[2023-06-05 04:13:55,148] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:13:55,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:13:55,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference
[2023-06-05 04:13:56,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:13:56,320] [INFO] Task started: Prodigal
[2023-06-05 04:13:56,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d46bd4b-073c-428b-a3de-d581e234bb22/GCA_902522535.1_AG-895-B18_genomic.fna.gz | prodigal -d GCA_902522535.1_AG-895-B18_genomic.fna/cds.fna -a GCA_902522535.1_AG-895-B18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:13:57,530] [INFO] Task succeeded: Prodigal
[2023-06-05 04:13:57,531] [INFO] Task started: HMMsearch
[2023-06-05 04:13:57,531] [INFO] Running command: hmmsearch --tblout GCA_902522535.1_AG-895-B18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/reference_markers.hmm GCA_902522535.1_AG-895-B18_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:13:57,733] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:13:57,735] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8d46bd4b-073c-428b-a3de-d581e234bb22/GCA_902522535.1_AG-895-B18_genomic.fna.gz]
[2023-06-05 04:13:57,750] [INFO] Query marker FASTA was written to GCA_902522535.1_AG-895-B18_genomic.fna/markers.fasta
[2023-06-05 04:13:57,751] [INFO] Task started: Blastn
[2023-06-05 04:13:57,751] [INFO] Running command: blastn -query GCA_902522535.1_AG-895-B18_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/reference_markers.fasta -out GCA_902522535.1_AG-895-B18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:13:58,253] [INFO] Task succeeded: Blastn
[2023-06-05 04:13:58,311] [INFO] Selected 2 target genomes.
[2023-06-05 04:13:58,312] [INFO] Target genome list was writen to GCA_902522535.1_AG-895-B18_genomic.fna/target_genomes.txt
[2023-06-05 04:13:58,314] [INFO] Task started: fastANI
[2023-06-05 04:13:58,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d46bd4b-073c-428b-a3de-d581e234bb22/GCA_902522535.1_AG-895-B18_genomic.fna.gz --refList GCA_902522535.1_AG-895-B18_genomic.fna/target_genomes.txt --output GCA_902522535.1_AG-895-B18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:13:58,940] [INFO] Task succeeded: fastANI
[2023-06-05 04:13:58,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:13:58,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:13:58,945] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:13:58,946] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:13:58,946] [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 04:13:58,948] [INFO] DFAST Taxonomy check result was written to GCA_902522535.1_AG-895-B18_genomic.fna/tc_result.tsv
[2023-06-05 04:13:58,949] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:13:58,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:13:58,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/checkm_data
[2023-06-05 04:13:58,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:13:58,968] [INFO] Task started: CheckM
[2023-06-05 04:13:58,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902522535.1_AG-895-B18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902522535.1_AG-895-B18_genomic.fna/checkm_input GCA_902522535.1_AG-895-B18_genomic.fna/checkm_result
[2023-06-05 04:14:10,816] [INFO] Task succeeded: CheckM
[2023-06-05 04:14:10,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:14:10,838] [INFO] ===== Completeness check finished =====
[2023-06-05 04:14:10,839] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:14:10,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902522535.1_AG-895-B18_genomic.fna/markers.fasta)
[2023-06-05 04:14:10,839] [INFO] Task started: Blastn
[2023-06-05 04:14:10,839] [INFO] Running command: blastn -query GCA_902522535.1_AG-895-B18_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6c45a52-e885-49e2-a1fb-5fae6cfec8e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902522535.1_AG-895-B18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:11,395] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:11,490] [INFO] Selected 8 target genomes.
[2023-06-05 04:14:11,491] [INFO] Target genome list was writen to GCA_902522535.1_AG-895-B18_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:14:11,494] [INFO] Task started: fastANI
[2023-06-05 04:14:11,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d46bd4b-073c-428b-a3de-d581e234bb22/GCA_902522535.1_AG-895-B18_genomic.fna.gz --refList GCA_902522535.1_AG-895-B18_genomic.fna/target_genomes_gtdb.txt --output GCA_902522535.1_AG-895-B18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:14:13,613] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:13,626] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 04:14:13,626] [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_902584635.1	s__CACIJG01 sp902584635	88.0475	131	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703515.1	s__CACIJG01 sp002703515	88.0456	67	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619165.1	s__CACIJG01 sp902619165	88.0173	133	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556405.1	s__CACIJG01 sp902556405	86.5617	125	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574225.1	s__CACIJG01 sp902574225	86.4206	134	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531755.1	s__CACIJG01 sp902531755	84.975	95	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331935.1	s__CACIJG01 sp003331935	80.9486	103	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524845.1	s__CACIJG01 sp902524845	80.8269	103	192	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:14:13,628] [INFO] GTDB search result was written to GCA_902522535.1_AG-895-B18_genomic.fna/result_gtdb.tsv
[2023-06-05 04:14:13,629] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:14:13,631] [INFO] DFAST_QC result json was written to GCA_902522535.1_AG-895-B18_genomic.fna/dqc_result.json
[2023-06-05 04:14:13,632] [INFO] DFAST_QC completed!
[2023-06-05 04:14:13,632] [INFO] Total running time: 0h0m18s