[2024-01-24 12:29:37,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:37,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:37,121] [INFO] DQC Reference Directory: /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference
[2024-01-24 12:29:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:38,465] [INFO] Task started: Prodigal
[2024-01-24 12:29:38,467] [INFO] Running command: gunzip -c /var/lib/cwl/stgd00e45dc-d31e-4dd2-a868-e21717566f40/GCF_019655175.1_ASM1965517v1_genomic.fna.gz | prodigal -d GCF_019655175.1_ASM1965517v1_genomic.fna/cds.fna -a GCF_019655175.1_ASM1965517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:48,131] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:48,132] [INFO] Task started: HMMsearch
[2024-01-24 12:29:48,132] [INFO] Running command: hmmsearch --tblout GCF_019655175.1_ASM1965517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/reference_markers.hmm GCF_019655175.1_ASM1965517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:48,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:48,432] [INFO] Found 6/6 markers.
[2024-01-24 12:29:48,469] [INFO] Query marker FASTA was written to GCF_019655175.1_ASM1965517v1_genomic.fna/markers.fasta
[2024-01-24 12:29:48,469] [INFO] Task started: Blastn
[2024-01-24 12:29:48,469] [INFO] Running command: blastn -query GCF_019655175.1_ASM1965517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/reference_markers.fasta -out GCF_019655175.1_ASM1965517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:49,257] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:49,261] [INFO] Selected 16 target genomes.
[2024-01-24 12:29:49,262] [INFO] Target genome list was writen to GCF_019655175.1_ASM1965517v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:49,271] [INFO] Task started: fastANI
[2024-01-24 12:29:49,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00e45dc-d31e-4dd2-a868-e21717566f40/GCF_019655175.1_ASM1965517v1_genomic.fna.gz --refList GCF_019655175.1_ASM1965517v1_genomic.fna/target_genomes.txt --output GCF_019655175.1_ASM1965517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:03,263] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:03,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:03,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:03,279] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:03,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:03,280] [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 algidipiscicola	strain=LMG 23746	GCA_019655175.1	614070	614070	type	True	100.0	1334	1340	95	conclusive
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	99.9915	1327	1340	95	conclusive
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	80.3206	578	1340	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	79.7976	509	1340	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	79.7014	455	1340	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	79.54	464	1340	95	below_threshold
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	79.3368	486	1340	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	78.7635	286	1340	95	below_threshold
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	78.6787	321	1340	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	78.5485	295	1340	95	below_threshold
Shewanella hanedai	strain=JCM 20706	GCA_007197645.1	25	25	type	True	78.4421	304	1340	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	78.4409	330	1340	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	78.3084	276	1340	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.0383	197	1340	95	below_threshold
Shewanella marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	78.0043	162	1340	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	77.8124	228	1340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:03,281] [INFO] DFAST Taxonomy check result was written to GCF_019655175.1_ASM1965517v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:03,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:03,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:03,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/checkm_data
[2024-01-24 12:30:03,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:03,334] [INFO] Task started: CheckM
[2024-01-24 12:30:03,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019655175.1_ASM1965517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019655175.1_ASM1965517v1_genomic.fna/checkm_input GCF_019655175.1_ASM1965517v1_genomic.fna/checkm_result
[2024-01-24 12:30:37,129] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:37,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:37,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:37,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019655175.1_ASM1965517v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:37,155] [INFO] Task started: Blastn
[2024-01-24 12:30:37,155] [INFO] Running command: blastn -query GCF_019655175.1_ASM1965517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga65532c1-28c9-41b9-8a4e-57a49c08ec5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019655175.1_ASM1965517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:38,325] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:38,330] [INFO] Selected 15 target genomes.
[2024-01-24 12:30:38,330] [INFO] Target genome list was writen to GCF_019655175.1_ASM1965517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:38,342] [INFO] Task started: fastANI
[2024-01-24 12:30:38,342] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00e45dc-d31e-4dd2-a868-e21717566f40/GCF_019655175.1_ASM1965517v1_genomic.fna.gz --refList GCF_019655175.1_ASM1965517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019655175.1_ASM1965517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:51,500] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:51,513] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:51,513] [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_003605125.1	s__Shewanella algidipiscicola	99.9915	1327	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	conclusive
GCF_000518705.1	s__Shewanella colwelliana	80.3172	578	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_002215585.1	s__Shewanella marisflavi	79.7297	514	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_009831655.1	s__Shewanella insulae	79.5177	465	1340	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	79.5176	469	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016065.1	s__Shewanella loihica	79.3197	487	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_000518605.1	s__Shewanella fidelis	78.7635	286	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_003966265.1	s__Shewanella atlantica	78.6793	322	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	78.6497	338	1340	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	78.5122	342	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197645.1	s__Shewanella hanedai	78.4421	304	1340	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016765635.1	s__Shewanella schlegeliana	78.4193	327	1340	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	78.0241	161	1340	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	77.7787	229	1340	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	77.6891	197	1340	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 12:30:51,515] [INFO] GTDB search result was written to GCF_019655175.1_ASM1965517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:51,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:51,523] [INFO] DFAST_QC result json was written to GCF_019655175.1_ASM1965517v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:51,523] [INFO] DFAST_QC completed!
[2024-01-24 12:30:51,524] [INFO] Total running time: 0h1m14s