[2024-01-24 13:31:44,335] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,337] [INFO] DQC Reference Directory: /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference
[2024-01-24 13:31:45,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,597] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,598] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2da92fd-385b-4a83-92b6-b12d01ee83ef/GCF_009828585.1_ASM982858v1_genomic.fna.gz | prodigal -d GCF_009828585.1_ASM982858v1_genomic.fna/cds.fna -a GCF_009828585.1_ASM982858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,105] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,106] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,106] [INFO] Running command: hmmsearch --tblout GCF_009828585.1_ASM982858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/reference_markers.hmm GCF_009828585.1_ASM982858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,451] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,452] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,508] [INFO] Query marker FASTA was written to GCF_009828585.1_ASM982858v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,508] [INFO] Task started: Blastn
[2024-01-24 13:31:56,509] [INFO] Running command: blastn -query GCF_009828585.1_ASM982858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/reference_markers.fasta -out GCF_009828585.1_ASM982858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,379] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,382] [INFO] Selected 10 target genomes.
[2024-01-24 13:31:57,382] [INFO] Target genome list was writen to GCF_009828585.1_ASM982858v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,392] [INFO] Task started: fastANI
[2024-01-24 13:31:57,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2da92fd-385b-4a83-92b6-b12d01ee83ef/GCF_009828585.1_ASM982858v1_genomic.fna.gz --refList GCF_009828585.1_ASM982858v1_genomic.fna/target_genomes.txt --output GCF_009828585.1_ASM982858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:12,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:12,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:12,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:12,304] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:12,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:12,304] [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 litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	100.0	1498	1502	95	conclusive
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	99.9737	1486	1502	95	conclusive
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	88.9117	1208	1502	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	88.8771	1222	1502	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	88.8195	1200	1502	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	87.7895	1276	1502	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	87.7632	1287	1502	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	84.9133	1152	1502	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	84.625	1136	1502	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	81.3683	931	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:12,306] [INFO] DFAST Taxonomy check result was written to GCF_009828585.1_ASM982858v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:12,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:12,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:12,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/checkm_data
[2024-01-24 13:32:12,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:12,361] [INFO] Task started: CheckM
[2024-01-24 13:32:12,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828585.1_ASM982858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828585.1_ASM982858v1_genomic.fna/checkm_input GCF_009828585.1_ASM982858v1_genomic.fna/checkm_result
[2024-01-24 13:32:48,451] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:48,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:48,472] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:48,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:48,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828585.1_ASM982858v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:48,474] [INFO] Task started: Blastn
[2024-01-24 13:32:48,474] [INFO] Running command: blastn -query GCF_009828585.1_ASM982858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33c7ef0-cdb7-4244-9be0-d8ce2c6216f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828585.1_ASM982858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,704] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:49,705] [INFO] Target genome list was writen to GCF_009828585.1_ASM982858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:49,713] [INFO] Task started: fastANI
[2024-01-24 13:32:49,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2da92fd-385b-4a83-92b6-b12d01ee83ef/GCF_009828585.1_ASM982858v1_genomic.fna.gz --refList GCF_009828585.1_ASM982858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828585.1_ASM982858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:03,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,126] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:03,126] [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_009828585.1	s__Shewanella litoralis	100.0	1498	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014648295.1	s__Shewanella saliphila	88.8667	1221	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	88.8249	1200	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	87.7968	1275	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	84.8263	1157	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	82.1515	995	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	81.8872	969	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014164505.1	s__Shewanella sp014164505	81.5862	785	1502	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	78.5023	399	1502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663145.1	s__Shewanella sp009663145	78.2072	395	1502	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 13:33:03,129] [INFO] GTDB search result was written to GCF_009828585.1_ASM982858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:03,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:03,132] [INFO] DFAST_QC result json was written to GCF_009828585.1_ASM982858v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:03,133] [INFO] DFAST_QC completed!
[2024-01-24 13:33:03,133] [INFO] Total running time: 0h1m19s