[2023-06-27 08:37:21,924] [INFO] DFAST_QC pipeline started.
[2023-06-27 08:37:21,927] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 08:37:21,927] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference
[2023-06-27 08:37:23,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 08:37:23,251] [INFO] Task started: Prodigal
[2023-06-27 08:37:23,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg07a3a290-0767-47bb-8bde-0b6343017436/GCA_026706265.1_ASM2670626v1_genomic.fna.gz | prodigal -d GCA_026706265.1_ASM2670626v1_genomic.fna/cds.fna -a GCA_026706265.1_ASM2670626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 08:37:30,026] [INFO] Task succeeded: Prodigal
[2023-06-27 08:37:30,027] [INFO] Task started: HMMsearch
[2023-06-27 08:37:30,027] [INFO] Running command: hmmsearch --tblout GCA_026706265.1_ASM2670626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/reference_markers.hmm GCA_026706265.1_ASM2670626v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 08:37:30,247] [INFO] Task succeeded: HMMsearch
[2023-06-27 08:37:30,249] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg07a3a290-0767-47bb-8bde-0b6343017436/GCA_026706265.1_ASM2670626v1_genomic.fna.gz]
[2023-06-27 08:37:30,315] [INFO] Query marker FASTA was written to GCA_026706265.1_ASM2670626v1_genomic.fna/markers.fasta
[2023-06-27 08:37:30,316] [INFO] Task started: Blastn
[2023-06-27 08:37:30,316] [INFO] Running command: blastn -query GCA_026706265.1_ASM2670626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/reference_markers.fasta -out GCA_026706265.1_ASM2670626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:37:30,876] [INFO] Task succeeded: Blastn
[2023-06-27 08:37:30,881] [INFO] Selected 10 target genomes.
[2023-06-27 08:37:30,881] [INFO] Target genome list was writen to GCA_026706265.1_ASM2670626v1_genomic.fna/target_genomes.txt
[2023-06-27 08:37:30,883] [INFO] Task started: fastANI
[2023-06-27 08:37:30,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a3a290-0767-47bb-8bde-0b6343017436/GCA_026706265.1_ASM2670626v1_genomic.fna.gz --refList GCA_026706265.1_ASM2670626v1_genomic.fna/target_genomes.txt --output GCA_026706265.1_ASM2670626v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 08:37:38,133] [INFO] Task succeeded: fastANI
[2023-06-27 08:37:38,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 08:37:38,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 08:37:38,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 08:37:38,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 08:37:38,152] [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
--------------------------------------------------------------------------------
[2023-06-27 08:37:38,158] [INFO] DFAST Taxonomy check result was written to GCA_026706265.1_ASM2670626v1_genomic.fna/tc_result.tsv
[2023-06-27 08:37:38,159] [INFO] ===== Taxonomy check completed =====
[2023-06-27 08:37:38,160] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 08:37:38,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/checkm_data
[2023-06-27 08:37:38,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 08:37:38,197] [INFO] Task started: CheckM
[2023-06-27 08:37:38,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706265.1_ASM2670626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706265.1_ASM2670626v1_genomic.fna/checkm_input GCA_026706265.1_ASM2670626v1_genomic.fna/checkm_result
[2023-06-27 08:38:03,339] [INFO] Task succeeded: CheckM
[2023-06-27 08:38:03,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 08:38:03,365] [INFO] ===== Completeness check finished =====
[2023-06-27 08:38:03,366] [INFO] ===== Start GTDB Search =====
[2023-06-27 08:38:03,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706265.1_ASM2670626v1_genomic.fna/markers.fasta)
[2023-06-27 08:38:03,367] [INFO] Task started: Blastn
[2023-06-27 08:38:03,367] [INFO] Running command: blastn -query GCA_026706265.1_ASM2670626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6eaa456-6f27-4d82-860c-7f48bbf0fe8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706265.1_ASM2670626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:38:04,059] [INFO] Task succeeded: Blastn
[2023-06-27 08:38:04,064] [INFO] Selected 10 target genomes.
[2023-06-27 08:38:04,064] [INFO] Target genome list was writen to GCA_026706265.1_ASM2670626v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 08:38:04,074] [INFO] Task started: fastANI
[2023-06-27 08:38:04,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a3a290-0767-47bb-8bde-0b6343017436/GCA_026706265.1_ASM2670626v1_genomic.fna.gz --refList GCA_026706265.1_ASM2670626v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706265.1_ASM2670626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 08:38:10,855] [INFO] Task succeeded: fastANI
[2023-06-27 08:38:10,862] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 08:38:10,862] [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_009839425.1	s__UBA11872 sp009839425	86.9934	418	721	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523785.1	s__UBA11872 sp011523785	85.8781	474	721	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 08:38:10,865] [INFO] GTDB search result was written to GCA_026706265.1_ASM2670626v1_genomic.fna/result_gtdb.tsv
[2023-06-27 08:38:10,866] [INFO] ===== GTDB Search completed =====
[2023-06-27 08:38:10,869] [INFO] DFAST_QC result json was written to GCA_026706265.1_ASM2670626v1_genomic.fna/dqc_result.json
[2023-06-27 08:38:10,869] [INFO] DFAST_QC completed!
[2023-06-27 08:38:10,869] [INFO] Total running time: 0h0m49s