[2024-01-24 12:39:48,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:48,187] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:48,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference
[2024-01-24 12:39:49,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:49,372] [INFO] Task started: Prodigal
[2024-01-24 12:39:49,372] [INFO] Running command: gunzip -c /var/lib/cwl/stgad435446-8fec-4ef6-8576-207842600598/GCF_004143605.1_ASM414360v1_genomic.fna.gz | prodigal -d GCF_004143605.1_ASM414360v1_genomic.fna/cds.fna -a GCF_004143605.1_ASM414360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:56,633] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:56,634] [INFO] Task started: HMMsearch
[2024-01-24 12:39:56,634] [INFO] Running command: hmmsearch --tblout GCF_004143605.1_ASM414360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/reference_markers.hmm GCF_004143605.1_ASM414360v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:56,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:56,821] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgad435446-8fec-4ef6-8576-207842600598/GCF_004143605.1_ASM414360v1_genomic.fna.gz]
[2024-01-24 12:39:56,854] [INFO] Query marker FASTA was written to GCF_004143605.1_ASM414360v1_genomic.fna/markers.fasta
[2024-01-24 12:39:56,854] [INFO] Task started: Blastn
[2024-01-24 12:39:56,854] [INFO] Running command: blastn -query GCF_004143605.1_ASM414360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/reference_markers.fasta -out GCF_004143605.1_ASM414360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:57,321] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:57,324] [INFO] Selected 9 target genomes.
[2024-01-24 12:39:57,325] [INFO] Target genome list was writen to GCF_004143605.1_ASM414360v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:57,331] [INFO] Task started: fastANI
[2024-01-24 12:39:57,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgad435446-8fec-4ef6-8576-207842600598/GCF_004143605.1_ASM414360v1_genomic.fna.gz --refList GCF_004143605.1_ASM414360v1_genomic.fna/target_genomes.txt --output GCF_004143605.1_ASM414360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:02,194] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:02,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:02,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:02,200] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:02,200] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:02,200] [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
Desulforamulus ruminis	strain=DSM 2154	GCA_000215085.1	1564	1564	type	True	78.3618	179	1155	95	below_threshold
Desulforamulus profundi	strain=Bs107	GCA_002607855.1	1383067	1383067	type	True	78.3357	160	1155	95	below_threshold
Desulfotomaculum nigrificans	strain=DSM 574	GCA_000189755.3	1565	1565	type	True	77.6597	156	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:02,202] [INFO] DFAST Taxonomy check result was written to GCF_004143605.1_ASM414360v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:02,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:02,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:02,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/checkm_data
[2024-01-24 12:40:02,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:02,247] [INFO] Task started: CheckM
[2024-01-24 12:40:02,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004143605.1_ASM414360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004143605.1_ASM414360v1_genomic.fna/checkm_input GCF_004143605.1_ASM414360v1_genomic.fna/checkm_result
[2024-01-24 12:40:28,680] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:28,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:28,726] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:28,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:28,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004143605.1_ASM414360v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:28,727] [INFO] Task started: Blastn
[2024-01-24 12:40:28,727] [INFO] Running command: blastn -query GCF_004143605.1_ASM414360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a09c2dc-b296-4113-8b45-bec7c8fb739b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004143605.1_ASM414360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:29,194] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:29,198] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:29,199] [INFO] Target genome list was writen to GCF_004143605.1_ASM414360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:29,226] [INFO] Task started: fastANI
[2024-01-24 12:40:29,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgad435446-8fec-4ef6-8576-207842600598/GCF_004143605.1_ASM414360v1_genomic.fna.gz --refList GCF_004143605.1_ASM414360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004143605.1_ASM414360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:37,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:37,193] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:37,193] [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
GCA_004143605.1	s__Desulfotomaculum aquiferis	100.0	1154	1155	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000215085.1	s__Desulfotomaculum ruminis	78.3618	179	1155	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002607855.1	s__Desulfotomaculum profundi	78.3123	161	1155	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189755.2	s__Desulfotomaculum nigrificans	77.6763	156	1155	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	98.87	98.87	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:37,195] [INFO] GTDB search result was written to GCF_004143605.1_ASM414360v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:37,195] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:37,202] [INFO] DFAST_QC result json was written to GCF_004143605.1_ASM414360v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:37,202] [INFO] DFAST_QC completed!
[2024-01-24 12:40:37,202] [INFO] Total running time: 0h0m49s