[2024-01-24 14:19:34,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:34,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:34,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference
[2024-01-24 14:19:36,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:36,235] [INFO] Task started: Prodigal
[2024-01-24 14:19:36,235] [INFO] Running command: gunzip -c /var/lib/cwl/stgee03ee0f-20ce-44f7-ae90-afc24c439864/GCF_000010665.1_ASM1066v1_genomic.fna.gz | prodigal -d GCF_000010665.1_ASM1066v1_genomic.fna/cds.fna -a GCF_000010665.1_ASM1066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:54,019] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:54,019] [INFO] Task started: HMMsearch
[2024-01-24 14:19:54,020] [INFO] Running command: hmmsearch --tblout GCF_000010665.1_ASM1066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/reference_markers.hmm GCF_000010665.1_ASM1066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:54,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:54,370] [INFO] Found 6/6 markers.
[2024-01-24 14:19:54,428] [INFO] Query marker FASTA was written to GCF_000010665.1_ASM1066v1_genomic.fna/markers.fasta
[2024-01-24 14:19:54,428] [INFO] Task started: Blastn
[2024-01-24 14:19:54,428] [INFO] Running command: blastn -query GCF_000010665.1_ASM1066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/reference_markers.fasta -out GCF_000010665.1_ASM1066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:55,187] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:55,190] [INFO] Selected 7 target genomes.
[2024-01-24 14:19:55,190] [INFO] Target genome list was writen to GCF_000010665.1_ASM1066v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:55,214] [INFO] Task started: fastANI
[2024-01-24 14:19:55,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgee03ee0f-20ce-44f7-ae90-afc24c439864/GCF_000010665.1_ASM1066v1_genomic.fna.gz --refList GCF_000010665.1_ASM1066v1_genomic.fna/target_genomes.txt --output GCF_000010665.1_ASM1066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:05,542] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:05,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:05,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:05,550] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:05,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:05,550] [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
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	100.0	1769	1770	95	conclusive
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	94.4604	1326	1770	95	below_threshold
Solidesulfovibrio aerotolerans	strain=DSM 16695	GCA_009856865.1	295255	295255	type	True	82.9761	1056	1770	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	82.297	936	1770	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	81.901	974	1770	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	81.649	909	1770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:05,552] [INFO] DFAST Taxonomy check result was written to GCF_000010665.1_ASM1066v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:05,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:05,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:05,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/checkm_data
[2024-01-24 14:20:05,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:05,607] [INFO] Task started: CheckM
[2024-01-24 14:20:05,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000010665.1_ASM1066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000010665.1_ASM1066v1_genomic.fna/checkm_input GCF_000010665.1_ASM1066v1_genomic.fna/checkm_result
[2024-01-24 14:20:54,971] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:54,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:54,994] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:54,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:54,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000010665.1_ASM1066v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:54,995] [INFO] Task started: Blastn
[2024-01-24 14:20:54,996] [INFO] Running command: blastn -query GCF_000010665.1_ASM1066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3859c009-5c00-45ee-89f4-5a4ed47c4028/dqc_reference/reference_markers_gtdb.fasta -out GCF_000010665.1_ASM1066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:56,154] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:56,157] [INFO] Selected 9 target genomes.
[2024-01-24 14:20:56,158] [INFO] Target genome list was writen to GCF_000010665.1_ASM1066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:56,168] [INFO] Task started: fastANI
[2024-01-24 14:20:56,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgee03ee0f-20ce-44f7-ae90-afc24c439864/GCF_000010665.1_ASM1066v1_genomic.fna.gz --refList GCF_000010665.1_ASM1066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000010665.1_ASM1066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:09,232] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:09,240] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:09,241] [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_000010665.1	s__Solidesulfovibrio magneticus	100.0	1769	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004135975.1	s__Solidesulfovibrio carbinolicus	94.4604	1326	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482565.1	s__Solidesulfovibrio magneticus_B	93.7264	1123	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307955.1	s__Solidesulfovibrio magneticus_A	92.4641	1070	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526455.1	s__Solidesulfovibrio magneticus_C	84.5459	1103	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001936595.1	s__Solidesulfovibrio sp001936595	83.9412	1070	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801335.2	s__Solidesulfovibrio sp000801335	83.1817	1143	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245055.1	s__Solidesulfovibrio sp000245055	82.089	964	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376475.1	s__Desulfolutivibrio sulfoxidireducens	78.7804	510	1770	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.21	99.21	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:09,243] [INFO] GTDB search result was written to GCF_000010665.1_ASM1066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:09,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:09,247] [INFO] DFAST_QC result json was written to GCF_000010665.1_ASM1066v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:09,247] [INFO] DFAST_QC completed!
[2024-01-24 14:21:09,247] [INFO] Total running time: 0h1m34s