[2024-01-25 19:33:20,948] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:20,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:20,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference
[2024-01-25 19:33:22,146] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,147] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,147] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2be617b-341a-4212-9a45-e2aa01b72908/GCF_003627965.1_ASM362796v1_genomic.fna.gz | prodigal -d GCF_003627965.1_ASM362796v1_genomic.fna/cds.fna -a GCF_003627965.1_ASM362796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:29,167] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:29,167] [INFO] Task started: HMMsearch
[2024-01-25 19:33:29,167] [INFO] Running command: hmmsearch --tblout GCF_003627965.1_ASM362796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/reference_markers.hmm GCF_003627965.1_ASM362796v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:29,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:29,390] [INFO] Found 6/6 markers.
[2024-01-25 19:33:29,414] [INFO] Query marker FASTA was written to GCF_003627965.1_ASM362796v1_genomic.fna/markers.fasta
[2024-01-25 19:33:29,414] [INFO] Task started: Blastn
[2024-01-25 19:33:29,414] [INFO] Running command: blastn -query GCF_003627965.1_ASM362796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/reference_markers.fasta -out GCF_003627965.1_ASM362796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:29,969] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:29,971] [INFO] Selected 8 target genomes.
[2024-01-25 19:33:29,972] [INFO] Target genome list was writen to GCF_003627965.1_ASM362796v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:29,975] [INFO] Task started: fastANI
[2024-01-25 19:33:29,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be617b-341a-4212-9a45-e2aa01b72908/GCF_003627965.1_ASM362796v1_genomic.fna.gz --refList GCF_003627965.1_ASM362796v1_genomic.fna/target_genomes.txt --output GCF_003627965.1_ASM362796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:35,438] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:35,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:35,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:35,444] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:35,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:35,444] [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	100.0	957	958	95	conclusive
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	92.3659	758	958	95	below_threshold
Desulfofundulus thermocisternus	strain=DSM 10259	GCA_000686645.1	42471	42471	type	True	84.6942	619	958	95	below_threshold
Desulfofundulus australicus	strain=DSM 11792	GCA_900129285.1	1566	1566	type	True	84.1304	602	958	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	77.7723	270	958	95	below_threshold
Desulfurispora thermophila	strain=DSM 16022	GCA_000376385.1	265470	265470	type	True	77.2541	129	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:35,445] [INFO] DFAST Taxonomy check result was written to GCF_003627965.1_ASM362796v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:35,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:35,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:35,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/checkm_data
[2024-01-25 19:33:35,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:35,477] [INFO] Task started: CheckM
[2024-01-25 19:33:35,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003627965.1_ASM362796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003627965.1_ASM362796v1_genomic.fna/checkm_input GCF_003627965.1_ASM362796v1_genomic.fna/checkm_result
[2024-01-25 19:33:59,304] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:59,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:59,322] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:59,322] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:59,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003627965.1_ASM362796v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:59,323] [INFO] Task started: Blastn
[2024-01-25 19:33:59,323] [INFO] Running command: blastn -query GCF_003627965.1_ASM362796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg845c5c8e-0862-40b7-b8d9-fbbe9b834fd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003627965.1_ASM362796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:00,106] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:00,113] [INFO] Selected 10 target genomes.
[2024-01-25 19:34:00,113] [INFO] Target genome list was writen to GCF_003627965.1_ASM362796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:00,119] [INFO] Task started: fastANI
[2024-01-25 19:34:00,119] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2be617b-341a-4212-9a45-e2aa01b72908/GCF_003627965.1_ASM362796v1_genomic.fna.gz --refList GCF_003627965.1_ASM362796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003627965.1_ASM362796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:07,497] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:07,502] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:07,502] [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	100.0	957	958	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000214705.1	s__Desulfofundulus kuznetsovii	93.2392	766	958	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	92.3491	759	958	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	84.1219	604	958	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	80.6	454	958	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	77.7587	271	958	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfovirgula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:07,504] [INFO] GTDB search result was written to GCF_003627965.1_ASM362796v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:07,505] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:07,507] [INFO] DFAST_QC result json was written to GCF_003627965.1_ASM362796v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:07,507] [INFO] DFAST_QC completed!
[2024-01-25 19:34:07,507] [INFO] Total running time: 0h0m47s