[2023-06-19 13:53:51,298] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:53:51,300] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:53:51,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference
[2023-06-19 13:53:53,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:53:53,210] [INFO] Task started: Prodigal
[2023-06-19 13:53:53,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg083d7c01-0811-4c38-a6ad-e9e40ea59ef7/GCA_013360445.1_ASM1336044v1_genomic.fna.gz | prodigal -d GCA_013360445.1_ASM1336044v1_genomic.fna/cds.fna -a GCA_013360445.1_ASM1336044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:08,263] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:08,263] [INFO] Task started: HMMsearch
[2023-06-19 13:54:08,263] [INFO] Running command: hmmsearch --tblout GCA_013360445.1_ASM1336044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/reference_markers.hmm GCA_013360445.1_ASM1336044v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:08,497] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:08,498] [INFO] Found 6/6 markers.
[2023-06-19 13:54:08,538] [INFO] Query marker FASTA was written to GCA_013360445.1_ASM1336044v1_genomic.fna/markers.fasta
[2023-06-19 13:54:08,538] [INFO] Task started: Blastn
[2023-06-19 13:54:08,538] [INFO] Running command: blastn -query GCA_013360445.1_ASM1336044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/reference_markers.fasta -out GCA_013360445.1_ASM1336044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:09,118] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:09,122] [INFO] Selected 20 target genomes.
[2023-06-19 13:54:09,122] [INFO] Target genome list was writen to GCA_013360445.1_ASM1336044v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:09,124] [INFO] Task started: fastANI
[2023-06-19 13:54:09,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg083d7c01-0811-4c38-a6ad-e9e40ea59ef7/GCA_013360445.1_ASM1336044v1_genomic.fna.gz --refList GCA_013360445.1_ASM1336044v1_genomic.fna/target_genomes.txt --output GCA_013360445.1_ASM1336044v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:22,027] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:22,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:22,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:22,029] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:22,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:54:22,029] [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
--------------------------------------------------------------------------------
[2023-06-19 13:54:22,032] [INFO] DFAST Taxonomy check result was written to GCA_013360445.1_ASM1336044v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:22,033] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:22,033] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:22,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/checkm_data
[2023-06-19 13:54:22,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:22,088] [INFO] Task started: CheckM
[2023-06-19 13:54:22,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013360445.1_ASM1336044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013360445.1_ASM1336044v1_genomic.fna/checkm_input GCA_013360445.1_ASM1336044v1_genomic.fna/checkm_result
[2023-06-19 13:55:06,166] [INFO] Task succeeded: CheckM
[2023-06-19 13:55:06,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:55:06,224] [INFO] ===== Completeness check finished =====
[2023-06-19 13:55:06,225] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:55:06,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013360445.1_ASM1336044v1_genomic.fna/markers.fasta)
[2023-06-19 13:55:06,225] [INFO] Task started: Blastn
[2023-06-19 13:55:06,226] [INFO] Running command: blastn -query GCA_013360445.1_ASM1336044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3e7829-ec30-4637-890a-727e0cef4cbe/dqc_reference/reference_markers_gtdb.fasta -out GCA_013360445.1_ASM1336044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:07,102] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:07,106] [INFO] Selected 21 target genomes.
[2023-06-19 13:55:07,106] [INFO] Target genome list was writen to GCA_013360445.1_ASM1336044v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:07,135] [INFO] Task started: fastANI
[2023-06-19 13:55:07,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg083d7c01-0811-4c38-a6ad-e9e40ea59ef7/GCA_013360445.1_ASM1336044v1_genomic.fna.gz --refList GCA_013360445.1_ASM1336044v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013360445.1_ASM1336044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:20,628] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:20,633] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:20,633] [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_013360445.1	s__JABWBP01 sp013360445	100.0	1914	1923	d__Bacteria;p__Calditrichota;c__Calditrichia;o__RBG-13-44-9;f__J042;g__JABWBP01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011526015.1	s__JABWBP01 sp011526015	90.6615	1121	1923	d__Bacteria;p__Calditrichota;c__Calditrichia;o__RBG-13-44-9;f__J042;g__JABWBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696445.1	s__J042 sp003696445	75.8777	51	1923	d__Bacteria;p__Calditrichota;c__Calditrichia;o__RBG-13-44-9;f__J042;g__J042	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:20,635] [INFO] GTDB search result was written to GCA_013360445.1_ASM1336044v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:20,636] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:20,639] [INFO] DFAST_QC result json was written to GCA_013360445.1_ASM1336044v1_genomic.fna/dqc_result.json
[2023-06-19 13:55:20,639] [INFO] DFAST_QC completed!
[2023-06-19 13:55:20,639] [INFO] Total running time: 0h1m29s