[2024-01-24 13:56:12,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference
[2024-01-24 13:56:14,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,423] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg89930fd1-df8a-4410-b5f5-14e823c831b8/GCF_000429345.1_ASM42934v1_genomic.fna.gz | prodigal -d GCF_000429345.1_ASM42934v1_genomic.fna/cds.fna -a GCF_000429345.1_ASM42934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:22,632] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:22,632] [INFO] Task started: HMMsearch
[2024-01-24 13:56:22,632] [INFO] Running command: hmmsearch --tblout GCF_000429345.1_ASM42934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/reference_markers.hmm GCF_000429345.1_ASM42934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:22,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:22,933] [INFO] Found 6/6 markers.
[2024-01-24 13:56:22,969] [INFO] Query marker FASTA was written to GCF_000429345.1_ASM42934v1_genomic.fna/markers.fasta
[2024-01-24 13:56:22,970] [INFO] Task started: Blastn
[2024-01-24 13:56:22,970] [INFO] Running command: blastn -query GCF_000429345.1_ASM42934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/reference_markers.fasta -out GCF_000429345.1_ASM42934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:23,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:23,611] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:23,612] [INFO] Target genome list was writen to GCF_000429345.1_ASM42934v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:23,617] [INFO] Task started: fastANI
[2024-01-24 13:56:23,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg89930fd1-df8a-4410-b5f5-14e823c831b8/GCF_000429345.1_ASM42934v1_genomic.fna.gz --refList GCF_000429345.1_ASM42934v1_genomic.fna/target_genomes.txt --output GCF_000429345.1_ASM42934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:31,436] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:31,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:31,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:31,450] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:31,450] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:31,450] [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
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	100.0	943	949	95	conclusive
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	77.8824	276	949	95	below_threshold
Desulfofundulus thermocisternus	strain=DSM 10259	GCA_000686645.1	42471	42471	type	True	77.8666	220	949	95	below_threshold
Desulfofundulus australicus	strain=DSM 11792	GCA_900129285.1	1566	1566	type	True	77.8065	236	949	95	below_threshold
Desulfofundulus salinum	strain=435	GCA_003627965.1	2419843	2419843	type	True	77.7821	266	949	95	below_threshold
Desulfurispora thermophila	strain=DSM 16022	GCA_000376385.1	265470	265470	type	True	76.6946	114	949	95	below_threshold
Ammonifex thiophilus	strain=SR	GCA_003368535.1	444093	444093	type	True	76.6634	69	949	95	below_threshold
Desulfoscipio geothermicus	strain=DSM 3669	GCA_900115975.1	39060	39060	type	True	76.1839	73	949	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.8828	71	949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:31,455] [INFO] DFAST Taxonomy check result was written to GCF_000429345.1_ASM42934v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:31,456] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:31,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:31,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/checkm_data
[2024-01-24 13:56:31,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:31,500] [INFO] Task started: CheckM
[2024-01-24 13:56:31,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429345.1_ASM42934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429345.1_ASM42934v1_genomic.fna/checkm_input GCF_000429345.1_ASM42934v1_genomic.fna/checkm_result
[2024-01-24 13:56:59,873] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:59,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:59,898] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:59,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:59,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429345.1_ASM42934v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:59,900] [INFO] Task started: Blastn
[2024-01-24 13:56:59,900] [INFO] Running command: blastn -query GCF_000429345.1_ASM42934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg339f8bda-a6ca-4ae1-9277-938d20d87617/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429345.1_ASM42934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:00,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:00,831] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:00,832] [INFO] Target genome list was writen to GCF_000429345.1_ASM42934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:00,849] [INFO] Task started: fastANI
[2024-01-24 13:57:00,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg89930fd1-df8a-4410-b5f5-14e823c831b8/GCF_000429345.1_ASM42934v1_genomic.fna.gz --refList GCF_000429345.1_ASM42934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429345.1_ASM42934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:09,613] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:09,622] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:09,622] [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_000429345.1	s__Desulfovirgula thermocuniculi	100.0	943	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfovirgula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000214705.1	s__Desulfofundulus kuznetsovii	78.0774	311	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	97.21	97.21	0.77	0.77	2	-
GCF_900142025.1	s__Desulfofundulus thermosubterraneus	77.8715	278	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627965.1	s__Desulfofundulus salinum	77.8107	264	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129285.1	s__Desulfofundulus australicus	77.7827	236	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	96.88	96.67	0.83	0.80	3	-
GCF_009428905.1	s__Desulfofundulus_A thermobenzoicus	77.7785	267	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A	95.0	96.96	95.37	0.88	0.86	3	-
GCF_001655685.1	s__Desulfotomaculum_G copahuensis	77.2296	162	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfotomaculum_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376385.1	s__Desulfurispora thermophila	76.6745	115	949	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfurisporaceae;g__Desulfurispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184705.1	s__Thermaerobacter marianensis	75.8634	72	949	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:09,624] [INFO] GTDB search result was written to GCF_000429345.1_ASM42934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:09,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:09,630] [INFO] DFAST_QC result json was written to GCF_000429345.1_ASM42934v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:09,631] [INFO] DFAST_QC completed!
[2024-01-24 13:57:09,631] [INFO] Total running time: 0h0m57s