[2024-01-24 12:53:36,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,617] [INFO] DQC Reference Directory: /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference
[2024-01-24 12:53:37,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,880] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f27d9fc-e2d8-49ef-9d3d-ad0c40fa76cb/GCF_000233715.2_ASM23371v3_genomic.fna.gz | prodigal -d GCF_000233715.2_ASM23371v3_genomic.fna/cds.fna -a GCF_000233715.2_ASM23371v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:49,903] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:49,904] [INFO] Task started: HMMsearch
[2024-01-24 12:53:49,904] [INFO] Running command: hmmsearch --tblout GCF_000233715.2_ASM23371v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/reference_markers.hmm GCF_000233715.2_ASM23371v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:50,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:50,187] [INFO] Found 6/6 markers.
[2024-01-24 12:53:50,227] [INFO] Query marker FASTA was written to GCF_000233715.2_ASM23371v3_genomic.fna/markers.fasta
[2024-01-24 12:53:50,227] [INFO] Task started: Blastn
[2024-01-24 12:53:50,227] [INFO] Running command: blastn -query GCF_000233715.2_ASM23371v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/reference_markers.fasta -out GCF_000233715.2_ASM23371v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:50,806] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:50,810] [INFO] Selected 18 target genomes.
[2024-01-24 12:53:50,810] [INFO] Target genome list was writen to GCF_000233715.2_ASM23371v3_genomic.fna/target_genomes.txt
[2024-01-24 12:53:50,818] [INFO] Task started: fastANI
[2024-01-24 12:53:50,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f27d9fc-e2d8-49ef-9d3d-ad0c40fa76cb/GCF_000233715.2_ASM23371v3_genomic.fna.gz --refList GCF_000233715.2_ASM23371v3_genomic.fna/target_genomes.txt --output GCF_000233715.2_ASM23371v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:59,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:59,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:59,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:59,574] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:59,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:59,574] [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
Sporotomaculum syntrophicum	strain=FB	GCA_009932395.1	182264	182264	type	True	79.4155	390	1618	95	below_threshold
Desulfocucumis palustris	strain=NAW-5	GCA_002933875.1	1898651	1898651	type	True	78.7778	84	1618	95	below_threshold
Desulfoscipio geothermicus	strain=DSM 3669	GCA_900115975.1	39060	39060	type	True	77.8534	281	1618	95	below_threshold
Desulfofundulus salinum	strain=435	GCA_003627965.1	2419843	2419843	type	True	76.7688	61	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:59,576] [INFO] DFAST Taxonomy check result was written to GCF_000233715.2_ASM23371v3_genomic.fna/tc_result.tsv
[2024-01-24 12:53:59,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:59,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:59,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/checkm_data
[2024-01-24 12:53:59,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:59,622] [INFO] Task started: CheckM
[2024-01-24 12:53:59,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000233715.2_ASM23371v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000233715.2_ASM23371v3_genomic.fna/checkm_input GCF_000233715.2_ASM23371v3_genomic.fna/checkm_result
[2024-01-24 12:54:37,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:37,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:37,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:37,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:37,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000233715.2_ASM23371v3_genomic.fna/markers.fasta)
[2024-01-24 12:54:37,558] [INFO] Task started: Blastn
[2024-01-24 12:54:37,558] [INFO] Running command: blastn -query GCF_000233715.2_ASM23371v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdddba82c-cec0-4267-bb7f-9933d6429037/dqc_reference/reference_markers_gtdb.fasta -out GCF_000233715.2_ASM23371v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:38,378] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:38,381] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:38,382] [INFO] Target genome list was writen to GCF_000233715.2_ASM23371v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:38,393] [INFO] Task started: fastANI
[2024-01-24 12:54:38,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f27d9fc-e2d8-49ef-9d3d-ad0c40fa76cb/GCF_000233715.2_ASM23371v3_genomic.fna.gz --refList GCF_000233715.2_ASM23371v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000233715.2_ASM23371v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:46,112] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:46,122] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:46,122] [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_000233715.2	s__Sporotomaculum gibsoniae	100.0	1618	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016841205.1	s__Sporotomaculum geothermicum_A	80.8665	554	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841645.1	s__Sporotomaculum geothermicum_B	80.6615	523	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124625.1	s__Sporotomaculum thermosapovorans	80.5509	550	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932395.1	s__Sporotomaculum syntrophicum	79.4536	387	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841905.1	s__Sporotomaculum geothermicum_C	79.3436	397	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115975.1	s__Desulfoscipio geothermicus	77.8126	283	1618	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Desulfoscipio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:46,123] [INFO] GTDB search result was written to GCF_000233715.2_ASM23371v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:46,124] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:46,126] [INFO] DFAST_QC result json was written to GCF_000233715.2_ASM23371v3_genomic.fna/dqc_result.json
[2024-01-24 12:54:46,126] [INFO] DFAST_QC completed!
[2024-01-24 12:54:46,126] [INFO] Total running time: 0h1m10s