[2024-01-24 12:14:33,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,687] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference
[2024-01-24 12:14:34,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,990] [INFO] Running command: gunzip -c /var/lib/cwl/stgdef24fdd-5b1b-4331-9eab-983ef5071ba9/GCF_014648295.1_ASM1464829v1_genomic.fna.gz | prodigal -d GCF_014648295.1_ASM1464829v1_genomic.fna/cds.fna -a GCF_014648295.1_ASM1464829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,727] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,728] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,728] [INFO] Running command: hmmsearch --tblout GCF_014648295.1_ASM1464829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/reference_markers.hmm GCF_014648295.1_ASM1464829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,961] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,962] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,013] [INFO] Query marker FASTA was written to GCF_014648295.1_ASM1464829v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,013] [INFO] Task started: Blastn
[2024-01-24 12:14:44,013] [INFO] Running command: blastn -query GCF_014648295.1_ASM1464829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/reference_markers.fasta -out GCF_014648295.1_ASM1464829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,716] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:44,716] [INFO] Target genome list was writen to GCF_014648295.1_ASM1464829v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,720] [INFO] Task started: fastANI
[2024-01-24 12:14:44,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef24fdd-5b1b-4331-9eab-983ef5071ba9/GCF_014648295.1_ASM1464829v1_genomic.fna.gz --refList GCF_014648295.1_ASM1464829v1_genomic.fna/target_genomes.txt --output GCF_014648295.1_ASM1464829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:58,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:58,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:58,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:58,783] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:14:58,783] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:14:58,783] [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 saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	100.0	1477	1481	95	inconclusive
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	99.9923	1461	1481	95	inconclusive
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	95.0406	1298	1481	95	inconclusive
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	88.8256	1218	1481	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	88.7791	1215	1481	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	85.0112	1095	1481	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	84.8516	1163	1481	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	84.8124	1165	1481	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	83.9957	1059	1481	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	80.8814	846	1481	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_003026365.1	661	661	type	True	76.1336	62	1481	95	below_threshold
Photobacterium angustum	strain=ATCC 25915	GCA_000950005.1	661	661	type	True	75.9924	61	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:58,785] [INFO] DFAST Taxonomy check result was written to GCF_014648295.1_ASM1464829v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:58,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:58,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:58,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/checkm_data
[2024-01-24 12:14:58,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:58,830] [INFO] Task started: CheckM
[2024-01-24 12:14:58,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648295.1_ASM1464829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648295.1_ASM1464829v1_genomic.fna/checkm_input GCF_014648295.1_ASM1464829v1_genomic.fna/checkm_result
[2024-01-24 12:15:28,186] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:28,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,202] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:28,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:28,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648295.1_ASM1464829v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:28,203] [INFO] Task started: Blastn
[2024-01-24 12:15:28,203] [INFO] Running command: blastn -query GCF_014648295.1_ASM1464829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6326c8-d70e-48d3-aee4-7a44738173d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648295.1_ASM1464829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:29,280] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:29,282] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:29,282] [INFO] Target genome list was writen to GCF_014648295.1_ASM1464829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:29,288] [INFO] Task started: fastANI
[2024-01-24 12:15:29,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef24fdd-5b1b-4331-9eab-983ef5071ba9/GCF_014648295.1_ASM1464829v1_genomic.fna.gz --refList GCF_014648295.1_ASM1464829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648295.1_ASM1464829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:39,975] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:39,982] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:39,982] [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_014648295.1	s__Shewanella saliphila	100.0	1477	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	conclusive
GCF_014648035.1	s__Shewanella algicola	95.0406	1298	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	88.8023	1213	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641855.1	s__Shewanella inventionis	84.9155	1120	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	84.8127	1165	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	81.2081	867	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_000217915.1	s__Shewanella sp000217915	78.2296	264	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	76.1769	70	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026365.1	s__Photobacterium angustum	76.1467	61	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.76	95.45	0.92	0.87	27	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:39,984] [INFO] GTDB search result was written to GCF_014648295.1_ASM1464829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:39,985] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:39,987] [INFO] DFAST_QC result json was written to GCF_014648295.1_ASM1464829v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:39,987] [INFO] DFAST_QC completed!
[2024-01-24 12:15:39,987] [INFO] Total running time: 0h1m6s