[2023-06-07 19:05:01,825] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:05:01,828] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:05:01,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference
[2023-06-07 19:05:03,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:05:03,460] [INFO] Task started: Prodigal
[2023-06-07 19:05:03,461] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe7cb62c-0031-44a6-8b6d-37aac3655ccc/GCA_902614945.1_AG-919-D04_genomic.fna.gz | prodigal -d GCA_902614945.1_AG-919-D04_genomic.fna/cds.fna -a GCA_902614945.1_AG-919-D04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:05:05,951] [INFO] Task succeeded: Prodigal
[2023-06-07 19:05:05,952] [INFO] Task started: HMMsearch
[2023-06-07 19:05:05,952] [INFO] Running command: hmmsearch --tblout GCA_902614945.1_AG-919-D04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/reference_markers.hmm GCA_902614945.1_AG-919-D04_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:05:06,182] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:05:06,184] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfe7cb62c-0031-44a6-8b6d-37aac3655ccc/GCA_902614945.1_AG-919-D04_genomic.fna.gz]
[2023-06-07 19:05:06,208] [INFO] Query marker FASTA was written to GCA_902614945.1_AG-919-D04_genomic.fna/markers.fasta
[2023-06-07 19:05:06,208] [INFO] Task started: Blastn
[2023-06-07 19:05:06,208] [INFO] Running command: blastn -query GCA_902614945.1_AG-919-D04_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/reference_markers.fasta -out GCA_902614945.1_AG-919-D04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:07,246] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:07,254] [INFO] Selected 15 target genomes.
[2023-06-07 19:05:07,255] [INFO] Target genome list was writen to GCA_902614945.1_AG-919-D04_genomic.fna/target_genomes.txt
[2023-06-07 19:05:07,281] [INFO] Task started: fastANI
[2023-06-07 19:05:07,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe7cb62c-0031-44a6-8b6d-37aac3655ccc/GCA_902614945.1_AG-919-D04_genomic.fna.gz --refList GCA_902614945.1_AG-919-D04_genomic.fna/target_genomes.txt --output GCA_902614945.1_AG-919-D04_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:05:13,670] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:13,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:05:13,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:05:13,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:05:13,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:05:13,674] [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
--------------------------------------------------------------------------------
[2023-06-07 19:05:13,676] [INFO] DFAST Taxonomy check result was written to GCA_902614945.1_AG-919-D04_genomic.fna/tc_result.tsv
[2023-06-07 19:05:13,677] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:05:13,678] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:05:13,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/checkm_data
[2023-06-07 19:05:13,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:05:13,708] [INFO] Task started: CheckM
[2023-06-07 19:05:13,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614945.1_AG-919-D04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614945.1_AG-919-D04_genomic.fna/checkm_input GCA_902614945.1_AG-919-D04_genomic.fna/checkm_result
[2023-06-07 19:05:29,739] [INFO] Task succeeded: CheckM
[2023-06-07 19:05:29,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:05:29,762] [INFO] ===== Completeness check finished =====
[2023-06-07 19:05:29,763] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:05:29,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614945.1_AG-919-D04_genomic.fna/markers.fasta)
[2023-06-07 19:05:29,763] [INFO] Task started: Blastn
[2023-06-07 19:05:29,764] [INFO] Running command: blastn -query GCA_902614945.1_AG-919-D04_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b8453cf-0dab-4c3b-98b5-71e652eb2a8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614945.1_AG-919-D04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:05:30,498] [INFO] Task succeeded: Blastn
[2023-06-07 19:05:30,504] [INFO] Selected 10 target genomes.
[2023-06-07 19:05:30,504] [INFO] Target genome list was writen to GCA_902614945.1_AG-919-D04_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:05:30,511] [INFO] Task started: fastANI
[2023-06-07 19:05:30,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe7cb62c-0031-44a6-8b6d-37aac3655ccc/GCA_902614945.1_AG-919-D04_genomic.fna.gz --refList GCA_902614945.1_AG-919-D04_genomic.fna/target_genomes_gtdb.txt --output GCA_902614945.1_AG-919-D04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:05:33,456] [INFO] Task succeeded: fastANI
[2023-06-07 19:05:33,467] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:05:33,467] [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_902611605.1	s__CACIIZ01 sp902611605	96.3471	249	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.35	96.35	0.51	0.51	2	conclusive
GCA_902570265.1	s__CACIIZ01 sp902570265	93.6944	326	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902562285.1	s__CACIIZ01 sp902562285	91.4978	279	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573735.1	s__CACIIZ01 sp902573735	82.3985	257	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578545.1	s__CACIIZ01 sp902578545	81.4692	250	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.87	95.99	0.65	0.64	7	-
GCA_902625475.1	s__CACIIZ01 sp902625475	80.8818	176	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:05:33,469] [INFO] GTDB search result was written to GCA_902614945.1_AG-919-D04_genomic.fna/result_gtdb.tsv
[2023-06-07 19:05:33,470] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:05:33,473] [INFO] DFAST_QC result json was written to GCA_902614945.1_AG-919-D04_genomic.fna/dqc_result.json
[2023-06-07 19:05:33,473] [INFO] DFAST_QC completed!
[2023-06-07 19:05:33,473] [INFO] Total running time: 0h0m32s