[2023-06-28 11:24:15,747] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:24:15,749] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:24:15,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference
[2023-06-28 11:24:16,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:24:16,982] [INFO] Task started: Prodigal
[2023-06-28 11:24:16,983] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7c79d81-2f1d-4fb4-b83f-fae140b32b25/GCA_020723985.1_ASM2072398v1_genomic.fna.gz | prodigal -d GCA_020723985.1_ASM2072398v1_genomic.fna/cds.fna -a GCA_020723985.1_ASM2072398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:24:20,875] [INFO] Task succeeded: Prodigal
[2023-06-28 11:24:20,875] [INFO] Task started: HMMsearch
[2023-06-28 11:24:20,876] [INFO] Running command: hmmsearch --tblout GCA_020723985.1_ASM2072398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/reference_markers.hmm GCA_020723985.1_ASM2072398v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:24:21,108] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:24:21,110] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7c79d81-2f1d-4fb4-b83f-fae140b32b25/GCA_020723985.1_ASM2072398v1_genomic.fna.gz]
[2023-06-28 11:24:21,134] [INFO] Query marker FASTA was written to GCA_020723985.1_ASM2072398v1_genomic.fna/markers.fasta
[2023-06-28 11:24:21,135] [INFO] Task started: Blastn
[2023-06-28 11:24:21,135] [INFO] Running command: blastn -query GCA_020723985.1_ASM2072398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/reference_markers.fasta -out GCA_020723985.1_ASM2072398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:24:21,730] [INFO] Task succeeded: Blastn
[2023-06-28 11:24:21,734] [INFO] Selected 20 target genomes.
[2023-06-28 11:24:21,734] [INFO] Target genome list was writen to GCA_020723985.1_ASM2072398v1_genomic.fna/target_genomes.txt
[2023-06-28 11:24:21,742] [INFO] Task started: fastANI
[2023-06-28 11:24:21,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7c79d81-2f1d-4fb4-b83f-fae140b32b25/GCA_020723985.1_ASM2072398v1_genomic.fna.gz --refList GCA_020723985.1_ASM2072398v1_genomic.fna/target_genomes.txt --output GCA_020723985.1_ASM2072398v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:24:33,963] [INFO] Task succeeded: fastANI
[2023-06-28 11:24:33,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:24:33,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:24:33,965] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:24:33,965] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:24:33,965] [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
--------------------------------------------------------------------------------
[2023-06-28 11:24:33,967] [INFO] DFAST Taxonomy check result was written to GCA_020723985.1_ASM2072398v1_genomic.fna/tc_result.tsv
[2023-06-28 11:24:33,968] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:24:33,968] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:24:33,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/checkm_data
[2023-06-28 11:24:33,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:24:34,005] [INFO] Task started: CheckM
[2023-06-28 11:24:34,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020723985.1_ASM2072398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020723985.1_ASM2072398v1_genomic.fna/checkm_input GCA_020723985.1_ASM2072398v1_genomic.fna/checkm_result
[2023-06-28 11:24:53,796] [INFO] Task succeeded: CheckM
[2023-06-28 11:24:53,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:24:53,824] [INFO] ===== Completeness check finished =====
[2023-06-28 11:24:53,824] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:24:53,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020723985.1_ASM2072398v1_genomic.fna/markers.fasta)
[2023-06-28 11:24:53,825] [INFO] Task started: Blastn
[2023-06-28 11:24:53,825] [INFO] Running command: blastn -query GCA_020723985.1_ASM2072398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27e0c681-7289-49a8-b03c-d14140e95c50/dqc_reference/reference_markers_gtdb.fasta -out GCA_020723985.1_ASM2072398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:24:54,582] [INFO] Task succeeded: Blastn
[2023-06-28 11:24:54,588] [INFO] Selected 23 target genomes.
[2023-06-28 11:24:54,588] [INFO] Target genome list was writen to GCA_020723985.1_ASM2072398v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:24:54,638] [INFO] Task started: fastANI
[2023-06-28 11:24:54,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7c79d81-2f1d-4fb4-b83f-fae140b32b25/GCA_020723985.1_ASM2072398v1_genomic.fna.gz --refList GCA_020723985.1_ASM2072398v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020723985.1_ASM2072398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:25:06,615] [INFO] Task succeeded: fastANI
[2023-06-28 11:25:06,622] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 11:25:06,623] [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_016873845.1	s__JAHJVF01 sp016873845	76.9693	90	651	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ch128b;f__Ch128b;g__JAHJVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011047755.1	s__Ch128b sp011047755	75.6941	56	651	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ch128b;f__Ch128b;g__Ch128b	95.0	99.97	99.95	0.97	0.97	3	-
GCA_013177855.1	s__Ch128b sp013177855	75.6779	54	651	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ch128b;f__Ch128b;g__Ch128b	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 11:25:06,626] [INFO] GTDB search result was written to GCA_020723985.1_ASM2072398v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:25:06,627] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:25:06,630] [INFO] DFAST_QC result json was written to GCA_020723985.1_ASM2072398v1_genomic.fna/dqc_result.json
[2023-06-28 11:25:06,630] [INFO] DFAST_QC completed!
[2023-06-28 11:25:06,630] [INFO] Total running time: 0h0m51s