[2023-06-08 12:31:40,261] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:40,265] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:40,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference
[2023-06-08 12:31:41,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:41,594] [INFO] Task started: Prodigal
[2023-06-08 12:31:41,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg8445a977-e057-469b-9225-bb629aa7e4bf/GCA_902520255.1_AG-333-I06_genomic.fna.gz | prodigal -d GCA_902520255.1_AG-333-I06_genomic.fna/cds.fna -a GCA_902520255.1_AG-333-I06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:42,792] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:42,792] [INFO] Task started: HMMsearch
[2023-06-08 12:31:42,793] [INFO] Running command: hmmsearch --tblout GCA_902520255.1_AG-333-I06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/reference_markers.hmm GCA_902520255.1_AG-333-I06_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:42,919] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:42,920] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg8445a977-e057-469b-9225-bb629aa7e4bf/GCA_902520255.1_AG-333-I06_genomic.fna.gz]
[2023-06-08 12:31:42,937] [INFO] Query marker FASTA was written to GCA_902520255.1_AG-333-I06_genomic.fna/markers.fasta
[2023-06-08 12:31:42,938] [INFO] Task started: Blastn
[2023-06-08 12:31:42,938] [INFO] Running command: blastn -query GCA_902520255.1_AG-333-I06_genomic.fna/markers.fasta -db /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/reference_markers.fasta -out GCA_902520255.1_AG-333-I06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:43,413] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:43,419] [INFO] Selected 4 target genomes.
[2023-06-08 12:31:43,420] [INFO] Target genome list was writen to GCA_902520255.1_AG-333-I06_genomic.fna/target_genomes.txt
[2023-06-08 12:31:43,421] [INFO] Task started: fastANI
[2023-06-08 12:31:43,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg8445a977-e057-469b-9225-bb629aa7e4bf/GCA_902520255.1_AG-333-I06_genomic.fna.gz --refList GCA_902520255.1_AG-333-I06_genomic.fna/target_genomes.txt --output GCA_902520255.1_AG-333-I06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:31:44,676] [INFO] Task succeeded: fastANI
[2023-06-08 12:31:44,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:31:44,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:31:44,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:31:44,680] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:31:44,680] [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
--------------------------------------------------------------------------------
[2023-06-08 12:31:44,682] [INFO] DFAST Taxonomy check result was written to GCA_902520255.1_AG-333-I06_genomic.fna/tc_result.tsv
[2023-06-08 12:31:44,683] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:31:44,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:31:44,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/checkm_data
[2023-06-08 12:31:44,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:31:44,700] [INFO] Task started: CheckM
[2023-06-08 12:31:44,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902520255.1_AG-333-I06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902520255.1_AG-333-I06_genomic.fna/checkm_input GCA_902520255.1_AG-333-I06_genomic.fna/checkm_result
[2023-06-08 12:31:56,293] [INFO] Task succeeded: CheckM
[2023-06-08 12:31:56,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:31:56,315] [INFO] ===== Completeness check finished =====
[2023-06-08 12:31:56,315] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:31:56,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902520255.1_AG-333-I06_genomic.fna/markers.fasta)
[2023-06-08 12:31:56,316] [INFO] Task started: Blastn
[2023-06-08 12:31:56,316] [INFO] Running command: blastn -query GCA_902520255.1_AG-333-I06_genomic.fna/markers.fasta -db /var/lib/cwl/stg6409e58a-10a5-4575-8705-6d12de5e1654/dqc_reference/reference_markers_gtdb.fasta -out GCA_902520255.1_AG-333-I06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:56,778] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:56,782] [INFO] Selected 5 target genomes.
[2023-06-08 12:31:56,783] [INFO] Target genome list was writen to GCA_902520255.1_AG-333-I06_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:31:56,785] [INFO] Task started: fastANI
[2023-06-08 12:31:56,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg8445a977-e057-469b-9225-bb629aa7e4bf/GCA_902520255.1_AG-333-I06_genomic.fna.gz --refList GCA_902520255.1_AG-333-I06_genomic.fna/target_genomes_gtdb.txt --output GCA_902520255.1_AG-333-I06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:31:57,997] [INFO] Task succeeded: fastANI
[2023-06-08 12:31:58,008] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:31:58,008] [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_003216375.1	s__Prochlorococcus_B sp003216375	85.5348	90	110	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	96.01	95.77	0.86	0.84	6	-
GCF_000757865.1	s__Prochlorococcus_B sp000757865	84.7741	88	110	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216955.1	s__Prochlorococcus_B sp003216955	84.3051	86	110	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003280445.1	s__Prochlorococcus_B sp003280445	83.9315	58	110	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:31:58,010] [INFO] GTDB search result was written to GCA_902520255.1_AG-333-I06_genomic.fna/result_gtdb.tsv
[2023-06-08 12:31:58,011] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:31:58,014] [INFO] DFAST_QC result json was written to GCA_902520255.1_AG-333-I06_genomic.fna/dqc_result.json
[2023-06-08 12:31:58,014] [INFO] DFAST_QC completed!
[2023-06-08 12:31:58,014] [INFO] Total running time: 0h0m18s