[2023-06-05 18:12:32,539] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:12:32,546] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:12:32,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference
[2023-06-05 18:12:35,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:12:35,073] [INFO] Task started: Prodigal
[2023-06-05 18:12:35,073] [INFO] Running command: gunzip -c /var/lib/cwl/stga1a24b2f-f430-4ca8-be33-2892231d89c7/GCA_902524045.1_AG-337-C07_genomic.fna.gz | prodigal -d GCA_902524045.1_AG-337-C07_genomic.fna/cds.fna -a GCA_902524045.1_AG-337-C07_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:12:37,393] [INFO] Task succeeded: Prodigal
[2023-06-05 18:12:37,394] [INFO] Task started: HMMsearch
[2023-06-05 18:12:37,394] [INFO] Running command: hmmsearch --tblout GCA_902524045.1_AG-337-C07_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/reference_markers.hmm GCA_902524045.1_AG-337-C07_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:12:37,681] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:12:37,682] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga1a24b2f-f430-4ca8-be33-2892231d89c7/GCA_902524045.1_AG-337-C07_genomic.fna.gz]
[2023-06-05 18:12:37,694] [INFO] Query marker FASTA was written to GCA_902524045.1_AG-337-C07_genomic.fna/markers.fasta
[2023-06-05 18:12:37,694] [INFO] Task started: Blastn
[2023-06-05 18:12:37,694] [INFO] Running command: blastn -query GCA_902524045.1_AG-337-C07_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/reference_markers.fasta -out GCA_902524045.1_AG-337-C07_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:12:40,253] [INFO] Task succeeded: Blastn
[2023-06-05 18:12:40,257] [INFO] Selected 7 target genomes.
[2023-06-05 18:12:40,257] [INFO] Target genome list was writen to GCA_902524045.1_AG-337-C07_genomic.fna/target_genomes.txt
[2023-06-05 18:12:40,300] [INFO] Task started: fastANI
[2023-06-05 18:12:40,300] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a24b2f-f430-4ca8-be33-2892231d89c7/GCA_902524045.1_AG-337-C07_genomic.fna.gz --refList GCA_902524045.1_AG-337-C07_genomic.fna/target_genomes.txt --output GCA_902524045.1_AG-337-C07_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:12:43,981] [INFO] Task succeeded: fastANI
[2023-06-05 18:12:43,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:12:43,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:12:43,983] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:12:43,983] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:12:43,984] [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
--------------------------------------------------------------------------------
[2023-06-05 18:12:43,985] [INFO] DFAST Taxonomy check result was written to GCA_902524045.1_AG-337-C07_genomic.fna/tc_result.tsv
[2023-06-05 18:12:43,986] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:12:43,986] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:12:43,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/checkm_data
[2023-06-05 18:12:43,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:12:44,003] [INFO] Task started: CheckM
[2023-06-05 18:12:44,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902524045.1_AG-337-C07_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902524045.1_AG-337-C07_genomic.fna/checkm_input GCA_902524045.1_AG-337-C07_genomic.fna/checkm_result
[2023-06-05 18:13:08,266] [INFO] Task succeeded: CheckM
[2023-06-05 18:13:08,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.91%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:13:08,392] [INFO] ===== Completeness check finished =====
[2023-06-05 18:13:08,392] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:13:08,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902524045.1_AG-337-C07_genomic.fna/markers.fasta)
[2023-06-05 18:13:08,393] [INFO] Task started: Blastn
[2023-06-05 18:13:08,393] [INFO] Running command: blastn -query GCA_902524045.1_AG-337-C07_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f862ac-775a-403e-96aa-f17cc5d7086e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902524045.1_AG-337-C07_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:13:09,364] [INFO] Task succeeded: Blastn
[2023-06-05 18:13:09,369] [INFO] Selected 8 target genomes.
[2023-06-05 18:13:09,369] [INFO] Target genome list was writen to GCA_902524045.1_AG-337-C07_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:13:09,372] [INFO] Task started: fastANI
[2023-06-05 18:13:09,373] [INFO] Running command: fastANI --query /var/lib/cwl/stga1a24b2f-f430-4ca8-be33-2892231d89c7/GCA_902524045.1_AG-337-C07_genomic.fna.gz --refList GCA_902524045.1_AG-337-C07_genomic.fna/target_genomes_gtdb.txt --output GCA_902524045.1_AG-337-C07_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:13:11,311] [INFO] Task succeeded: fastANI
[2023-06-05 18:13:11,320] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:13:11,320] [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_902524045.1	s__Pelagibacter sp902524045	99.9999	213	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902579925.1	s__Pelagibacter sp902579925	91.4749	157	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.80	96.31	0.69	0.68	3	-
GCA_902514945.1	s__Pelagibacter sp902514945	91.3271	142	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902633585.1	s__Pelagibacter sp902633585	85.5041	128	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582845.1	s__Pelagibacter sp902582845	84.5789	136	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580895.1	s__Pelagibacter sp902580895	84.4379	157	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.12	99.12	0.86	0.86	2	-
GCA_902572925.1	s__Pelagibacter sp902572925	84.1721	102	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515095.1	s__Pelagibacter sp902515095	84.0169	168	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:13:11,326] [INFO] GTDB search result was written to GCA_902524045.1_AG-337-C07_genomic.fna/result_gtdb.tsv
[2023-06-05 18:13:11,327] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:13:11,339] [INFO] DFAST_QC result json was written to GCA_902524045.1_AG-337-C07_genomic.fna/dqc_result.json
[2023-06-05 18:13:11,339] [INFO] DFAST_QC completed!
[2023-06-05 18:13:11,340] [INFO] Total running time: 0h0m39s