[2023-06-08 06:29:54,976] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:29:54,978] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:29:54,978] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference
[2023-06-08 06:29:56,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:29:56,297] [INFO] Task started: Prodigal
[2023-06-08 06:29:56,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e4e8a30-e1f5-4e83-8623-c50d08c0c37d/GCA_902528435.1_AG-896-K04_genomic.fna.gz | prodigal -d GCA_902528435.1_AG-896-K04_genomic.fna/cds.fna -a GCA_902528435.1_AG-896-K04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:29:57,793] [INFO] Task succeeded: Prodigal
[2023-06-08 06:29:57,794] [INFO] Task started: HMMsearch
[2023-06-08 06:29:57,794] [INFO] Running command: hmmsearch --tblout GCA_902528435.1_AG-896-K04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/reference_markers.hmm GCA_902528435.1_AG-896-K04_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:29:57,948] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:29:57,949] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6e4e8a30-e1f5-4e83-8623-c50d08c0c37d/GCA_902528435.1_AG-896-K04_genomic.fna.gz]
[2023-06-08 06:29:57,960] [INFO] Query marker FASTA was written to GCA_902528435.1_AG-896-K04_genomic.fna/markers.fasta
[2023-06-08 06:29:57,960] [INFO] Task started: Blastn
[2023-06-08 06:29:57,961] [INFO] Running command: blastn -query GCA_902528435.1_AG-896-K04_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/reference_markers.fasta -out GCA_902528435.1_AG-896-K04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:29:59,349] [INFO] Task succeeded: Blastn
[2023-06-08 06:29:59,353] [INFO] Selected 10 target genomes.
[2023-06-08 06:29:59,354] [INFO] Target genome list was writen to GCA_902528435.1_AG-896-K04_genomic.fna/target_genomes.txt
[2023-06-08 06:29:59,356] [INFO] Task started: fastANI
[2023-06-08 06:29:59,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e4e8a30-e1f5-4e83-8623-c50d08c0c37d/GCA_902528435.1_AG-896-K04_genomic.fna.gz --refList GCA_902528435.1_AG-896-K04_genomic.fna/target_genomes.txt --output GCA_902528435.1_AG-896-K04_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:30:02,349] [INFO] Task succeeded: fastANI
[2023-06-08 06:30:02,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:30:02,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:30:02,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 06:30:02,351] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 06:30:02,351] [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 06:30:02,353] [INFO] DFAST Taxonomy check result was written to GCA_902528435.1_AG-896-K04_genomic.fna/tc_result.tsv
[2023-06-08 06:30:02,354] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:30:02,354] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:30:02,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/checkm_data
[2023-06-08 06:30:02,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:30:02,370] [INFO] Task started: CheckM
[2023-06-08 06:30:02,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528435.1_AG-896-K04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528435.1_AG-896-K04_genomic.fna/checkm_input GCA_902528435.1_AG-896-K04_genomic.fna/checkm_result
[2023-06-08 06:30:14,921] [INFO] Task succeeded: CheckM
[2023-06-08 06:30:14,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:30:14,943] [INFO] ===== Completeness check finished =====
[2023-06-08 06:30:14,943] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:30:14,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528435.1_AG-896-K04_genomic.fna/markers.fasta)
[2023-06-08 06:30:14,944] [INFO] Task started: Blastn
[2023-06-08 06:30:14,944] [INFO] Running command: blastn -query GCA_902528435.1_AG-896-K04_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7230d54-6cb5-4448-a1dd-cb9ff8ebdedd/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528435.1_AG-896-K04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:30:15,508] [INFO] Task succeeded: Blastn
[2023-06-08 06:30:15,512] [INFO] Selected 9 target genomes.
[2023-06-08 06:30:15,513] [INFO] Target genome list was writen to GCA_902528435.1_AG-896-K04_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:30:15,516] [INFO] Task started: fastANI
[2023-06-08 06:30:15,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e4e8a30-e1f5-4e83-8623-c50d08c0c37d/GCA_902528435.1_AG-896-K04_genomic.fna.gz --refList GCA_902528435.1_AG-896-K04_genomic.fna/target_genomes_gtdb.txt --output GCA_902528435.1_AG-896-K04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:30:17,200] [INFO] Task succeeded: fastANI
[2023-06-08 06:30:17,213] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 06:30:17,213] [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_001704065.1	s__Pelagibacter sp001704065	94.4268	124	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.46	95.21	0.83	0.78	7	-
GCA_902564385.1	s__Pelagibacter sp902564385	94.1148	90	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542975.1	s__Pelagibacter sp902542975	94.0342	127	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902617975.1	s__Pelagibacter sp902617975	93.6999	109	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532525.1	s__Pelagibacter sp902532525	93.6269	113	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543575.1	s__Pelagibacter sp902543575	93.62	112	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.66	97.41	0.82	0.80	3	-
GCA_902533775.1	s__Pelagibacter sp902533775	93.4143	102	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541285.1	s__Pelagibacter sp902541285	93.3386	114	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902534735.1	s__Pelagibacter sp902534735	93.0627	119	149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.80	99.78	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-08 06:30:17,216] [INFO] GTDB search result was written to GCA_902528435.1_AG-896-K04_genomic.fna/result_gtdb.tsv
[2023-06-08 06:30:17,217] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:30:17,221] [INFO] DFAST_QC result json was written to GCA_902528435.1_AG-896-K04_genomic.fna/dqc_result.json
[2023-06-08 06:30:17,221] [INFO] DFAST_QC completed!
[2023-06-08 06:30:17,222] [INFO] Total running time: 0h0m22s