[2024-01-24 15:18:22,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:22,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:22,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference
[2024-01-24 15:18:25,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,006] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,007] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7c779c-055e-490c-bce0-3af1ca35a3c1/GCF_014648035.1_ASM1464803v1_genomic.fna.gz | prodigal -d GCF_014648035.1_ASM1464803v1_genomic.fna/cds.fna -a GCF_014648035.1_ASM1464803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:36,254] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:36,254] [INFO] Task started: HMMsearch
[2024-01-24 15:18:36,255] [INFO] Running command: hmmsearch --tblout GCF_014648035.1_ASM1464803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/reference_markers.hmm GCF_014648035.1_ASM1464803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:36,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:36,634] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d7c779c-055e-490c-bce0-3af1ca35a3c1/GCF_014648035.1_ASM1464803v1_genomic.fna.gz]
[2024-01-24 15:18:36,719] [INFO] Query marker FASTA was written to GCF_014648035.1_ASM1464803v1_genomic.fna/markers.fasta
[2024-01-24 15:18:36,719] [INFO] Task started: Blastn
[2024-01-24 15:18:36,719] [INFO] Running command: blastn -query GCF_014648035.1_ASM1464803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/reference_markers.fasta -out GCF_014648035.1_ASM1464803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:37,509] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:37,512] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:37,512] [INFO] Target genome list was writen to GCF_014648035.1_ASM1464803v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:37,518] [INFO] Task started: fastANI
[2024-01-24 15:18:37,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7c779c-055e-490c-bce0-3af1ca35a3c1/GCF_014648035.1_ASM1464803v1_genomic.fna.gz --refList GCF_014648035.1_ASM1464803v1_genomic.fna/target_genomes.txt --output GCF_014648035.1_ASM1464803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:51,492] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:51,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:51,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:51,508] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:18:51,508] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:18:51,509] [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 algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	100.0	1559	1565	95	inconclusive
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	95.1245	1291	1565	95	inconclusive
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	95.1181	1296	1565	95	inconclusive
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	88.7868	1205	1565	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	88.6435	1210	1565	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	84.9208	1099	1565	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	84.8845	1120	1565	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	84.8561	1158	1565	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	84.8446	1169	1565	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	83.9514	1065	1565	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	79.4688	487	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:51,519] [INFO] DFAST Taxonomy check result was written to GCF_014648035.1_ASM1464803v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:51,520] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:51,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:51,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/checkm_data
[2024-01-24 15:18:51,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:51,576] [INFO] Task started: CheckM
[2024-01-24 15:18:51,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648035.1_ASM1464803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648035.1_ASM1464803v1_genomic.fna/checkm_input GCF_014648035.1_ASM1464803v1_genomic.fna/checkm_result
[2024-01-24 15:19:28,107] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:28,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,127] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:28,127] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:28,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648035.1_ASM1464803v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:28,128] [INFO] Task started: Blastn
[2024-01-24 15:19:28,128] [INFO] Running command: blastn -query GCF_014648035.1_ASM1464803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8847885a-e18a-4d6a-8884-dfb1638277e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648035.1_ASM1464803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:29,255] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:29,259] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:29,260] [INFO] Target genome list was writen to GCF_014648035.1_ASM1464803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:29,265] [INFO] Task started: fastANI
[2024-01-24 15:19:29,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7c779c-055e-490c-bce0-3af1ca35a3c1/GCF_014648035.1_ASM1464803v1_genomic.fna.gz --refList GCF_014648035.1_ASM1464803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648035.1_ASM1464803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:37,151] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:37,162] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:19:37,162] [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_014648035.1	s__Shewanella algicola	100.0	1559	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014648295.1	s__Shewanella saliphila	95.129	1295	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	inconclusive
GCF_009828585.1	s__Shewanella litoralis	88.783	1206	1565	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	84.8941	1119	1565	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	84.8554	1168	1565	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	81.7495	949	1565	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:37,164] [INFO] GTDB search result was written to GCF_014648035.1_ASM1464803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:37,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:37,167] [INFO] DFAST_QC result json was written to GCF_014648035.1_ASM1464803v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:37,167] [INFO] DFAST_QC completed!
[2024-01-24 15:19:37,168] [INFO] Total running time: 0h1m15s