[2024-01-24 12:14:48,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,900] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference
[2024-01-24 12:14:50,317] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,318] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,319] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e6064c4-eb1e-4511-ac92-b9cae114c18b/GCF_023283595.1_ASM2328359v1_genomic.fna.gz | prodigal -d GCF_023283595.1_ASM2328359v1_genomic.fna/cds.fna -a GCF_023283595.1_ASM2328359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:01,116] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:01,116] [INFO] Task started: HMMsearch
[2024-01-24 12:15:01,116] [INFO] Running command: hmmsearch --tblout GCF_023283595.1_ASM2328359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/reference_markers.hmm GCF_023283595.1_ASM2328359v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:01,444] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:01,445] [INFO] Found 6/6 markers.
[2024-01-24 12:15:01,501] [INFO] Query marker FASTA was written to GCF_023283595.1_ASM2328359v1_genomic.fna/markers.fasta
[2024-01-24 12:15:01,501] [INFO] Task started: Blastn
[2024-01-24 12:15:01,501] [INFO] Running command: blastn -query GCF_023283595.1_ASM2328359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/reference_markers.fasta -out GCF_023283595.1_ASM2328359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:02,293] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:02,296] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:02,296] [INFO] Target genome list was writen to GCF_023283595.1_ASM2328359v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:02,300] [INFO] Task started: fastANI
[2024-01-24 12:15:02,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e6064c4-eb1e-4511-ac92-b9cae114c18b/GCF_023283595.1_ASM2328359v1_genomic.fna.gz --refList GCF_023283595.1_ASM2328359v1_genomic.fna/target_genomes.txt --output GCF_023283595.1_ASM2328359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:15,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:15,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:15,863] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:15,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:15,864] [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 inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	100.0	1481	1490	95	conclusive
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	99.9966	1485	1490	95	conclusive
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	85.0564	1127	1490	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	84.9039	1101	1490	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	84.8488	1105	1490	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	84.8448	1103	1490	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	84.8292	1141	1490	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	84.7822	1131	1490	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	84.77	1163	1490	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	84.7548	1121	1490	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	80.9623	838	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,866] [INFO] DFAST Taxonomy check result was written to GCF_023283595.1_ASM2328359v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:15,866] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:15,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:15,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/checkm_data
[2024-01-24 12:15:15,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:15,916] [INFO] Task started: CheckM
[2024-01-24 12:15:15,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283595.1_ASM2328359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283595.1_ASM2328359v1_genomic.fna/checkm_input GCF_023283595.1_ASM2328359v1_genomic.fna/checkm_result
[2024-01-24 12:15:51,231] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:51,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,256] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:51,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:51,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283595.1_ASM2328359v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:51,257] [INFO] Task started: Blastn
[2024-01-24 12:15:51,257] [INFO] Running command: blastn -query GCF_023283595.1_ASM2328359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bd88cdd-bc5c-4d4d-8613-32a99d918f0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283595.1_ASM2328359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:52,413] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:52,418] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:52,418] [INFO] Target genome list was writen to GCF_023283595.1_ASM2328359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:52,423] [INFO] Task started: fastANI
[2024-01-24 12:15:52,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e6064c4-eb1e-4511-ac92-b9cae114c18b/GCF_023283595.1_ASM2328359v1_genomic.fna.gz --refList GCF_023283595.1_ASM2328359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283595.1_ASM2328359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:03,694] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:03,712] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:03,712] [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_014641855.1	s__Shewanella inventionis	99.9966	1485	1490	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_014648295.1	s__Shewanella saliphila	84.8467	1102	1490	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	84.8465	1105	1490	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	84.7774	1133	1490	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	84.7745	1163	1490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003855395.1	s__Shewanella livingstonensis	81.3063	880	1490	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	81.2967	875	1490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_006385555.1	s__Shewanella polaris	80.9451	810	1490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_014164505.1	s__Shewanella sp014164505	80.9435	743	1490	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	78.4718	291	1490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:03,714] [INFO] GTDB search result was written to GCF_023283595.1_ASM2328359v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:03,715] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:03,718] [INFO] DFAST_QC result json was written to GCF_023283595.1_ASM2328359v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:03,718] [INFO] DFAST_QC completed!
[2024-01-24 12:16:03,718] [INFO] Total running time: 0h1m15s