[2023-06-18 12:03:58,453] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:03:58,457] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:03:58,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference
[2023-06-18 12:03:59,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:03:59,739] [INFO] Task started: Prodigal
[2023-06-18 12:03:59,739] [INFO] Running command: gunzip -c /var/lib/cwl/stge03b086e-08bb-4863-84bf-95e38a9f662f/GCA_018052995.1_ASM1805299v1_genomic.fna.gz | prodigal -d GCA_018052995.1_ASM1805299v1_genomic.fna/cds.fna -a GCA_018052995.1_ASM1805299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:04:03,616] [INFO] Task succeeded: Prodigal
[2023-06-18 12:04:03,616] [INFO] Task started: HMMsearch
[2023-06-18 12:04:03,616] [INFO] Running command: hmmsearch --tblout GCA_018052995.1_ASM1805299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/reference_markers.hmm GCA_018052995.1_ASM1805299v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:04:03,864] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:04:03,865] [INFO] Found 6/6 markers.
[2023-06-18 12:04:03,890] [INFO] Query marker FASTA was written to GCA_018052995.1_ASM1805299v1_genomic.fna/markers.fasta
[2023-06-18 12:04:03,890] [INFO] Task started: Blastn
[2023-06-18 12:04:03,891] [INFO] Running command: blastn -query GCA_018052995.1_ASM1805299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/reference_markers.fasta -out GCA_018052995.1_ASM1805299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:04:04,471] [INFO] Task succeeded: Blastn
[2023-06-18 12:04:04,478] [INFO] Selected 18 target genomes.
[2023-06-18 12:04:04,479] [INFO] Target genome list was writen to GCA_018052995.1_ASM1805299v1_genomic.fna/target_genomes.txt
[2023-06-18 12:04:04,483] [INFO] Task started: fastANI
[2023-06-18 12:04:04,483] [INFO] Running command: fastANI --query /var/lib/cwl/stge03b086e-08bb-4863-84bf-95e38a9f662f/GCA_018052995.1_ASM1805299v1_genomic.fna.gz --refList GCA_018052995.1_ASM1805299v1_genomic.fna/target_genomes.txt --output GCA_018052995.1_ASM1805299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:04:13,281] [INFO] Task succeeded: fastANI
[2023-06-18 12:04:13,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:04:13,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:04:13,283] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:04:13,284] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:04:13,284] [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
--------------------------------------------------------------------------------
[2023-06-18 12:04:13,286] [INFO] DFAST Taxonomy check result was written to GCA_018052995.1_ASM1805299v1_genomic.fna/tc_result.tsv
[2023-06-18 12:04:13,287] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:04:13,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:04:13,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/checkm_data
[2023-06-18 12:04:13,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:04:13,323] [INFO] Task started: CheckM
[2023-06-18 12:04:13,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018052995.1_ASM1805299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018052995.1_ASM1805299v1_genomic.fna/checkm_input GCA_018052995.1_ASM1805299v1_genomic.fna/checkm_result
[2023-06-18 12:04:32,504] [INFO] Task succeeded: CheckM
[2023-06-18 12:04:32,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:04:32,535] [INFO] ===== Completeness check finished =====
[2023-06-18 12:04:32,535] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:04:32,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018052995.1_ASM1805299v1_genomic.fna/markers.fasta)
[2023-06-18 12:04:32,536] [INFO] Task started: Blastn
[2023-06-18 12:04:32,536] [INFO] Running command: blastn -query GCA_018052995.1_ASM1805299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf546b5e-755f-4501-aa14-b29272fb943e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018052995.1_ASM1805299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:04:33,314] [INFO] Task succeeded: Blastn
[2023-06-18 12:04:33,320] [INFO] Selected 19 target genomes.
[2023-06-18 12:04:33,321] [INFO] Target genome list was writen to GCA_018052995.1_ASM1805299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:04:33,337] [INFO] Task started: fastANI
[2023-06-18 12:04:33,338] [INFO] Running command: fastANI --query /var/lib/cwl/stge03b086e-08bb-4863-84bf-95e38a9f662f/GCA_018052995.1_ASM1805299v1_genomic.fna.gz --refList GCA_018052995.1_ASM1805299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018052995.1_ASM1805299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:04:41,564] [INFO] Task succeeded: fastANI
[2023-06-18 12:04:41,571] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:04:41,571] [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_018052995.1	s__DTOV01 sp018052995	100.0	606	608	d__Bacteria;p__Desulfobacterota_G;c__Syntrophorhabdia;o__Syntrophorhabdales;f__Syntrophorhabdaceae;g__DTOV01	95.0	99.57	99.57	0.93	0.93	2	conclusive
GCA_011388995.1	s__DTOV01 sp011388995	77.1639	148	608	d__Bacteria;p__Desulfobacterota_G;c__Syntrophorhabdia;o__Syntrophorhabdales;f__Syntrophorhabdaceae;g__DTOV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:04:41,573] [INFO] GTDB search result was written to GCA_018052995.1_ASM1805299v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:04:41,574] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:04:41,576] [INFO] DFAST_QC result json was written to GCA_018052995.1_ASM1805299v1_genomic.fna/dqc_result.json
[2023-06-18 12:04:41,576] [INFO] DFAST_QC completed!
[2023-06-18 12:04:41,576] [INFO] Total running time: 0h0m43s