[2024-01-24 13:28:29,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference
[2024-01-24 13:28:30,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,378] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg038540ec-a5cd-4225-b05d-3c8b876112db/GCF_032464635.1_ASM3246463v1_genomic.fna.gz | prodigal -d GCF_032464635.1_ASM3246463v1_genomic.fna/cds.fna -a GCF_032464635.1_ASM3246463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,013] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,013] [INFO] Running command: hmmsearch --tblout GCF_032464635.1_ASM3246463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/reference_markers.hmm GCF_032464635.1_ASM3246463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,329] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg038540ec-a5cd-4225-b05d-3c8b876112db/GCF_032464635.1_ASM3246463v1_genomic.fna.gz]
[2024-01-24 13:28:41,369] [INFO] Query marker FASTA was written to GCF_032464635.1_ASM3246463v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,370] [INFO] Task started: Blastn
[2024-01-24 13:28:41,370] [INFO] Running command: blastn -query GCF_032464635.1_ASM3246463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/reference_markers.fasta -out GCF_032464635.1_ASM3246463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:41,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:41,997] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:41,997] [INFO] Target genome list was writen to GCF_032464635.1_ASM3246463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,010] [INFO] Task started: fastANI
[2024-01-24 13:28:42,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg038540ec-a5cd-4225-b05d-3c8b876112db/GCF_032464635.1_ASM3246463v1_genomic.fna.gz --refList GCF_032464635.1_ASM3246463v1_genomic.fna/target_genomes.txt --output GCF_032464635.1_ASM3246463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:53,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:53,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:53,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:53,310] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:53,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:53,311] [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
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	79.0058	236	1630	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	78.9986	211	1630	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.9019	436	1630	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	78.4015	271	1630	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	78.3795	214	1630	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.3053	85	1630	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	78.2806	127	1630	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	78.1458	183	1630	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	76.4799	54	1630	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	76.3066	64	1630	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.2262	67	1630	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	76.1	54	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,312] [INFO] DFAST Taxonomy check result was written to GCF_032464635.1_ASM3246463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:53,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:53,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:53,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/checkm_data
[2024-01-24 13:28:53,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:53,370] [INFO] Task started: CheckM
[2024-01-24 13:28:53,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032464635.1_ASM3246463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032464635.1_ASM3246463v1_genomic.fna/checkm_input GCF_032464635.1_ASM3246463v1_genomic.fna/checkm_result
[2024-01-24 13:29:29,328] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:29,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:29,352] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:29,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:29,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032464635.1_ASM3246463v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:29,353] [INFO] Task started: Blastn
[2024-01-24 13:29:29,354] [INFO] Running command: blastn -query GCF_032464635.1_ASM3246463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09da8702-67f8-4791-9895-688b51ce3725/dqc_reference/reference_markers_gtdb.fasta -out GCF_032464635.1_ASM3246463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:30,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:30,317] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:30,317] [INFO] Target genome list was writen to GCF_032464635.1_ASM3246463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:30,338] [INFO] Task started: fastANI
[2024-01-24 13:29:30,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg038540ec-a5cd-4225-b05d-3c8b876112db/GCF_032464635.1_ASM3246463v1_genomic.fna.gz --refList GCF_032464635.1_ASM3246463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032464635.1_ASM3246463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:44,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:44,074] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:44,075] [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_009796765.1	s__Paraglaciecola sp009796765	80.0319	645	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360155.1	s__Paraglaciecola sp004360155	79.0083	235	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	78.9732	213	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	78.9334	147	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	78.7528	255	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	78.4905	247	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314995.1	s__Paraglaciecola arctica	78.4113	270	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	78.2938	179	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	78.2806	127	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	77.9553	65	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993955.1	s__Paraglaciecola sp009993955	77.6321	119	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002836255.1	s__Colwellia sp002836255	76.643	52	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	76.3164	65	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:44,077] [INFO] GTDB search result was written to GCF_032464635.1_ASM3246463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:44,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:44,080] [INFO] DFAST_QC result json was written to GCF_032464635.1_ASM3246463v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:44,081] [INFO] DFAST_QC completed!
[2024-01-24 13:29:44,081] [INFO] Total running time: 0h1m15s