[2024-01-24 14:15:33,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:33,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:33,852] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference
[2024-01-24 14:15:35,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,259] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dab12eb-c195-4174-8fda-1da0db0b26f6/GCF_015775515.1_ASM1577551v1_genomic.fna.gz | prodigal -d GCF_015775515.1_ASM1577551v1_genomic.fna/cds.fna -a GCF_015775515.1_ASM1577551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:42,109] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:42,110] [INFO] Task started: HMMsearch
[2024-01-24 14:15:42,110] [INFO] Running command: hmmsearch --tblout GCF_015775515.1_ASM1577551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/reference_markers.hmm GCF_015775515.1_ASM1577551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:42,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:42,431] [INFO] Found 6/6 markers.
[2024-01-24 14:15:42,457] [INFO] Query marker FASTA was written to GCF_015775515.1_ASM1577551v1_genomic.fna/markers.fasta
[2024-01-24 14:15:42,458] [INFO] Task started: Blastn
[2024-01-24 14:15:42,458] [INFO] Running command: blastn -query GCF_015775515.1_ASM1577551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/reference_markers.fasta -out GCF_015775515.1_ASM1577551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:43,057] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:43,061] [INFO] Selected 6 target genomes.
[2024-01-24 14:15:43,061] [INFO] Target genome list was writen to GCF_015775515.1_ASM1577551v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:43,064] [INFO] Task started: fastANI
[2024-01-24 14:15:43,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dab12eb-c195-4174-8fda-1da0db0b26f6/GCF_015775515.1_ASM1577551v1_genomic.fna.gz --refList GCF_015775515.1_ASM1577551v1_genomic.fna/target_genomes.txt --output GCF_015775515.1_ASM1577551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:48,958] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:48,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:48,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:48,966] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:48,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:48,967] [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
Atribacter laminatus	strain=RT761	GCA_015775515.1	2847778	2847778	type	True	100.0	1033	1033	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:15:48,969] [INFO] DFAST Taxonomy check result was written to GCF_015775515.1_ASM1577551v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:48,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:48,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:48,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/checkm_data
[2024-01-24 14:15:48,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:49,008] [INFO] Task started: CheckM
[2024-01-24 14:15:49,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015775515.1_ASM1577551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015775515.1_ASM1577551v1_genomic.fna/checkm_input GCF_015775515.1_ASM1577551v1_genomic.fna/checkm_result
[2024-01-24 14:16:17,525] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:17,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,548] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:17,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:17,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015775515.1_ASM1577551v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:17,549] [INFO] Task started: Blastn
[2024-01-24 14:16:17,549] [INFO] Running command: blastn -query GCF_015775515.1_ASM1577551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5b30c2-e661-4787-94fa-f7094ac76a40/dqc_reference/reference_markers_gtdb.fasta -out GCF_015775515.1_ASM1577551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:18,409] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:18,412] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:18,413] [INFO] Target genome list was writen to GCF_015775515.1_ASM1577551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:18,463] [INFO] Task started: fastANI
[2024-01-24 14:16:18,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dab12eb-c195-4174-8fda-1da0db0b26f6/GCF_015775515.1_ASM1577551v1_genomic.fna.gz --refList GCF_015775515.1_ASM1577551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015775515.1_ASM1577551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:26,700] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:26,706] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:26,706] [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_015775515.1	s__Atribacter laminatus	100.0	1033	1033	d__Bacteria;p__Atribacterota;c__Atribacteria;o__Atribacterales;f__Atribacteraceae;g__Atribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003542295.1	s__Atribacter sp003542295	91.6359	513	1033	d__Bacteria;p__Atribacterota;c__Atribacteria;o__Atribacterales;f__Atribacteraceae;g__Atribacter	95.0	98.98	98.98	0.72	0.72	2	-
GCA_002069605.1	s__Atribacter sp002069605	88.2752	646	1033	d__Bacteria;p__Atribacterota;c__Atribacteria;o__Atribacterales;f__Atribacteraceae;g__Atribacter	95.0	99.08	99.08	0.83	0.83	2	-
GCA_012517635.1	s__Atribacter sp012517635	84.7539	504	1033	d__Bacteria;p__Atribacterota;c__Atribacteria;o__Atribacterales;f__Atribacteraceae;g__Atribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517485.1	s__Atribacter sp012517485	83.0232	433	1033	d__Bacteria;p__Atribacterota;c__Atribacteria;o__Atribacterales;f__Atribacteraceae;g__Atribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:26,710] [INFO] GTDB search result was written to GCF_015775515.1_ASM1577551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:26,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:26,713] [INFO] DFAST_QC result json was written to GCF_015775515.1_ASM1577551v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:26,714] [INFO] DFAST_QC completed!
[2024-01-24 14:16:26,714] [INFO] Total running time: 0h0m53s