[2023-06-08 03:14:38,398] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:38,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:38,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference
[2023-06-08 03:14:39,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:39,750] [INFO] Task started: Prodigal
[2023-06-08 03:14:39,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ade65ad-f452-4386-b91f-0b31ae688a1e/GCA_902615795.1_AG-892-A05_genomic.fna.gz | prodigal -d GCA_902615795.1_AG-892-A05_genomic.fna/cds.fna -a GCA_902615795.1_AG-892-A05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:40,570] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:40,571] [INFO] Task started: HMMsearch
[2023-06-08 03:14:40,571] [INFO] Running command: hmmsearch --tblout GCA_902615795.1_AG-892-A05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/reference_markers.hmm GCA_902615795.1_AG-892-A05_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:40,699] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:40,700] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2ade65ad-f452-4386-b91f-0b31ae688a1e/GCA_902615795.1_AG-892-A05_genomic.fna.gz]
[2023-06-08 03:14:40,708] [INFO] Query marker FASTA was written to GCA_902615795.1_AG-892-A05_genomic.fna/markers.fasta
[2023-06-08 03:14:40,709] [INFO] Task started: Blastn
[2023-06-08 03:14:40,709] [INFO] Running command: blastn -query GCA_902615795.1_AG-892-A05_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/reference_markers.fasta -out GCA_902615795.1_AG-892-A05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:42,500] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:42,504] [INFO] Selected 1 target genomes.
[2023-06-08 03:14:42,505] [INFO] Target genome list was writen to GCA_902615795.1_AG-892-A05_genomic.fna/target_genomes.txt
[2023-06-08 03:14:42,507] [INFO] Task started: fastANI
[2023-06-08 03:14:42,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ade65ad-f452-4386-b91f-0b31ae688a1e/GCA_902615795.1_AG-892-A05_genomic.fna.gz --refList GCA_902615795.1_AG-892-A05_genomic.fna/target_genomes.txt --output GCA_902615795.1_AG-892-A05_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:42,697] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:42,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:42,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:42,700] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:42,701] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:14:42,701] [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 03:14:42,710] [INFO] DFAST Taxonomy check result was written to GCA_902615795.1_AG-892-A05_genomic.fna/tc_result.tsv
[2023-06-08 03:14:42,711] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:42,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:42,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/checkm_data
[2023-06-08 03:14:42,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:42,724] [INFO] Task started: CheckM
[2023-06-08 03:14:42,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902615795.1_AG-892-A05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902615795.1_AG-892-A05_genomic.fna/checkm_input GCA_902615795.1_AG-892-A05_genomic.fna/checkm_result
[2023-06-08 03:14:53,412] [INFO] Task succeeded: CheckM
[2023-06-08 03:14:53,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 4.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:14:53,430] [INFO] ===== Completeness check finished =====
[2023-06-08 03:14:53,431] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:14:53,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902615795.1_AG-892-A05_genomic.fna/markers.fasta)
[2023-06-08 03:14:53,431] [INFO] Task started: Blastn
[2023-06-08 03:14:53,432] [INFO] Running command: blastn -query GCA_902615795.1_AG-892-A05_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f9f460-6f12-45f9-a62c-08a64b15fef2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902615795.1_AG-892-A05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:54,027] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:54,031] [INFO] Selected 8 target genomes.
[2023-06-08 03:14:54,032] [INFO] Target genome list was writen to GCA_902615795.1_AG-892-A05_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:14:54,033] [INFO] Task started: fastANI
[2023-06-08 03:14:54,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ade65ad-f452-4386-b91f-0b31ae688a1e/GCA_902615795.1_AG-892-A05_genomic.fna.gz --refList GCA_902615795.1_AG-892-A05_genomic.fna/target_genomes_gtdb.txt --output GCA_902615795.1_AG-892-A05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:14:55,212] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:55,217] [INFO] Found 4 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 03:14:55,218] [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_902560185.1	s__Pelagibacter sp902560185	95.9018	62	80	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.62	95.09	0.64	0.62	5	inconclusive
GCA_003212275.1	s__Pelagibacter sp003212275	95.1307	67	80	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCA_902597675.1	s__Pelagibacter sp902597675	94.6656	60	80	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.60	95.15	0.72	0.69	5	-
GCA_902627805.1	s__Pelagibacter sp902627805	90.4584	73	80	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:14:55,220] [INFO] GTDB search result was written to GCA_902615795.1_AG-892-A05_genomic.fna/result_gtdb.tsv
[2023-06-08 03:14:55,220] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:14:55,223] [INFO] DFAST_QC result json was written to GCA_902615795.1_AG-892-A05_genomic.fna/dqc_result.json
[2023-06-08 03:14:55,223] [INFO] DFAST_QC completed!
[2023-06-08 03:14:55,224] [INFO] Total running time: 0h0m17s