[2023-03-18 23:44:06,378] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,378] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference
[2023-03-18 23:44:07,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,567] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,567] [INFO] Running command: cat /var/lib/cwl/stg3f38b457-8b2a-4d66-8d93-d4f70cf48365/OceanDNA-b16144.fa | prodigal -d OceanDNA-b16144/cds.fna -a OceanDNA-b16144/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:19,942] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:19,942] [INFO] Task started: HMMsearch
[2023-03-18 23:44:19,942] [INFO] Running command: hmmsearch --tblout OceanDNA-b16144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/reference_markers.hmm OceanDNA-b16144/protein.faa > /dev/null
[2023-03-18 23:44:20,148] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:20,148] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3f38b457-8b2a-4d66-8d93-d4f70cf48365/OceanDNA-b16144.fa]
[2023-03-18 23:44:20,175] [INFO] Query marker FASTA was written to OceanDNA-b16144/markers.fasta
[2023-03-18 23:44:20,176] [INFO] Task started: Blastn
[2023-03-18 23:44:20,176] [INFO] Running command: blastn -query OceanDNA-b16144/markers.fasta -db /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/reference_markers.fasta -out OceanDNA-b16144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:20,606] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:20,606] [INFO] Selected 8 target genomes.
[2023-03-18 23:44:20,607] [INFO] Target genome list was writen to OceanDNA-b16144/target_genomes.txt
[2023-03-18 23:44:20,612] [INFO] Task started: fastANI
[2023-03-18 23:44:20,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f38b457-8b2a-4d66-8d93-d4f70cf48365/OceanDNA-b16144.fa --refList OceanDNA-b16144/target_genomes.txt --output OceanDNA-b16144/fastani_result.tsv --threads 1
[2023-03-18 23:44:24,875] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:24,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:24,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:24,879] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:24,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:24,880] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	78.9908	311	566	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:24,880] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16144/tc_result.tsv
[2023-03-18 23:44:24,880] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:24,880] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:24,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/checkm_data
[2023-03-18 23:44:24,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:25,040] [INFO] Task started: CheckM
[2023-03-18 23:44:25,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16144/checkm_input OceanDNA-b16144/checkm_result
[2023-03-18 23:45:00,080] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:00,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:00,086] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:00,087] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:00,087] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16144/markers.fasta)
[2023-03-18 23:45:00,088] [INFO] Task started: Blastn
[2023-03-18 23:45:00,088] [INFO] Running command: blastn -query OceanDNA-b16144/markers.fasta -db /var/lib/cwl/stgc762f973-c204-422a-9c13-0883c6dd33e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:00,534] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:00,537] [INFO] Selected 14 target genomes.
[2023-03-18 23:45:00,537] [INFO] Target genome list was writen to OceanDNA-b16144/target_genomes_gtdb.txt
[2023-03-18 23:45:00,546] [INFO] Task started: fastANI
[2023-03-18 23:45:00,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f38b457-8b2a-4d66-8d93-d4f70cf48365/OceanDNA-b16144.fa --refList OceanDNA-b16144/target_genomes_gtdb.txt --output OceanDNA-b16144/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:10,599] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:10,603] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:45:10,603] [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_015207195.1	s__Pleurocapsa sp015207195	77.0583	157	566	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	76.7333	142	566	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	76.6188	118	566	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_002368355.1	s__Pleurocapsa sp002368355	76.4843	126	566	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756305.1	s__Myxosarcina sp000756305	76.0027	76	566	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:10,604] [INFO] GTDB search result was written to OceanDNA-b16144/result_gtdb.tsv
[2023-03-18 23:45:10,604] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:10,605] [INFO] DFAST_QC result json was written to OceanDNA-b16144/dqc_result.json
[2023-03-18 23:45:10,605] [INFO] DFAST_QC completed!
[2023-03-18 23:45:10,605] [INFO] Total running time: 0h1m4s