[2024-01-24 14:39:02,747] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:02,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:02,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference
[2024-01-24 14:39:04,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,248] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb59779e-4346-44c1-8c28-a0574a641191/GCF_004358445.1_ASM435844v1_genomic.fna.gz | prodigal -d GCF_004358445.1_ASM435844v1_genomic.fna/cds.fna -a GCF_004358445.1_ASM435844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:13,326] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:13,326] [INFO] Task started: HMMsearch
[2024-01-24 14:39:13,326] [INFO] Running command: hmmsearch --tblout GCF_004358445.1_ASM435844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/reference_markers.hmm GCF_004358445.1_ASM435844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:13,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:13,619] [INFO] Found 6/6 markers.
[2024-01-24 14:39:13,657] [INFO] Query marker FASTA was written to GCF_004358445.1_ASM435844v1_genomic.fna/markers.fasta
[2024-01-24 14:39:13,658] [INFO] Task started: Blastn
[2024-01-24 14:39:13,658] [INFO] Running command: blastn -query GCF_004358445.1_ASM435844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/reference_markers.fasta -out GCF_004358445.1_ASM435844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:14,537] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:14,541] [INFO] Selected 22 target genomes.
[2024-01-24 14:39:14,542] [INFO] Target genome list was writen to GCF_004358445.1_ASM435844v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:14,562] [INFO] Task started: fastANI
[2024-01-24 14:39:14,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb59779e-4346-44c1-8c28-a0574a641191/GCF_004358445.1_ASM435844v1_genomic.fna.gz --refList GCF_004358445.1_ASM435844v1_genomic.fna/target_genomes.txt --output GCF_004358445.1_ASM435844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:33,280] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:33,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:33,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:33,298] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:33,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:33,299] [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
Parashewanella tropica	strain=MEBiC05444	GCA_004358445.1	2547970	2547970	type	True	100.0	1405	1407	95	conclusive
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	83.7447	866	1407	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	79.5165	145	1407	95	below_threshold
Shewanella maritima	strain=D4-2	GCA_004295345.1	2520507	2520507	type	True	79.4012	173	1407	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.1392	70	1407	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	78.9192	71	1407	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	78.8461	58	1407	95	below_threshold
Parashewanella spongiae	strain=HJ039	GCA_004358345.1	342950	342950	type	True	78.7595	245	1407	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	78.6761	69	1407	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	78.6675	73	1407	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	78.5238	147	1407	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	78.4903	283	1407	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	78.2751	123	1407	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	78.2501	130	1407	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	78.1766	151	1407	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	78.0667	152	1407	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	77.9511	129	1407	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	77.9496	151	1407	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	77.8873	152	1407	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	77.8517	152	1407	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	77.7689	148	1407	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	77.6466	163	1407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:33,302] [INFO] DFAST Taxonomy check result was written to GCF_004358445.1_ASM435844v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:33,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:33,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:33,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/checkm_data
[2024-01-24 14:39:33,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:33,352] [INFO] Task started: CheckM
[2024-01-24 14:39:33,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358445.1_ASM435844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358445.1_ASM435844v1_genomic.fna/checkm_input GCF_004358445.1_ASM435844v1_genomic.fna/checkm_result
[2024-01-24 14:40:05,753] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:05,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:05,771] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:05,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:05,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358445.1_ASM435844v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:05,772] [INFO] Task started: Blastn
[2024-01-24 14:40:05,772] [INFO] Running command: blastn -query GCF_004358445.1_ASM435844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852985f0-0a88-46cf-b758-2a892b714668/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358445.1_ASM435844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:06,973] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:06,976] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:06,976] [INFO] Target genome list was writen to GCF_004358445.1_ASM435844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:07,006] [INFO] Task started: fastANI
[2024-01-24 14:40:07,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb59779e-4346-44c1-8c28-a0574a641191/GCF_004358445.1_ASM435844v1_genomic.fna.gz --refList GCF_004358445.1_ASM435844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358445.1_ASM435844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:22,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:22,777] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:22,778] [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_004358445.1	s__Parashewanella tropica	100.0	1405	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003675895.1	s__Parashewanella curva	83.7472	867	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216875.1	s__Shewanella bicestrii	79.7924	156	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_000018285.1	s__Shewanella pealeana	79.4672	147	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295345.1	s__Shewanella maritima	79.3106	171	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.24	98.24	0.95	0.95	2	-
GCF_002838165.1	s__Shewanella sp002838165	78.9724	154	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_004358345.1	s__Parashewanella spongiae	78.6864	248	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900456975.1	s__Shewanella baltica	78.6785	157	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_004168585.1	s__Parashewanella sp004168585	78.5811	277	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900895.1	s__Parashewanella sp016900895	78.4948	284	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	78.4588	154	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_002873615.1	s__Shewanella sp002873615	78.3189	150	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647135.1	s__Shewanella xiamenensis	78.1477	148	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_009663145.1	s__Shewanella sp009663145	78.0625	151	1407	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	77.9619	130	1407	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	77.9476	129	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_002873135.1	s__Shewanella sp002873135	77.9063	144	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
GCF_000518605.1	s__Shewanella fidelis	77.9022	149	1407	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	77.8548	155	1407	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 14:40:22,783] [INFO] GTDB search result was written to GCF_004358445.1_ASM435844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:22,783] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:22,788] [INFO] DFAST_QC result json was written to GCF_004358445.1_ASM435844v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:22,788] [INFO] DFAST_QC completed!
[2024-01-24 14:40:22,788] [INFO] Total running time: 0h1m20s