1_ASM1705166v1_genomic.fna.gz | prodigal -d GCF_017051665.1_ASM1705166v1_genomic.fna/cds.fna -a GCF_017051665.1_ASM1705166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:25,464] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:25,464] [INFO] Task started: HMMsearch
[2024-01-24 13:24:25,465] [INFO] Running command: hmmsearch --tblout GCF_017051665.1_ASM1705166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/reference_markers.hmm GCF_017051665.1_ASM1705166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:25,690] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:25,691] [INFO] Found 6/6 markers.
[2024-01-24 13:24:25,731] [INFO] Query marker FASTA was written to GCF_017051665.1_ASM1705166v1_genomic.fna/markers.fasta
[2024-01-24 13:24:25,731] [INFO] Task started: Blastn
[2024-01-24 13:24:25,731] [INFO] Running command: blastn -query GCF_017051665.1_ASM1705166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/reference_markers.fasta -out GCF_017051665.1_ASM1705166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:26,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:26,362] [INFO] Selected 19 target genomes.
[2024-01-24 13:24:26,362] [INFO] Target genome list was writen to GCF_017051665.1_ASM1705166v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:26,378] [INFO] Task started: fastANI
[2024-01-24 13:24:26,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg70641573-8aab-45d2-9b1c-9a5f30f877a1/GCF_017051665.1_ASM1705166v1_genomic.fna.gz --refList GCF_017051665.1_ASM1705166v1_genomic.fna/target_genomes.txt --output GCF_017051665.1_ASM1705166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:39,264] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:39,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:39,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:39,274] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:39,274] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:39,274] [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 spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	100.0	1628	1628	95	conclusive
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	81.9875	1081	1628	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	78.7693	260	1628	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	78.6946	257	1628	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	78.469	164	1628	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	78.441	194	1628	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	78.3802	195	1628	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	78.3098	236	1628	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	78.2799	225	1628	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	76.6932	91	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:39,276] [INFO] DFAST Taxonomy check result was written to GCF_017051665.1_ASM1705166v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:39,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:39,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:39,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/checkm_data
[2024-01-24 13:24:39,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:39,322] [INFO] Task started: CheckM
[2024-01-24 13:24:39,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017051665.1_ASM1705166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017051665.1_ASM1705166v1_genomic.fna/checkm_input GCF_017051665.1_ASM1705166v1_genomic.fna/checkm_result
[2024-01-24 13:25:17,681] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:17,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:17,700] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:17,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:17,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017051665.1_ASM1705166v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:17,701] [INFO] Task started: Blastn
[2024-01-24 13:25:17,701] [INFO] Running command: blastn -query GCF_017051665.1_ASM1705166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b0c079e-9b4c-4553-ad79-992277afa41e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017051665.1_ASM1705166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:18,670] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:18,673] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:18,673] [INFO] Target genome list was writen to GCF_017051665.1_ASM1705166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:18,703] [INFO] Task started: fastANI
[2024-01-24 13:25:18,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg70641573-8aab-45d2-9b1c-9a5f30f877a1/GCF_017051665.1_ASM1705166v1_genomic.fna.gz --refList GCF_017051665.1_ASM1705166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017051665.1_ASM1705166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:32,601] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:32,612] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:32,612] [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_017051665.1	s__Amphritea spongicola	100.0	1628	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003858655.1	s__Amphritea balenae	78.7692	260	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003957515.1	s__Amphritea opalescens	78.469	164	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592435.1	s__Amphritea japonica	78.4243	195	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018860855.1	s__Amphritea atlantica_A	78.3699	177	1628	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	78.3632	141	1628	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	78.3248	186	1628	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	78.3154	231	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_900111095.1	s__Amphritea atlantica	78.2834	225	1628	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	78.1736	233	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000691225.1	s__Nitrincola lacisaponensis	76.7275	92	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053805.1	s__Pseudomonas_E sp003053805	76.151	61	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.38	98.38	0.96	0.96	2	-
GCF_009903625.1	s__Microbulbifer sp009903625	75.6782	62	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:32,614] [INFO] GTDB search result was written to GCF_017051665.1_ASM1705166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:32,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:32,619] [INFO] DFAST_QC result json was written to GCF_017051665.1_ASM1705166v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:32,619] [INFO] DFAST_QC completed!
[2024-01-24 13:25:32,619] [INFO] Total running time: 0h1m20s