[2023-06-07 19:37:19,977] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:37:19,979] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:37:19,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference
[2023-06-07 19:37:21,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:37:21,351] [INFO] Task started: Prodigal
[2023-06-07 19:37:21,352] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b4456e5-1d4d-4656-9179-7cbd024139a3/GCA_902520155.1_AG-333-G22_genomic.fna.gz | prodigal -d GCA_902520155.1_AG-333-G22_genomic.fna/cds.fna -a GCA_902520155.1_AG-333-G22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:37:23,015] [INFO] Task succeeded: Prodigal
[2023-06-07 19:37:23,015] [INFO] Task started: HMMsearch
[2023-06-07 19:37:23,015] [INFO] Running command: hmmsearch --tblout GCA_902520155.1_AG-333-G22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/reference_markers.hmm GCA_902520155.1_AG-333-G22_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:37:23,184] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:37:23,186] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6b4456e5-1d4d-4656-9179-7cbd024139a3/GCA_902520155.1_AG-333-G22_genomic.fna.gz]
[2023-06-07 19:37:23,202] [INFO] Query marker FASTA was written to GCA_902520155.1_AG-333-G22_genomic.fna/markers.fasta
[2023-06-07 19:37:23,203] [INFO] Task started: Blastn
[2023-06-07 19:37:23,203] [INFO] Running command: blastn -query GCA_902520155.1_AG-333-G22_genomic.fna/markers.fasta -db /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/reference_markers.fasta -out GCA_902520155.1_AG-333-G22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:37:23,692] [INFO] Task succeeded: Blastn
[2023-06-07 19:37:23,698] [INFO] Selected 5 target genomes.
[2023-06-07 19:37:23,698] [INFO] Target genome list was writen to GCA_902520155.1_AG-333-G22_genomic.fna/target_genomes.txt
[2023-06-07 19:37:23,700] [INFO] Task started: fastANI
[2023-06-07 19:37:23,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b4456e5-1d4d-4656-9179-7cbd024139a3/GCA_902520155.1_AG-333-G22_genomic.fna.gz --refList GCA_902520155.1_AG-333-G22_genomic.fna/target_genomes.txt --output GCA_902520155.1_AG-333-G22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:37:26,295] [INFO] Task succeeded: fastANI
[2023-06-07 19:37:26,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:37:26,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:37:26,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:37:26,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 19:37:26,298] [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 19:37:26,300] [INFO] DFAST Taxonomy check result was written to GCA_902520155.1_AG-333-G22_genomic.fna/tc_result.tsv
[2023-06-07 19:37:26,300] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:37:26,300] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:37:26,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/checkm_data
[2023-06-07 19:37:26,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:37:26,317] [INFO] Task started: CheckM
[2023-06-07 19:37:26,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520155.1_AG-333-G22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520155.1_AG-333-G22_genomic.fna/checkm_input GCA_902520155.1_AG-333-G22_genomic.fna/checkm_result
[2023-06-07 19:37:39,812] [INFO] Task succeeded: CheckM
[2023-06-07 19:37:39,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 26.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:37:39,834] [INFO] ===== Completeness check finished =====
[2023-06-07 19:37:39,835] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:37:39,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520155.1_AG-333-G22_genomic.fna/markers.fasta)
[2023-06-07 19:37:39,836] [INFO] Task started: Blastn
[2023-06-07 19:37:39,836] [INFO] Running command: blastn -query GCA_902520155.1_AG-333-G22_genomic.fna/markers.fasta -db /var/lib/cwl/stg923b4f3f-6aa9-40bb-acd1-40146d777215/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520155.1_AG-333-G22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:37:40,339] [INFO] Task succeeded: Blastn
[2023-06-07 19:37:40,348] [INFO] Selected 7 target genomes.
[2023-06-07 19:37:40,349] [INFO] Target genome list was writen to GCA_902520155.1_AG-333-G22_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:37:40,350] [INFO] Task started: fastANI
[2023-06-07 19:37:40,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b4456e5-1d4d-4656-9179-7cbd024139a3/GCA_902520155.1_AG-333-G22_genomic.fna.gz --refList GCA_902520155.1_AG-333-G22_genomic.fna/target_genomes_gtdb.txt --output GCA_902520155.1_AG-333-G22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:37:41,671] [INFO] Task succeeded: fastANI
[2023-06-07 19:37:41,679] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 19:37:41,680] [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_902595725.1	s__Pelagibacter sp902595725	89.2071	134	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519625.1	s__Pelagibacter sp902519625	88.9558	87	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.78	98.78	0.51	0.51	2	-
GCA_902569415.1	s__Pelagibacter sp902569415	88.5671	103	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902634305.1	s__Pelagibacter sp902634305	88.5487	130	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902529715.1	s__Pelagibacter sp902529715	88.2349	110	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556825.1	s__Pelagibacter sp902556825	87.8301	68	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559305.1	s__Pelagibacter sp902559305	85.3636	125	177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:37:41,682] [INFO] GTDB search result was written to GCA_902520155.1_AG-333-G22_genomic.fna/result_gtdb.tsv
[2023-06-07 19:37:41,683] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:37:41,686] [INFO] DFAST_QC result json was written to GCA_902520155.1_AG-333-G22_genomic.fna/dqc_result.json
[2023-06-07 19:37:41,686] [INFO] DFAST_QC completed!
[2023-06-07 19:37:41,686] [INFO] Total running time: 0h0m22s