[2024-01-25 18:56:05,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference
[2024-01-25 18:56:06,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,829] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,829] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6c89a1c-ac55-4ed9-9e42-cddbfb9594ff/GCF_025971955.1_ASM2597195v1_genomic.fna.gz | prodigal -d GCF_025971955.1_ASM2597195v1_genomic.fna/cds.fna -a GCF_025971955.1_ASM2597195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:14,697] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:14,698] [INFO] Task started: HMMsearch
[2024-01-25 18:56:14,698] [INFO] Running command: hmmsearch --tblout GCF_025971955.1_ASM2597195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/reference_markers.hmm GCF_025971955.1_ASM2597195v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:14,946] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:14,947] [INFO] Found 6/6 markers.
[2024-01-25 18:56:14,979] [INFO] Query marker FASTA was written to GCF_025971955.1_ASM2597195v1_genomic.fna/markers.fasta
[2024-01-25 18:56:14,979] [INFO] Task started: Blastn
[2024-01-25 18:56:14,979] [INFO] Running command: blastn -query GCF_025971955.1_ASM2597195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/reference_markers.fasta -out GCF_025971955.1_ASM2597195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:15,673] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:15,675] [INFO] Selected 17 target genomes.
[2024-01-25 18:56:15,676] [INFO] Target genome list was writen to GCF_025971955.1_ASM2597195v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:15,692] [INFO] Task started: fastANI
[2024-01-25 18:56:15,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c89a1c-ac55-4ed9-9e42-cddbfb9594ff/GCF_025971955.1_ASM2597195v1_genomic.fna.gz --refList GCF_025971955.1_ASM2597195v1_genomic.fna/target_genomes.txt --output GCF_025971955.1_ASM2597195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:28,798] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:28,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:28,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:28,809] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:28,809] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:28,809] [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
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	88.3797	1115	1347	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	88.3406	1118	1347	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	81.4856	815	1347	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.6434	466	1347	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	79.6405	471	1347	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	79.5877	471	1347	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	79.538	484	1347	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	79.505	465	1347	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	79.4876	474	1347	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	79.4723	463	1347	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	79.4513	489	1347	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	79.4446	473	1347	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	79.3437	464	1347	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	79.0414	445	1347	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	78.9959	438	1347	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	78.2299	272	1347	95	below_threshold
Parashewanella spongiae	strain=KCTC 22492	GCA_023283745.1	342950	342950	type	True	77.7887	143	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:28,811] [INFO] DFAST Taxonomy check result was written to GCF_025971955.1_ASM2597195v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:28,811] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:28,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:28,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/checkm_data
[2024-01-25 18:56:28,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:28,868] [INFO] Task started: CheckM
[2024-01-25 18:56:28,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025971955.1_ASM2597195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025971955.1_ASM2597195v1_genomic.fna/checkm_input GCF_025971955.1_ASM2597195v1_genomic.fna/checkm_result
[2024-01-25 18:56:56,191] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:56,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:56,213] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:56,213] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:56,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025971955.1_ASM2597195v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:56,213] [INFO] Task started: Blastn
[2024-01-25 18:56:56,214] [INFO] Running command: blastn -query GCF_025971955.1_ASM2597195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc835ed34-9d3b-499f-a043-72a9df02a578/dqc_reference/reference_markers_gtdb.fasta -out GCF_025971955.1_ASM2597195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:57,268] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:57,272] [INFO] Selected 18 target genomes.
[2024-01-25 18:56:57,272] [INFO] Target genome list was writen to GCF_025971955.1_ASM2597195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:57,291] [INFO] Task started: fastANI
[2024-01-25 18:56:57,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c89a1c-ac55-4ed9-9e42-cddbfb9594ff/GCF_025971955.1_ASM2597195v1_genomic.fna.gz --refList GCF_025971955.1_ASM2597195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025971955.1_ASM2597195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:12,460] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:12,471] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:57:12,472] [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_014647215.1	s__Shewanella aestuarii	88.3797	1115	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	81.0373	670	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	79.6402	472	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	79.4832	467	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	79.4723	463	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_009828585.1	s__Shewanella litoralis	79.4366	491	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648035.1	s__Shewanella algicola	79.4093	479	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	79.4011	462	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	79.3854	475	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_010092445.1	s__Shewanella sp002836315	79.2432	476	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_006385555.1	s__Shewanella polaris	79.14	474	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_003855155.1	s__Shewanella sp002836275	79.0373	445	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_002873135.1	s__Shewanella sp002873135	78.8468	378	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
GCF_001957135.1	s__Shewanella sp001957135	78.7865	381	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014163735.1	s__Shewanella sp014163735	78.7224	301	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.5207	328	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000518705.1	s__Shewanella colwelliana	78.1384	210	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_004358345.1	s__Parashewanella spongiae	77.8469	148	1347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:12,474] [INFO] GTDB search result was written to GCF_025971955.1_ASM2597195v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:12,475] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:12,478] [INFO] DFAST_QC result json was written to GCF_025971955.1_ASM2597195v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:12,478] [INFO] DFAST_QC completed!
[2024-01-25 18:57:12,478] [INFO] Total running time: 0h1m7s