[2024-01-24 14:39:15,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference
[2024-01-24 14:39:16,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,546] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,547] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea92b8f-647d-4e74-a64d-3249a06cb054/GCF_007991235.1_ASM799123v1_genomic.fna.gz | prodigal -d GCF_007991235.1_ASM799123v1_genomic.fna/cds.fna -a GCF_007991235.1_ASM799123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:24,730] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:24,731] [INFO] Task started: HMMsearch
[2024-01-24 14:39:24,731] [INFO] Running command: hmmsearch --tblout GCF_007991235.1_ASM799123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/reference_markers.hmm GCF_007991235.1_ASM799123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:24,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:24,997] [INFO] Found 6/6 markers.
[2024-01-24 14:39:25,033] [INFO] Query marker FASTA was written to GCF_007991235.1_ASM799123v1_genomic.fna/markers.fasta
[2024-01-24 14:39:25,033] [INFO] Task started: Blastn
[2024-01-24 14:39:25,033] [INFO] Running command: blastn -query GCF_007991235.1_ASM799123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/reference_markers.fasta -out GCF_007991235.1_ASM799123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:25,764] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:25,767] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:25,768] [INFO] Target genome list was writen to GCF_007991235.1_ASM799123v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:25,777] [INFO] Task started: fastANI
[2024-01-24 14:39:25,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea92b8f-647d-4e74-a64d-3249a06cb054/GCF_007991235.1_ASM799123v1_genomic.fna.gz --refList GCF_007991235.1_ASM799123v1_genomic.fna/target_genomes.txt --output GCF_007991235.1_ASM799123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:35,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:35,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:35,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:35,132] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:39:35,132] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:39:35,132] [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
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	100.0	1313	1316	95	inconclusive
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	99.9947	1314	1316	95	inconclusive
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	98.2844	1225	1316	95	inconclusive
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	98.1847	1240	1316	95	inconclusive
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	90.7582	1144	1316	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	81.6856	763	1316	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	81.2006	641	1316	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.4652	66	1316	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.2622	62	1316	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	76.0153	58	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,134] [INFO] DFAST Taxonomy check result was written to GCF_007991235.1_ASM799123v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:35,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:35,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:35,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/checkm_data
[2024-01-24 14:39:35,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:35,183] [INFO] Task started: CheckM
[2024-01-24 14:39:35,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991235.1_ASM799123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991235.1_ASM799123v1_genomic.fna/checkm_input GCF_007991235.1_ASM799123v1_genomic.fna/checkm_result
[2024-01-24 14:40:04,342] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:04,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:04,363] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:04,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:04,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991235.1_ASM799123v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:04,364] [INFO] Task started: Blastn
[2024-01-24 14:40:04,364] [INFO] Running command: blastn -query GCF_007991235.1_ASM799123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23659ee-8601-4f58-a9ee-acbb8cd4d3b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991235.1_ASM799123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:05,522] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:05,525] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:05,525] [INFO] Target genome list was writen to GCF_007991235.1_ASM799123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:05,533] [INFO] Task started: fastANI
[2024-01-24 14:40:05,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea92b8f-647d-4e74-a64d-3249a06cb054/GCF_007991235.1_ASM799123v1_genomic.fna.gz --refList GCF_007991235.1_ASM799123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991235.1_ASM799123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:16,221] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,231] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:16,231] [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_002310835.1	s__Pseudoalteromonas tetraodonis	99.9947	1314	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	conclusive
GCA_018402495.1	s__Pseudoalteromonas sp018402495	92.6027	1023	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238275.3	s__Pseudoalteromonas undina	90.7582	1144	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	90.4004	1095	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	81.9608	722	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_002221505.1	s__Pseudoalteromonas nigrifaciens	81.8758	772	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	98.65	98.00	0.90	0.81	15	-
GCA_000814675.1	s__Pseudoalteromonas distincta	81.682	764	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_000238335.3	s__Pseudoalteromonas marina	81.4379	758	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_000238395.3	s__Pseudoalteromonas arctica	81.4219	768	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	81.2964	766	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905615.1	s__Pseudoalteromonas aliena	81.1458	772	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,233] [INFO] GTDB search result was written to GCF_007991235.1_ASM799123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:16,233] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:16,237] [INFO] DFAST_QC result json was written to GCF_007991235.1_ASM799123v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:16,237] [INFO] DFAST_QC completed!
[2024-01-24 14:40:16,237] [INFO] Total running time: 0h1m1s