[2024-01-25 19:04:20,680] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:20,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:20,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference
[2024-01-25 19:04:21,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:21,824] [INFO] Task started: Prodigal
[2024-01-25 19:04:21,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg27ea2773-a57b-431b-b561-41c3b2f2cceb/GCF_000753795.1_ASM75379v1_genomic.fna.gz | prodigal -d GCF_000753795.1_ASM75379v1_genomic.fna/cds.fna -a GCF_000753795.1_ASM75379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:31,760] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:31,761] [INFO] Task started: HMMsearch
[2024-01-25 19:04:31,761] [INFO] Running command: hmmsearch --tblout GCF_000753795.1_ASM75379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/reference_markers.hmm GCF_000753795.1_ASM75379v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:31,995] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:31,997] [INFO] Found 6/6 markers.
[2024-01-25 19:04:32,031] [INFO] Query marker FASTA was written to GCF_000753795.1_ASM75379v1_genomic.fna/markers.fasta
[2024-01-25 19:04:32,031] [INFO] Task started: Blastn
[2024-01-25 19:04:32,031] [INFO] Running command: blastn -query GCF_000753795.1_ASM75379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/reference_markers.fasta -out GCF_000753795.1_ASM75379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:32,761] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:32,764] [INFO] Selected 20 target genomes.
[2024-01-25 19:04:32,765] [INFO] Target genome list was writen to GCF_000753795.1_ASM75379v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:32,777] [INFO] Task started: fastANI
[2024-01-25 19:04:32,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ea2773-a57b-431b-b561-41c3b2f2cceb/GCF_000753795.1_ASM75379v1_genomic.fna.gz --refList GCF_000753795.1_ASM75379v1_genomic.fna/target_genomes.txt --output GCF_000753795.1_ASM75379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:47,149] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:47,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:47,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:47,161] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:47,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:47,162] [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 mangrovi	strain=YQH10	GCA_000753795.1	1515746	1515746	type	True	100.0	1384	1386	95	conclusive
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	82.6712	910	1386	95	below_threshold
Shewanella yunxiaonensis	strain=FJAT-54481	GCA_018223345.1	2829809	2829809	type	True	78.6284	312	1386	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	78.3417	221	1386	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	78.3042	217	1386	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	78.2416	225	1386	95	below_threshold
Shewanella dokdonensis	strain=DSM 23626	GCA_018394335.1	712036	712036	type	True	78.1624	333	1386	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.1245	162	1386	95	below_threshold
Shewanella litorisediminis	strain=SMK1-12	GCA_016834455.1	1173586	1173586	type	True	78.1109	163	1386	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	78.0924	213	1386	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.9189	170	1386	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	77.6215	196	1386	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	77.5846	126	1386	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	77.5007	116	1386	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	77.4341	124	1386	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	77.3782	180	1386	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	77.3024	127	1386	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	76.5764	53	1386	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.4497	50	1386	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	75.3784	60	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:47,163] [INFO] DFAST Taxonomy check result was written to GCF_000753795.1_ASM75379v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:47,164] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:47,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:47,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/checkm_data
[2024-01-25 19:04:47,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:47,205] [INFO] Task started: CheckM
[2024-01-25 19:04:47,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000753795.1_ASM75379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000753795.1_ASM75379v1_genomic.fna/checkm_input GCF_000753795.1_ASM75379v1_genomic.fna/checkm_result
[2024-01-25 19:05:19,209] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:19,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:19,229] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:19,229] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:19,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000753795.1_ASM75379v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:19,229] [INFO] Task started: Blastn
[2024-01-25 19:05:19,229] [INFO] Running command: blastn -query GCF_000753795.1_ASM75379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59e02f06-1445-4e6a-b3c5-c56496873bcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000753795.1_ASM75379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:20,363] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:20,365] [INFO] Selected 19 target genomes.
[2024-01-25 19:05:20,366] [INFO] Target genome list was writen to GCF_000753795.1_ASM75379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:20,388] [INFO] Task started: fastANI
[2024-01-25 19:05:20,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ea2773-a57b-431b-b561-41c3b2f2cceb/GCF_000753795.1_ASM75379v1_genomic.fna.gz --refList GCF_000753795.1_ASM75379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000753795.1_ASM75379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:34,610] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:34,622] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:34,622] [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_000753795.1	s__Shewanella mangrovi	100.0	1384	1386	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_017354945.1	s__Shewanella sp017354945	82.6754	909	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018223345.1	s__Shewanella sp018223345	78.6388	312	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183365.2	s__Shewanella algae	78.344	223	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002836975.1	s__Shewanella indica	78.3017	216	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_018394335.1	s__Shewanella dokdonensis	78.1631	333	1386	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	78.1109	163	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002777975.1	s__Shewanella carassii	78.102	215	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014651955.1	s__Shewanella fodinae	78.0999	309	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.57	97.13	0.90	0.90	3	-
GCF_000485795.1	s__Shewanella decolorationis	78.0709	196	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_000203935.1	s__Shewanella sp000203935	78.0239	227	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_002836945.1	s__Shewanella chilikensis	77.9061	217	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_004358445.1	s__Parashewanella tropica	77.8233	104	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	77.6215	196	1386	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	77.4464	96	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016065.1	s__Shewanella loihica	77.4352	142	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_000614975.1	s__Shewanella marina	77.4124	129	1386	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	77.2914	126	1386	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	77.2534	127	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:34,624] [INFO] GTDB search result was written to GCF_000753795.1_ASM75379v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:34,625] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:34,629] [INFO] DFAST_QC result json was written to GCF_000753795.1_ASM75379v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:34,629] [INFO] DFAST_QC completed!
[2024-01-25 19:05:34,629] [INFO] Total running time: 0h1m14s