[2024-01-24 12:36:24,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,846] [INFO] DQC Reference Directory: /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference
[2024-01-24 12:36:26,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,162] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,163] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5924815-f92c-472d-8e9e-6e84798ac9c9/GCF_023283645.1_ASM2328364v1_genomic.fna.gz | prodigal -d GCF_023283645.1_ASM2328364v1_genomic.fna/cds.fna -a GCF_023283645.1_ASM2328364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:35,655] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:35,656] [INFO] Task started: HMMsearch
[2024-01-24 12:36:35,656] [INFO] Running command: hmmsearch --tblout GCF_023283645.1_ASM2328364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/reference_markers.hmm GCF_023283645.1_ASM2328364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:35,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:35,923] [INFO] Found 6/6 markers.
[2024-01-24 12:36:35,957] [INFO] Query marker FASTA was written to GCF_023283645.1_ASM2328364v1_genomic.fna/markers.fasta
[2024-01-24 12:36:35,958] [INFO] Task started: Blastn
[2024-01-24 12:36:35,958] [INFO] Running command: blastn -query GCF_023283645.1_ASM2328364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/reference_markers.fasta -out GCF_023283645.1_ASM2328364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:36,730] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:36,734] [INFO] Selected 21 target genomes.
[2024-01-24 12:36:36,735] [INFO] Target genome list was writen to GCF_023283645.1_ASM2328364v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:36,746] [INFO] Task started: fastANI
[2024-01-24 12:36:36,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5924815-f92c-472d-8e9e-6e84798ac9c9/GCF_023283645.1_ASM2328364v1_genomic.fna.gz --refList GCF_023283645.1_ASM2328364v1_genomic.fna/target_genomes.txt --output GCF_023283645.1_ASM2328364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:52,253] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:52,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:52,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:52,269] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:36:52,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:52,269] [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 gelidii	strain=KCTC 42663	GCA_023283645.1	1642821	1642821	type	True	100.0	1281	1285	95	conclusive
Shewanella gelidii	strain=JCM 30804	GCA_014647855.1	1642821	1642821	type	True	99.9921	1279	1285	95	conclusive
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	78.3605	145	1285	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	78.2375	164	1285	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.187	154	1285	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	78.1612	165	1285	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	78.1572	178	1285	95	below_threshold
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	78.1569	166	1285	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	78.1166	197	1285	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	78.1062	162	1285	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	78.0834	171	1285	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	77.9793	183	1285	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	77.975	166	1285	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	77.9693	193	1285	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	77.9539	166	1285	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	77.9532	168	1285	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	77.9428	152	1285	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	77.8066	164	1285	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	77.7793	177	1285	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	77.5496	173	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:52,271] [INFO] DFAST Taxonomy check result was written to GCF_023283645.1_ASM2328364v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:52,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:52,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:52,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/checkm_data
[2024-01-24 12:36:52,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:52,312] [INFO] Task started: CheckM
[2024-01-24 12:36:52,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283645.1_ASM2328364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283645.1_ASM2328364v1_genomic.fna/checkm_input GCF_023283645.1_ASM2328364v1_genomic.fna/checkm_result
[2024-01-24 12:37:25,773] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:25,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:25,801] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:25,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:25,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283645.1_ASM2328364v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:25,803] [INFO] Task started: Blastn
[2024-01-24 12:37:25,803] [INFO] Running command: blastn -query GCF_023283645.1_ASM2328364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge07579ec-9c0a-405f-99e4-576fa439ee28/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283645.1_ASM2328364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:26,923] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:26,928] [INFO] Selected 24 target genomes.
[2024-01-24 12:37:26,928] [INFO] Target genome list was writen to GCF_023283645.1_ASM2328364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:26,949] [INFO] Task started: fastANI
[2024-01-24 12:37:26,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5924815-f92c-472d-8e9e-6e84798ac9c9/GCF_023283645.1_ASM2328364v1_genomic.fna.gz --refList GCF_023283645.1_ASM2328364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283645.1_ASM2328364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:44,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:44,906] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:44,906] [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_014647855.1	s__Shewanella gelidii	99.9921	1279	1285	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_014163735.1	s__Shewanella sp014163735	78.5166	137	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	78.3928	183	1285	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	78.3605	145	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003966225.1	s__Shewanella canadensis	78.3022	157	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406325.1	s__Shewanella putrefaciens	78.2928	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_016757755.1	s__Shewanella sp016757755	78.2371	183	1285	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	78.1851	164	1285	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	78.1666	166	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000018285.1	s__Shewanella pealeana	78.1378	179	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001957125.1	s__Shewanella sp001957125	78.1329	169	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	78.1143	196	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_016765635.1	s__Shewanella schlegeliana	78.0962	162	1285	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	78.0689	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_009663145.1	s__Shewanella sp009663145	78.0653	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	78.0628	172	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_000019525.1	s__Shewanella woodyi	78.0043	164	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_002075795.1	s__Shewanella japonica	77.9673	183	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_014647215.1	s__Shewanella aestuarii	77.9298	155	1285	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	77.9246	175	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	77.8695	161	1285	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	77.8536	126	1285	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	77.7793	177	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_000753795.1	s__Shewanella mangrovi	77.4256	105	1285	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 12:37:44,908] [INFO] GTDB search result was written to GCF_023283645.1_ASM2328364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:44,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:44,915] [INFO] DFAST_QC result json was written to GCF_023283645.1_ASM2328364v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:44,915] [INFO] DFAST_QC completed!
[2024-01-24 12:37:44,915] [INFO] Total running time: 0h1m20s