[2023-06-04 23:12:17,423] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:12:17,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:12:17,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference
[2023-06-04 23:12:18,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:12:18,926] [INFO] Task started: Prodigal
[2023-06-04 23:12:18,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgd858be28-eb9e-407d-b8b6-200f1af950ed/GCA_934489955.1_ERR7737968_bin.70_genomic.fna.gz | prodigal -d GCA_934489955.1_ERR7737968_bin.70_genomic.fna/cds.fna -a GCA_934489955.1_ERR7737968_bin.70_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:12:24,983] [INFO] Task succeeded: Prodigal
[2023-06-04 23:12:24,984] [INFO] Task started: HMMsearch
[2023-06-04 23:12:24,984] [INFO] Running command: hmmsearch --tblout GCA_934489955.1_ERR7737968_bin.70_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/reference_markers.hmm GCA_934489955.1_ERR7737968_bin.70_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:12:25,251] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:12:25,253] [INFO] Found 6/6 markers.
[2023-06-04 23:12:25,280] [INFO] Query marker FASTA was written to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/markers.fasta
[2023-06-04 23:12:25,281] [INFO] Task started: Blastn
[2023-06-04 23:12:25,283] [INFO] Running command: blastn -query GCA_934489955.1_ERR7737968_bin.70_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/reference_markers.fasta -out GCA_934489955.1_ERR7737968_bin.70_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:25,983] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:25,993] [INFO] Selected 26 target genomes.
[2023-06-04 23:12:25,994] [INFO] Target genome list was writen to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/target_genomes.txt
[2023-06-04 23:12:26,035] [INFO] Task started: fastANI
[2023-06-04 23:12:26,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgd858be28-eb9e-407d-b8b6-200f1af950ed/GCA_934489955.1_ERR7737968_bin.70_genomic.fna.gz --refList GCA_934489955.1_ERR7737968_bin.70_genomic.fna/target_genomes.txt --output GCA_934489955.1_ERR7737968_bin.70_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:12:42,425] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:42,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:12:42,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:12:42,429] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:12:42,429] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:12:42,429] [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
--------------------------------------------------------------------------------
[2023-06-04 23:12:42,432] [INFO] DFAST Taxonomy check result was written to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/tc_result.tsv
[2023-06-04 23:12:42,433] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:12:42,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:12:42,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/checkm_data
[2023-06-04 23:12:42,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:12:42,464] [INFO] Task started: CheckM
[2023-06-04 23:12:42,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934489955.1_ERR7737968_bin.70_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934489955.1_ERR7737968_bin.70_genomic.fna/checkm_input GCA_934489955.1_ERR7737968_bin.70_genomic.fna/checkm_result
[2023-06-04 23:13:06,705] [INFO] Task succeeded: CheckM
[2023-06-04 23:13:06,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:13:06,726] [INFO] ===== Completeness check finished =====
[2023-06-04 23:13:06,726] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:13:06,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934489955.1_ERR7737968_bin.70_genomic.fna/markers.fasta)
[2023-06-04 23:13:06,727] [INFO] Task started: Blastn
[2023-06-04 23:13:06,727] [INFO] Running command: blastn -query GCA_934489955.1_ERR7737968_bin.70_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd620a0-46a4-44d9-830b-4fdbe3207783/dqc_reference/reference_markers_gtdb.fasta -out GCA_934489955.1_ERR7737968_bin.70_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:13:07,482] [INFO] Task succeeded: Blastn
[2023-06-04 23:13:07,487] [INFO] Selected 38 target genomes.
[2023-06-04 23:13:07,487] [INFO] Target genome list was writen to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:13:07,526] [INFO] Task started: fastANI
[2023-06-04 23:13:07,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgd858be28-eb9e-407d-b8b6-200f1af950ed/GCA_934489955.1_ERR7737968_bin.70_genomic.fna.gz --refList GCA_934489955.1_ERR7737968_bin.70_genomic.fna/target_genomes_gtdb.txt --output GCA_934489955.1_ERR7737968_bin.70_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:13:21,041] [INFO] Task succeeded: fastANI
[2023-06-04 23:13:21,047] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 23:13:21,048] [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_010206265.1	s__CAG-41 sp010206265	76.5965	65	796	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	97.79	97.79	0.83	0.83	2	-
GCA_017443895.1	s__12844 sp017443895	75.9945	52	796	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__12844	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:13:21,050] [INFO] GTDB search result was written to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/result_gtdb.tsv
[2023-06-04 23:13:21,051] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:13:21,054] [INFO] DFAST_QC result json was written to GCA_934489955.1_ERR7737968_bin.70_genomic.fna/dqc_result.json
[2023-06-04 23:13:21,054] [INFO] DFAST_QC completed!
[2023-06-04 23:13:21,054] [INFO] Total running time: 0h1m4s