[2024-01-24 12:31:21,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference
[2024-01-24 12:31:22,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,575] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg14eb125a-67f4-491f-8f15-5362079389c0/GCF_000614975.1_ASM61497v1_genomic.fna.gz | prodigal -d GCF_000614975.1_ASM61497v1_genomic.fna/cds.fna -a GCF_000614975.1_ASM61497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:31,491] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:31,491] [INFO] Task started: HMMsearch
[2024-01-24 12:31:31,491] [INFO] Running command: hmmsearch --tblout GCF_000614975.1_ASM61497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/reference_markers.hmm GCF_000614975.1_ASM61497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:31,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:31,771] [INFO] Found 6/6 markers.
[2024-01-24 12:31:31,806] [INFO] Query marker FASTA was written to GCF_000614975.1_ASM61497v1_genomic.fna/markers.fasta
[2024-01-24 12:31:31,806] [INFO] Task started: Blastn
[2024-01-24 12:31:31,807] [INFO] Running command: blastn -query GCF_000614975.1_ASM61497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/reference_markers.fasta -out GCF_000614975.1_ASM61497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:32,548] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:32,552] [INFO] Selected 27 target genomes.
[2024-01-24 12:31:32,553] [INFO] Target genome list was writen to GCF_000614975.1_ASM61497v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:32,570] [INFO] Task started: fastANI
[2024-01-24 12:31:32,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg14eb125a-67f4-491f-8f15-5362079389c0/GCF_000614975.1_ASM61497v1_genomic.fna.gz --refList GCF_000614975.1_ASM61497v1_genomic.fna/target_genomes.txt --output GCF_000614975.1_ASM61497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:51,901] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:51,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:51,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:51,921] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:51,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:51,922] [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 marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	100.0	1432	1440	95	conclusive
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	78.8377	115	1440	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	78.5126	188	1440	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	78.4738	171	1440	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	78.4331	179	1440	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	78.4076	176	1440	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.3493	191	1440	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	78.2856	253	1440	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	78.2802	256	1440	95	below_threshold
Shewanella woodyi	strain=ATCC 51908	GCA_000019525.1	60961	60961	type	True	78.1983	192	1440	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	78.1824	188	1440	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	78.1123	176	1440	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	78.0895	189	1440	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	78.0704	206	1440	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.0162	193	1440	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.0007	196	1440	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	77.9739	194	1440	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	77.9588	261	1440	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_019655175.1	614070	614070	type	True	77.9543	176	1440	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	77.897	205	1440	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	77.8679	216	1440	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	77.8613	177	1440	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	77.8489	212	1440	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	77.8343	186	1440	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	77.6958	194	1440	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	77.6325	211	1440	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.4342	50	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,923] [INFO] DFAST Taxonomy check result was written to GCF_000614975.1_ASM61497v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:51,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:51,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:51,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/checkm_data
[2024-01-24 12:31:51,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:51,967] [INFO] Task started: CheckM
[2024-01-24 12:31:51,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000614975.1_ASM61497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000614975.1_ASM61497v1_genomic.fna/checkm_input GCF_000614975.1_ASM61497v1_genomic.fna/checkm_result
[2024-01-24 12:32:22,423] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:22,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:22,442] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:22,443] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:22,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000614975.1_ASM61497v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:22,443] [INFO] Task started: Blastn
[2024-01-24 12:32:22,443] [INFO] Running command: blastn -query GCF_000614975.1_ASM61497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4f847d3-2bb6-454a-9c39-78c8fe6fec32/dqc_reference/reference_markers_gtdb.fasta -out GCF_000614975.1_ASM61497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:23,456] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:23,461] [INFO] Selected 23 target genomes.
[2024-01-24 12:32:23,462] [INFO] Target genome list was writen to GCF_000614975.1_ASM61497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:23,476] [INFO] Task started: fastANI
[2024-01-24 12:32:23,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg14eb125a-67f4-491f-8f15-5362079389c0/GCF_000614975.1_ASM61497v1_genomic.fna.gz --refList GCF_000614975.1_ASM61497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000614975.1_ASM61497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:39,967] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:39,985] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:39,986] [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_000614975.1	s__Shewanella marina	100.0	1432	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000016065.1	s__Shewanella loihica	78.8011	116	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_016765635.1	s__Shewanella schlegeliana	78.5279	209	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	78.5268	211	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	78.4494	191	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_000203935.1	s__Shewanella sp000203935	78.4108	175	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_003797125.1	s__Shewanella frigidimarina	78.4069	200	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014164505.1	s__Shewanella sp014164505	78.386	160	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831655.1	s__Shewanella insulae	78.3533	119	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146165.2	s__Shewanella oneidensis	78.3427	179	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011765625.1	s__Shewanella aestuarii_A	78.298	197	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019525.1	s__Shewanella woodyi	78.1787	193	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_002838165.1	s__Shewanella sp002838165	78.1575	207	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_014648035.1	s__Shewanella algicola	78.12	206	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014647135.1	s__Shewanella xiamenensis	78.1123	176	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_006385555.1	s__Shewanella polaris	78.0562	208	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_900156405.1	s__Shewanella morhuae	77.9739	194	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000518605.1	s__Shewanella fidelis	77.9451	262	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_014641855.1	s__Shewanella inventionis	77.9311	203	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	77.883	215	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003605125.1	s__Shewanella algidipiscicola	77.8627	177	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_018221465.1	s__Shewanella intestini	77.807	210	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009663145.1	s__Shewanella sp009663145	77.7917	204	1440	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 12:32:39,987] [INFO] GTDB search result was written to GCF_000614975.1_ASM61497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:39,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:39,992] [INFO] DFAST_QC result json was written to GCF_000614975.1_ASM61497v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:39,993] [INFO] DFAST_QC completed!
[2024-01-24 12:32:39,993] [INFO] Total running time: 0h1m19s