[2024-01-25 18:40:50,721] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:50,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:50,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference
[2024-01-25 18:40:51,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:51,866] [INFO] Task started: Prodigal
[2024-01-25 18:40:51,866] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf8ccaad-f8c9-4560-be83-dfece38d8892/GCF_002282855.1_ASM228285v1_genomic.fna.gz | prodigal -d GCF_002282855.1_ASM228285v1_genomic.fna/cds.fna -a GCF_002282855.1_ASM228285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:01,245] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:01,246] [INFO] Task started: HMMsearch
[2024-01-25 18:41:01,246] [INFO] Running command: hmmsearch --tblout GCF_002282855.1_ASM228285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/reference_markers.hmm GCF_002282855.1_ASM228285v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:01,466] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:01,468] [INFO] Found 6/6 markers.
[2024-01-25 18:41:01,498] [INFO] Query marker FASTA was written to GCF_002282855.1_ASM228285v1_genomic.fna/markers.fasta
[2024-01-25 18:41:01,499] [INFO] Task started: Blastn
[2024-01-25 18:41:01,499] [INFO] Running command: blastn -query GCF_002282855.1_ASM228285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/reference_markers.fasta -out GCF_002282855.1_ASM228285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:02,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:02,255] [INFO] Selected 26 target genomes.
[2024-01-25 18:41:02,256] [INFO] Target genome list was writen to GCF_002282855.1_ASM228285v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:02,263] [INFO] Task started: fastANI
[2024-01-25 18:41:02,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf8ccaad-f8c9-4560-be83-dfece38d8892/GCF_002282855.1_ASM228285v1_genomic.fna.gz --refList GCF_002282855.1_ASM228285v1_genomic.fna/target_genomes.txt --output GCF_002282855.1_ASM228285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:23,365] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:23,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:23,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:23,378] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:23,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:23,378] [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
Paraferrimonas sedimenticola	strain=NBRC 101628	GCA_002282855.1	375674	375674	type	True	100.0	1255	1257	95	conclusive
Paraferrimonas haliotis	strain=AFRC7-2-1	GCA_002282895.1	2013866	2013866	type	True	78.5277	214	1257	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	77.3595	77	1257	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.2957	91	1257	95	below_threshold
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	77.2699	89	1257	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	77.2278	81	1257	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	77.192	94	1257	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	77.0681	95	1257	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	77.0634	97	1257	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	77.0235	100	1257	95	below_threshold
Shewanella litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	77.0148	101	1257	95	below_threshold
Ferrimonas aestuarii	strain=IMCC35002	GCA_005116665.1	2569539	2569539	type	True	76.8816	102	1257	95	below_threshold
Ferrimonas lipolytica	strain=S7	GCA_012295575.1	2724191	2724191	type	True	76.8373	72	1257	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	76.7748	51	1257	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	76.7709	74	1257	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	76.6821	128	1257	95	below_threshold
Ferrimonas balearica	strain=DSM 9799	GCA_000148645.1	44012	44012	type	True	76.5515	95	1257	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	76.3258	74	1257	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	76.0933	53	1257	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	76.0819	56	1257	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	76.0141	53	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:23,381] [INFO] DFAST Taxonomy check result was written to GCF_002282855.1_ASM228285v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:23,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:23,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:23,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/checkm_data
[2024-01-25 18:41:23,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:23,421] [INFO] Task started: CheckM
[2024-01-25 18:41:23,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002282855.1_ASM228285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002282855.1_ASM228285v1_genomic.fna/checkm_input GCF_002282855.1_ASM228285v1_genomic.fna/checkm_result
[2024-01-25 18:41:54,279] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:54,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:54,295] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:54,295] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:54,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002282855.1_ASM228285v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:54,296] [INFO] Task started: Blastn
[2024-01-25 18:41:54,296] [INFO] Running command: blastn -query GCF_002282855.1_ASM228285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7692e720-197b-4f23-9c48-c865cfbb4238/dqc_reference/reference_markers_gtdb.fasta -out GCF_002282855.1_ASM228285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:55,488] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:55,491] [INFO] Selected 25 target genomes.
[2024-01-25 18:41:55,491] [INFO] Target genome list was writen to GCF_002282855.1_ASM228285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:55,501] [INFO] Task started: fastANI
[2024-01-25 18:41:55,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf8ccaad-f8c9-4560-be83-dfece38d8892/GCF_002282855.1_ASM228285v1_genomic.fna.gz --refList GCF_002282855.1_ASM228285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002282855.1_ASM228285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:13,743] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:13,755] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:13,755] [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_002282855.1	s__Paraferrimonas sedimenticola	100.0	1255	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002282895.1	s__Paraferrimonas haliotis	78.5277	214	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	99.27	99.27	0.96	0.96	2	-
GCF_010993985.1	s__SM1919 sp010993985	77.8253	69	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__SM1919	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002777975.1	s__Shewanella carassii	77.3525	78	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000016065.1	s__Shewanella loihica	77.2309	96	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_003353085.1	s__Shewanella corallii	77.1385	98	1257	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	77.0609	98	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832025.1	s__Shewanella sp000832025	77.0578	88	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834455.1	s__Shewanella litorisediminis	77.0148	101	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966515.1	s__Shewanella sp002966515	76.954	77	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_005116665.1	s__Ferrimonas sp005116665	76.8796	101	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295575.1	s__Ferrimonas lipolytica	76.8373	72	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957745.1	s__Shewanella khirikhana	76.6821	128	1257	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	76.661	83	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_000148645.1	s__Ferrimonas balearica	76.5728	94	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	76.4094	84	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	76.3223	74	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_000176175.1	s__Vibrio furnissii	76.0933	53	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_002242685.1	s__Oceanimonas doudoroffii	75.5413	52	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:13,758] [INFO] GTDB search result was written to GCF_002282855.1_ASM228285v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:13,760] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:13,763] [INFO] DFAST_QC result json was written to GCF_002282855.1_ASM228285v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:13,763] [INFO] DFAST_QC completed!
[2024-01-25 18:42:13,763] [INFO] Total running time: 0h1m23s