[2023-06-16 20:50:29,581] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:50:29,593] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:50:29,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference
[2023-06-16 20:50:31,328] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:50:31,328] [INFO] Task started: Prodigal
[2023-06-16 20:50:31,329] [INFO] Running command: gunzip -c /var/lib/cwl/stg950edc6a-3274-4200-a1ee-c492085ed227/GCA_009993265.1_ASM999326v1_genomic.fna.gz | prodigal -d GCA_009993265.1_ASM999326v1_genomic.fna/cds.fna -a GCA_009993265.1_ASM999326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:50:34,461] [INFO] Task succeeded: Prodigal
[2023-06-16 20:50:34,461] [INFO] Task started: HMMsearch
[2023-06-16 20:50:34,462] [INFO] Running command: hmmsearch --tblout GCA_009993265.1_ASM999326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/reference_markers.hmm GCA_009993265.1_ASM999326v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:50:34,677] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:50:34,678] [INFO] Found 6/6 markers.
[2023-06-16 20:50:34,971] [INFO] Query marker FASTA was written to GCA_009993265.1_ASM999326v1_genomic.fna/markers.fasta
[2023-06-16 20:50:34,971] [INFO] Task started: Blastn
[2023-06-16 20:50:34,971] [INFO] Running command: blastn -query GCA_009993265.1_ASM999326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/reference_markers.fasta -out GCA_009993265.1_ASM999326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:50:35,497] [INFO] Task succeeded: Blastn
[2023-06-16 20:50:35,500] [INFO] Selected 20 target genomes.
[2023-06-16 20:50:35,501] [INFO] Target genome list was writen to GCA_009993265.1_ASM999326v1_genomic.fna/target_genomes.txt
[2023-06-16 20:50:35,504] [INFO] Task started: fastANI
[2023-06-16 20:50:35,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg950edc6a-3274-4200-a1ee-c492085ed227/GCA_009993265.1_ASM999326v1_genomic.fna.gz --refList GCA_009993265.1_ASM999326v1_genomic.fna/target_genomes.txt --output GCA_009993265.1_ASM999326v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:50:45,626] [INFO] Task succeeded: fastANI
[2023-06-16 20:50:45,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:50:45,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:50:45,628] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:50:45,628] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 20:50:45,628] [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
--------------------------------------------------------------------------------
[2023-06-16 20:50:45,630] [INFO] DFAST Taxonomy check result was written to GCA_009993265.1_ASM999326v1_genomic.fna/tc_result.tsv
[2023-06-16 20:50:45,630] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:50:45,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:50:45,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/checkm_data
[2023-06-16 20:50:45,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:50:45,654] [INFO] Task started: CheckM
[2023-06-16 20:50:45,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009993265.1_ASM999326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009993265.1_ASM999326v1_genomic.fna/checkm_input GCA_009993265.1_ASM999326v1_genomic.fna/checkm_result
[2023-06-16 20:51:01,687] [INFO] Task succeeded: CheckM
[2023-06-16 20:51:01,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:51:01,720] [INFO] ===== Completeness check finished =====
[2023-06-16 20:51:01,720] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:51:01,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009993265.1_ASM999326v1_genomic.fna/markers.fasta)
[2023-06-16 20:51:01,721] [INFO] Task started: Blastn
[2023-06-16 20:51:01,721] [INFO] Running command: blastn -query GCA_009993265.1_ASM999326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c50711-fed3-42be-974e-0e380926a090/dqc_reference/reference_markers_gtdb.fasta -out GCA_009993265.1_ASM999326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:51:02,483] [INFO] Task succeeded: Blastn
[2023-06-16 20:51:02,487] [INFO] Selected 7 target genomes.
[2023-06-16 20:51:02,487] [INFO] Target genome list was writen to GCA_009993265.1_ASM999326v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:51:02,491] [INFO] Task started: fastANI
[2023-06-16 20:51:02,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg950edc6a-3274-4200-a1ee-c492085ed227/GCA_009993265.1_ASM999326v1_genomic.fna.gz --refList GCA_009993265.1_ASM999326v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009993265.1_ASM999326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:51:05,402] [INFO] Task succeeded: fastANI
[2023-06-16 20:51:05,407] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:51:05,408] [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_001871685.1	s__UBA1546 sp001871685	99.6073	441	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	99.61	99.53	0.82	0.80	9	conclusive
GCA_016195565.1	s__UBA1546 sp016195565	87.2842	410	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001805105.1	s__UBA1546 sp001805105	87.1329	409	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	99.83	99.61	0.98	0.98	5	-
GCA_018896985.1	s__UBA1546 sp018896985	85.9743	259	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003535475.1	s__UBA1546 sp003535475	85.6963	238	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599795.1	s__UBA1546 sp003599795	84.328	226	521	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__UBA1546;g__UBA1546	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:51:05,409] [INFO] GTDB search result was written to GCA_009993265.1_ASM999326v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:51:05,410] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:51:05,412] [INFO] DFAST_QC result json was written to GCA_009993265.1_ASM999326v1_genomic.fna/dqc_result.json
[2023-06-16 20:51:05,412] [INFO] DFAST_QC completed!
[2023-06-16 20:51:05,412] [INFO] Total running time: 0h0m36s