[2023-06-14 01:07:04,185] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:04,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:04,188] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference
[2023-06-14 01:07:05,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:05,361] [INFO] Task started: Prodigal
[2023-06-14 01:07:05,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgb21cdc9c-3e0e-4df1-8451-1cfc0648f16b/GCA_003245855.1_ASM324585v1_genomic.fna.gz | prodigal -d GCA_003245855.1_ASM324585v1_genomic.fna/cds.fna -a GCA_003245855.1_ASM324585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:09,659] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:09,660] [INFO] Task started: HMMsearch
[2023-06-14 01:07:09,660] [INFO] Running command: hmmsearch --tblout GCA_003245855.1_ASM324585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/reference_markers.hmm GCA_003245855.1_ASM324585v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:09,868] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:09,869] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb21cdc9c-3e0e-4df1-8451-1cfc0648f16b/GCA_003245855.1_ASM324585v1_genomic.fna.gz]
[2023-06-14 01:07:09,893] [INFO] Query marker FASTA was written to GCA_003245855.1_ASM324585v1_genomic.fna/markers.fasta
[2023-06-14 01:07:09,893] [INFO] Task started: Blastn
[2023-06-14 01:07:09,893] [INFO] Running command: blastn -query GCA_003245855.1_ASM324585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/reference_markers.fasta -out GCA_003245855.1_ASM324585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:10,376] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:10,381] [INFO] Selected 5 target genomes.
[2023-06-14 01:07:10,382] [INFO] Target genome list was writen to GCA_003245855.1_ASM324585v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:10,385] [INFO] Task started: fastANI
[2023-06-14 01:07:10,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgb21cdc9c-3e0e-4df1-8451-1cfc0648f16b/GCA_003245855.1_ASM324585v1_genomic.fna.gz --refList GCA_003245855.1_ASM324585v1_genomic.fna/target_genomes.txt --output GCA_003245855.1_ASM324585v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:14,175] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:14,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:14,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:14,187] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:14,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:07:14,188] [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
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	82.8138	244	355	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	82.0404	246	355	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	77.9022	114	355	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	77.4909	116	355	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	77.2402	110	355	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:07:14,191] [INFO] DFAST Taxonomy check result was written to GCA_003245855.1_ASM324585v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:14,191] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:14,192] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:14,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/checkm_data
[2023-06-14 01:07:14,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:14,219] [INFO] Task started: CheckM
[2023-06-14 01:07:14,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003245855.1_ASM324585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003245855.1_ASM324585v1_genomic.fna/checkm_input GCA_003245855.1_ASM324585v1_genomic.fna/checkm_result
[2023-06-14 01:07:33,779] [INFO] Task succeeded: CheckM
[2023-06-14 01:07:33,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.28%
Contamintation: 12.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-14 01:07:33,804] [INFO] ===== Completeness check finished =====
[2023-06-14 01:07:33,804] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:07:33,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003245855.1_ASM324585v1_genomic.fna/markers.fasta)
[2023-06-14 01:07:33,805] [INFO] Task started: Blastn
[2023-06-14 01:07:33,805] [INFO] Running command: blastn -query GCA_003245855.1_ASM324585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9bb5271-eb3f-49af-a48f-35b825dc03cf/dqc_reference/reference_markers_gtdb.fasta -out GCA_003245855.1_ASM324585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:34,238] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:34,242] [INFO] Selected 5 target genomes.
[2023-06-14 01:07:34,242] [INFO] Target genome list was writen to GCA_003245855.1_ASM324585v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:07:34,245] [INFO] Task started: fastANI
[2023-06-14 01:07:34,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgb21cdc9c-3e0e-4df1-8451-1cfc0648f16b/GCA_003245855.1_ASM324585v1_genomic.fna.gz --refList GCA_003245855.1_ASM324585v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003245855.1_ASM324585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:07:37,552] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:37,561] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:07:37,561] [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_000429325.1	s__Fundidesulfovibrio putealis	82.8138	244	355	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773665.1	s__Fundidesulfovibrio sp009773665	82.1586	159	355	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013019105.1	s__Fundidesulfovibrio sp013019105	82.0928	244	355	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208105.1	s__Fundidesulfovibrio sp016208105	80.9949	193	355	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	99.98	99.98	0.95	0.95	2	-
GCF_000519125.1	s__Desulfocurvus vexinensis	77.8416	125	355	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:07:37,563] [INFO] GTDB search result was written to GCA_003245855.1_ASM324585v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:07:37,563] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:07:37,566] [INFO] DFAST_QC result json was written to GCA_003245855.1_ASM324585v1_genomic.fna/dqc_result.json
[2023-06-14 01:07:37,566] [INFO] DFAST_QC completed!
[2023-06-14 01:07:37,567] [INFO] Total running time: 0h0m33s