[2024-01-24 12:05:58,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,947] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference
[2024-01-24 12:06:00,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,331] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,331] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdbd07d5-6f93-4e96-8bf3-16e8d2963043/GCF_023284005.1_ASM2328400v1_genomic.fna.gz | prodigal -d GCF_023284005.1_ASM2328400v1_genomic.fna/cds.fna -a GCF_023284005.1_ASM2328400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:12,621] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:12,621] [INFO] Task started: HMMsearch
[2024-01-24 12:06:12,621] [INFO] Running command: hmmsearch --tblout GCF_023284005.1_ASM2328400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/reference_markers.hmm GCF_023284005.1_ASM2328400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:13,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:13,032] [INFO] Found 6/6 markers.
[2024-01-24 12:06:13,080] [INFO] Query marker FASTA was written to GCF_023284005.1_ASM2328400v1_genomic.fna/markers.fasta
[2024-01-24 12:06:13,081] [INFO] Task started: Blastn
[2024-01-24 12:06:13,081] [INFO] Running command: blastn -query GCF_023284005.1_ASM2328400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/reference_markers.fasta -out GCF_023284005.1_ASM2328400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:13,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:13,955] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:13,956] [INFO] Target genome list was writen to GCF_023284005.1_ASM2328400v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:13,970] [INFO] Task started: fastANI
[2024-01-24 12:06:13,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdbd07d5-6f93-4e96-8bf3-16e8d2963043/GCF_023284005.1_ASM2328400v1_genomic.fna.gz --refList GCF_023284005.1_ASM2328400v1_genomic.fna/target_genomes.txt --output GCF_023284005.1_ASM2328400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,045] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,069] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:35,069] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,070] [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 surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	100.0	1823	1840	95	conclusive
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	78.8228	157	1840	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	78.5766	182	1840	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	78.5102	178	1840	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	78.4812	183	1840	95	below_threshold
Shewanella piezotolerans	strain=WP3	GCA_000014885.1	404011	404011	type	True	78.4384	192	1840	95	below_threshold
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	78.4369	182	1840	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	78.4082	186	1840	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	78.338	183	1840	95	below_threshold
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	78.3331	186	1840	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	78.1929	193	1840	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	78.1887	191	1840	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	77.9577	159	1840	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	77.9482	156	1840	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	77.8613	156	1840	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	77.7291	174	1840	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	77.6419	158	1840	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	77.6371	169	1840	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	77.6366	151	1840	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	77.632	168	1840	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	77.5815	160	1840	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	77.5735	171	1840	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	77.4934	133	1840	95	below_threshold
Shewanella marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	77.3629	149	1840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,072] [INFO] DFAST Taxonomy check result was written to GCF_023284005.1_ASM2328400v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/checkm_data
[2024-01-24 12:06:35,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,147] [INFO] Task started: CheckM
[2024-01-24 12:06:35,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023284005.1_ASM2328400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023284005.1_ASM2328400v1_genomic.fna/checkm_input GCF_023284005.1_ASM2328400v1_genomic.fna/checkm_result
[2024-01-24 12:07:15,648] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:15,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,672] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:15,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:15,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023284005.1_ASM2328400v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:15,674] [INFO] Task started: Blastn
[2024-01-24 12:07:15,674] [INFO] Running command: blastn -query GCF_023284005.1_ASM2328400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7035bae-0198-4e3a-bf20-930593fc910f/dqc_reference/reference_markers_gtdb.fasta -out GCF_023284005.1_ASM2328400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,793] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,797] [INFO] Selected 29 target genomes.
[2024-01-24 12:07:16,797] [INFO] Target genome list was writen to GCF_023284005.1_ASM2328400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:16,819] [INFO] Task started: fastANI
[2024-01-24 12:07:16,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdbd07d5-6f93-4e96-8bf3-16e8d2963043/GCF_023284005.1_ASM2328400v1_genomic.fna.gz --refList GCF_023284005.1_ASM2328400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023284005.1_ASM2328400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:38,775] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:38,802] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:07:38,802] [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_003966265.1	s__Shewanella atlantica	78.7681	159	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	78.5772	193	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	78.5732	183	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605125.1	s__Shewanella algidipiscicola	78.4756	178	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_000014885.1	s__Shewanella piezotolerans	78.4589	192	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005305.1	s__Shewanella psychrophila	78.4216	180	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	78.3486	197	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_000018285.1	s__Shewanella pealeana	78.345	178	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518705.1	s__Shewanella colwelliana	78.3216	186	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_007197645.1	s__Shewanella hanedai	78.3153	192	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007004545.2	s__Shewanella sp007004545	78.2996	185	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000518605.1	s__Shewanella fidelis	78.0864	201	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_900456975.1	s__Shewanella baltica	77.9409	157	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_000172075.1	s__Shewanella benthica_A	77.8667	157	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCF_002873135.1	s__Shewanella sp002873135	77.8412	158	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
GCF_003797125.1	s__Shewanella frigidimarina	77.7847	157	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_001957135.1	s__Shewanella sp001957135	77.7574	170	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	77.7239	175	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_010092445.1	s__Shewanella sp002836315	77.6931	165	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_009663145.1	s__Shewanella sp009663145	77.6857	158	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217915.1	s__Shewanella sp000217915	77.6483	138	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647215.1	s__Shewanella aestuarii	77.638	152	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	77.6217	170	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_014648315.1	s__Shewanella ulleungensis	77.5843	171	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	77.5678	160	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCA_002783505.1	s__Shewanella sp002783505	77.3656	159	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614975.1	s__Shewanella marina	77.3629	149	1840	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	77.3424	157	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494715.1	s__Shewanella sp006494715	77.2386	137	1840	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:38,805] [INFO] GTDB search result was written to GCF_023284005.1_ASM2328400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:38,806] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:38,813] [INFO] DFAST_QC result json was written to GCF_023284005.1_ASM2328400v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:38,813] [INFO] DFAST_QC completed!
[2024-01-24 12:07:38,813] [INFO] Total running time: 0h1m40s