[2024-01-25 19:38:35,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference
[2024-01-25 19:38:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,769] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg6036c6e0-861a-4689-b20c-b646fd5899eb/GCF_030813795.1_ASM3081379v1_genomic.fna.gz | prodigal -d GCF_030813795.1_ASM3081379v1_genomic.fna/cds.fna -a GCF_030813795.1_ASM3081379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:43,653] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:43,654] [INFO] Task started: HMMsearch
[2024-01-25 19:38:43,654] [INFO] Running command: hmmsearch --tblout GCF_030813795.1_ASM3081379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/reference_markers.hmm GCF_030813795.1_ASM3081379v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:43,862] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:43,863] [INFO] Found 6/6 markers.
[2024-01-25 19:38:43,889] [INFO] Query marker FASTA was written to GCF_030813795.1_ASM3081379v1_genomic.fna/markers.fasta
[2024-01-25 19:38:43,889] [INFO] Task started: Blastn
[2024-01-25 19:38:43,889] [INFO] Running command: blastn -query GCF_030813795.1_ASM3081379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/reference_markers.fasta -out GCF_030813795.1_ASM3081379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:44,426] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:44,429] [INFO] Selected 9 target genomes.
[2024-01-25 19:38:44,430] [INFO] Target genome list was writen to GCF_030813795.1_ASM3081379v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:44,436] [INFO] Task started: fastANI
[2024-01-25 19:38:44,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg6036c6e0-861a-4689-b20c-b646fd5899eb/GCF_030813795.1_ASM3081379v1_genomic.fna.gz --refList GCF_030813795.1_ASM3081379v1_genomic.fna/target_genomes.txt --output GCF_030813795.1_ASM3081379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:50,024] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:50,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:50,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:50,031] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:38:50,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:38:50,032] [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
Desulfofundulus salinum	strain=435	GCA_003627965.1	2419843	2419843	type	True	93.1841	725	949	95	below_threshold
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	92.4803	762	949	95	below_threshold
Desulfofundulus australicus	strain=DSM 11792	GCA_900129285.1	1566	1566	type	True	84.2343	647	949	95	below_threshold
Desulfofundulus thermocisternus	strain=DSM 10259	GCA_000686645.1	42471	42471	type	True	84.0593	626	949	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	77.8065	267	949	95	below_threshold
Desulfoscipio geothermicus	strain=DSM 3669	GCA_900115975.1	39060	39060	type	True	76.4309	103	949	95	below_threshold
Desulforamulus ruminis	strain=DSM 2154	GCA_000215085.1	1564	1564	type	True	75.4295	52	949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:50,033] [INFO] DFAST Taxonomy check result was written to GCF_030813795.1_ASM3081379v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:50,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:50,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:50,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/checkm_data
[2024-01-25 19:38:50,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:50,065] [INFO] Task started: CheckM
[2024-01-25 19:38:50,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813795.1_ASM3081379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813795.1_ASM3081379v1_genomic.fna/checkm_input GCF_030813795.1_ASM3081379v1_genomic.fna/checkm_result
[2024-01-25 19:39:14,194] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:14,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:14,224] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:14,224] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:14,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813795.1_ASM3081379v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:14,225] [INFO] Task started: Blastn
[2024-01-25 19:39:14,225] [INFO] Running command: blastn -query GCF_030813795.1_ASM3081379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f776b75-19ae-4122-8fa1-1b710cb482d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813795.1_ASM3081379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:14,974] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:14,977] [INFO] Selected 9 target genomes.
[2024-01-25 19:39:14,977] [INFO] Target genome list was writen to GCF_030813795.1_ASM3081379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:14,980] [INFO] Task started: fastANI
[2024-01-25 19:39:14,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg6036c6e0-861a-4689-b20c-b646fd5899eb/GCF_030813795.1_ASM3081379v1_genomic.fna.gz --refList GCF_030813795.1_ASM3081379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813795.1_ASM3081379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:21,753] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:21,759] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:39:21,759] [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_003627965.1	s__Desulfofundulus salinum	93.1766	725	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	-
GCA_000214705.1	s__Desulfofundulus kuznetsovii	93.0148	788	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	92.4901	762	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	84.2764	644	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	80.4047	492	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_000429345.1	s__Desulfovirgula thermocuniculi	77.8094	266	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	-
GCF_001655685.1	s__Desulfotomaculum_G copahuensis	77.3796	230	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:21,762] [INFO] GTDB search result was written to GCF_030813795.1_ASM3081379v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:21,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:21,765] [INFO] DFAST_QC result json was written to GCF_030813795.1_ASM3081379v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:21,765] [INFO] DFAST_QC completed!
[2024-01-25 19:39:21,765] [INFO] Total running time: 0h0m46s