[2023-06-05 04:14:00,255] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:14:00,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:14:00,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference
[2023-06-05 04:14:01,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:14:01,481] [INFO] Task started: Prodigal
[2023-06-05 04:14:01,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd9e9831-5392-4eb2-9da1-4ef585f482a8/GCA_004562705.1_ASM456270v1_genomic.fna.gz | prodigal -d GCA_004562705.1_ASM456270v1_genomic.fna/cds.fna -a GCA_004562705.1_ASM456270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:14:04,419] [INFO] Task succeeded: Prodigal
[2023-06-05 04:14:04,420] [INFO] Task started: HMMsearch
[2023-06-05 04:14:04,420] [INFO] Running command: hmmsearch --tblout GCA_004562705.1_ASM456270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/reference_markers.hmm GCA_004562705.1_ASM456270v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:14:04,706] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:14:04,709] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcd9e9831-5392-4eb2-9da1-4ef585f482a8/GCA_004562705.1_ASM456270v1_genomic.fna.gz]
[2023-06-05 04:14:04,738] [INFO] Query marker FASTA was written to GCA_004562705.1_ASM456270v1_genomic.fna/markers.fasta
[2023-06-05 04:14:04,739] [INFO] Task started: Blastn
[2023-06-05 04:14:04,739] [INFO] Running command: blastn -query GCA_004562705.1_ASM456270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/reference_markers.fasta -out GCA_004562705.1_ASM456270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:05,533] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:05,538] [INFO] Selected 13 target genomes.
[2023-06-05 04:14:05,538] [INFO] Target genome list was writen to GCA_004562705.1_ASM456270v1_genomic.fna/target_genomes.txt
[2023-06-05 04:14:05,543] [INFO] Task started: fastANI
[2023-06-05 04:14:05,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd9e9831-5392-4eb2-9da1-4ef585f482a8/GCA_004562705.1_ASM456270v1_genomic.fna.gz --refList GCA_004562705.1_ASM456270v1_genomic.fna/target_genomes.txt --output GCA_004562705.1_ASM456270v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:14:11,372] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:11,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:14:11,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:14:11,377] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:14:11,378] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:14:11,378] [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
--------------------------------------------------------------------------------
[2023-06-05 04:14:11,509] [INFO] DFAST Taxonomy check result was written to GCA_004562705.1_ASM456270v1_genomic.fna/tc_result.tsv
[2023-06-05 04:14:11,509] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:14:11,510] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:14:11,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/checkm_data
[2023-06-05 04:14:11,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:14:11,530] [INFO] Task started: CheckM
[2023-06-05 04:14:11,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004562705.1_ASM456270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004562705.1_ASM456270v1_genomic.fna/checkm_input GCA_004562705.1_ASM456270v1_genomic.fna/checkm_result
[2023-06-05 04:14:28,481] [INFO] Task succeeded: CheckM
[2023-06-05 04:14:28,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:14:28,507] [INFO] ===== Completeness check finished =====
[2023-06-05 04:14:28,508] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:14:28,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004562705.1_ASM456270v1_genomic.fna/markers.fasta)
[2023-06-05 04:14:28,508] [INFO] Task started: Blastn
[2023-06-05 04:14:28,508] [INFO] Running command: blastn -query GCA_004562705.1_ASM456270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcfec7bb-30d2-4580-8bb8-e146fb5c87d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_004562705.1_ASM456270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:29,458] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:29,461] [INFO] Selected 18 target genomes.
[2023-06-05 04:14:29,462] [INFO] Target genome list was writen to GCA_004562705.1_ASM456270v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:14:29,471] [INFO] Task started: fastANI
[2023-06-05 04:14:29,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd9e9831-5392-4eb2-9da1-4ef585f482a8/GCA_004562705.1_ASM456270v1_genomic.fna.gz --refList GCA_004562705.1_ASM456270v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004562705.1_ASM456270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:14:35,868] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:35,873] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:14:35,873] [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_001940855.1	s__Phil1 sp001940855	97.1411	274	280	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Phil1	95.0	97.09	96.81	0.92	0.85	14	conclusive
GCA_004558525.1	s__Phil1 sp004558525	79.5829	156	280	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Phil1	95.0	98.96	98.54	0.91	0.86	6	-
--------------------------------------------------------------------------------
[2023-06-05 04:14:35,875] [INFO] GTDB search result was written to GCA_004562705.1_ASM456270v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:14:35,876] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:14:35,878] [INFO] DFAST_QC result json was written to GCA_004562705.1_ASM456270v1_genomic.fna/dqc_result.json
[2023-06-05 04:14:35,878] [INFO] DFAST_QC completed!
[2023-06-05 04:14:35,879] [INFO] Total running time: 0h0m36s