[2024-01-25 20:27:05,691] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:05,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:05,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference
[2024-01-25 20:27:06,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:06,844] [INFO] Task started: Prodigal
[2024-01-25 20:27:06,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c4f967f-9ecd-479e-ba57-08239f762365/GCF_009856865.1_ASM985686v1_genomic.fna.gz | prodigal -d GCF_009856865.1_ASM985686v1_genomic.fna/cds.fna -a GCF_009856865.1_ASM985686v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:19,303] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:19,303] [INFO] Task started: HMMsearch
[2024-01-25 20:27:19,303] [INFO] Running command: hmmsearch --tblout GCF_009856865.1_ASM985686v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/reference_markers.hmm GCF_009856865.1_ASM985686v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:19,551] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:19,552] [INFO] Found 6/6 markers.
[2024-01-25 20:27:19,589] [INFO] Query marker FASTA was written to GCF_009856865.1_ASM985686v1_genomic.fna/markers.fasta
[2024-01-25 20:27:19,589] [INFO] Task started: Blastn
[2024-01-25 20:27:19,590] [INFO] Running command: blastn -query GCF_009856865.1_ASM985686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/reference_markers.fasta -out GCF_009856865.1_ASM985686v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:20,251] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:20,256] [INFO] Selected 6 target genomes.
[2024-01-25 20:27:20,256] [INFO] Target genome list was writen to GCF_009856865.1_ASM985686v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:20,270] [INFO] Task started: fastANI
[2024-01-25 20:27:20,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4f967f-9ecd-479e-ba57-08239f762365/GCF_009856865.1_ASM985686v1_genomic.fna.gz --refList GCF_009856865.1_ASM985686v1_genomic.fna/target_genomes.txt --output GCF_009856865.1_ASM985686v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:27,893] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:27,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:27,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:27,900] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:27,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:27,900] [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 aerotolerans	strain=DSM 16695	GCA_009856865.1	295255	295255	type	True	99.9999	1466	1473	95	conclusive
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	83.1968	1024	1473	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	82.9223	1055	1473	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	81.1393	849	1473	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	80.5982	774	1473	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	80.3924	842	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:27,902] [INFO] DFAST Taxonomy check result was written to GCF_009856865.1_ASM985686v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:27,902] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:27,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:27,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/checkm_data
[2024-01-25 20:27:27,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:27,949] [INFO] Task started: CheckM
[2024-01-25 20:27:27,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009856865.1_ASM985686v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009856865.1_ASM985686v1_genomic.fna/checkm_input GCF_009856865.1_ASM985686v1_genomic.fna/checkm_result
[2024-01-25 20:28:03,918] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:03,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:03,935] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:03,935] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:03,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009856865.1_ASM985686v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:03,936] [INFO] Task started: Blastn
[2024-01-25 20:28:03,936] [INFO] Running command: blastn -query GCF_009856865.1_ASM985686v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00207001-ed60-4905-8b0f-3ae34d0ea705/dqc_reference/reference_markers_gtdb.fasta -out GCF_009856865.1_ASM985686v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:05,209] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:05,220] [INFO] Selected 9 target genomes.
[2024-01-25 20:28:05,220] [INFO] Target genome list was writen to GCF_009856865.1_ASM985686v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:05,234] [INFO] Task started: fastANI
[2024-01-25 20:28:05,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4f967f-9ecd-479e-ba57-08239f762365/GCF_009856865.1_ASM985686v1_genomic.fna.gz --refList GCF_009856865.1_ASM985686v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009856865.1_ASM985686v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:16,505] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:16,512] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:16,512] [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_009856865.1	s__Solidesulfovibrio aerotolerans	99.9999	1466	1473	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_000526455.1	s__Solidesulfovibrio magneticus_C	86.4296	1097	1473	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	85.3478	1043	1473	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	84.9118	1088	1473	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_004135975.1	s__Solidesulfovibrio carbinolicus	83.1937	1025	1473	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	83.0012	870	1473	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_000010665.1	s__Solidesulfovibrio magneticus	82.9247	1056	1473	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	82.9161	890	1473	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:16,514] [INFO] GTDB search result was written to GCF_009856865.1_ASM985686v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:16,514] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:16,517] [INFO] DFAST_QC result json was written to GCF_009856865.1_ASM985686v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:16,517] [INFO] DFAST_QC completed!
[2024-01-25 20:28:16,517] [INFO] Total running time: 0h1m11s