[2023-06-07 23:15:50,160] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:15:50,163] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:15:50,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference
[2023-06-07 23:15:53,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:15:53,488] [INFO] Task started: Prodigal
[2023-06-07 23:15:53,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c73c043-d0a8-4973-b0ec-fd7b9e1a4c33/GCA_902516175.1_AG-325-J04_genomic.fna.gz | prodigal -d GCA_902516175.1_AG-325-J04_genomic.fna/cds.fna -a GCA_902516175.1_AG-325-J04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:15:55,367] [INFO] Task succeeded: Prodigal
[2023-06-07 23:15:55,368] [INFO] Task started: HMMsearch
[2023-06-07 23:15:55,368] [INFO] Running command: hmmsearch --tblout GCA_902516175.1_AG-325-J04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/reference_markers.hmm GCA_902516175.1_AG-325-J04_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:15:55,550] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:15:55,552] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4c73c043-d0a8-4973-b0ec-fd7b9e1a4c33/GCA_902516175.1_AG-325-J04_genomic.fna.gz]
[2023-06-07 23:15:55,567] [INFO] Query marker FASTA was written to GCA_902516175.1_AG-325-J04_genomic.fna/markers.fasta
[2023-06-07 23:15:55,567] [INFO] Task started: Blastn
[2023-06-07 23:15:55,568] [INFO] Running command: blastn -query GCA_902516175.1_AG-325-J04_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/reference_markers.fasta -out GCA_902516175.1_AG-325-J04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:15:57,082] [INFO] Task succeeded: Blastn
[2023-06-07 23:15:57,086] [INFO] Selected 5 target genomes.
[2023-06-07 23:15:57,087] [INFO] Target genome list was writen to GCA_902516175.1_AG-325-J04_genomic.fna/target_genomes.txt
[2023-06-07 23:15:57,088] [INFO] Task started: fastANI
[2023-06-07 23:15:57,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c73c043-d0a8-4973-b0ec-fd7b9e1a4c33/GCA_902516175.1_AG-325-J04_genomic.fna.gz --refList GCA_902516175.1_AG-325-J04_genomic.fna/target_genomes.txt --output GCA_902516175.1_AG-325-J04_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:15:59,285] [INFO] Task succeeded: fastANI
[2023-06-07 23:15:59,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:15:59,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:15:59,292] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:15:59,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:15:59,292] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	79.1682	111	207	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:15:59,294] [INFO] DFAST Taxonomy check result was written to GCA_902516175.1_AG-325-J04_genomic.fna/tc_result.tsv
[2023-06-07 23:15:59,294] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:15:59,294] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:15:59,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/checkm_data
[2023-06-07 23:15:59,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:15:59,308] [INFO] Task started: CheckM
[2023-06-07 23:15:59,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902516175.1_AG-325-J04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902516175.1_AG-325-J04_genomic.fna/checkm_input GCA_902516175.1_AG-325-J04_genomic.fna/checkm_result
[2023-06-07 23:16:13,341] [INFO] Task succeeded: CheckM
[2023-06-07 23:16:13,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:16:13,364] [INFO] ===== Completeness check finished =====
[2023-06-07 23:16:13,365] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:16:13,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902516175.1_AG-325-J04_genomic.fna/markers.fasta)
[2023-06-07 23:16:13,366] [INFO] Task started: Blastn
[2023-06-07 23:16:13,367] [INFO] Running command: blastn -query GCA_902516175.1_AG-325-J04_genomic.fna/markers.fasta -db /var/lib/cwl/stgdac074d7-9ce8-40d4-94e4-cbcde1c5d80f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902516175.1_AG-325-J04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:16:14,082] [INFO] Task succeeded: Blastn
[2023-06-07 23:16:14,087] [INFO] Selected 5 target genomes.
[2023-06-07 23:16:14,087] [INFO] Target genome list was writen to GCA_902516175.1_AG-325-J04_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:16:14,089] [INFO] Task started: fastANI
[2023-06-07 23:16:14,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c73c043-d0a8-4973-b0ec-fd7b9e1a4c33/GCA_902516175.1_AG-325-J04_genomic.fna.gz --refList GCA_902516175.1_AG-325-J04_genomic.fna/target_genomes_gtdb.txt --output GCA_902516175.1_AG-325-J04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:16:14,968] [INFO] Task succeeded: fastANI
[2023-06-07 23:16:14,975] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:16:14,976] [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_902515625.1	s__Pelagibacter sp902515625	92.5148	116	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622795.1	s__Pelagibacter sp902622795	91.9776	151	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.61	99.61	0.85	0.85	2	-
GCA_902543535.1	s__Pelagibacter sp902543535	91.9463	148	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517175.1	s__Pelagibacter sp902517175	91.2917	117	207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578255.1	s__Pelagibacter sp902578255	90.9477	134	207	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 23:16:14,978] [INFO] GTDB search result was written to GCA_902516175.1_AG-325-J04_genomic.fna/result_gtdb.tsv
[2023-06-07 23:16:14,978] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:16:14,981] [INFO] DFAST_QC result json was written to GCA_902516175.1_AG-325-J04_genomic.fna/dqc_result.json
[2023-06-07 23:16:14,981] [INFO] DFAST_QC completed!
[2023-06-07 23:16:14,981] [INFO] Total running time: 0h0m25s