[2023-03-18 23:44:06,356] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference
[2023-03-18 23:44:07,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,620] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,620] [INFO] Running command: cat /var/lib/cwl/stgcc1196f6-9b50-4309-bfae-4f03fe168af3/OceanDNA-b16273.fa | prodigal -d OceanDNA-b16273/cds.fna -a OceanDNA-b16273/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:19,169] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:19,170] [INFO] Task started: HMMsearch
[2023-03-18 23:44:19,170] [INFO] Running command: hmmsearch --tblout OceanDNA-b16273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/reference_markers.hmm OceanDNA-b16273/protein.faa > /dev/null
[2023-03-18 23:44:19,343] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:19,344] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcc1196f6-9b50-4309-bfae-4f03fe168af3/OceanDNA-b16273.fa]
[2023-03-18 23:44:19,356] [INFO] Query marker FASTA was written to OceanDNA-b16273/markers.fasta
[2023-03-18 23:44:19,356] [INFO] Task started: Blastn
[2023-03-18 23:44:19,356] [INFO] Running command: blastn -query OceanDNA-b16273/markers.fasta -db /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/reference_markers.fasta -out OceanDNA-b16273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:19,961] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:19,962] [INFO] Selected 22 target genomes.
[2023-03-18 23:44:19,962] [INFO] Target genome list was writen to OceanDNA-b16273/target_genomes.txt
[2023-03-18 23:44:19,978] [INFO] Task started: fastANI
[2023-03-18 23:44:19,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1196f6-9b50-4309-bfae-4f03fe168af3/OceanDNA-b16273.fa --refList OceanDNA-b16273/target_genomes.txt --output OceanDNA-b16273/fastani_result.tsv --threads 1
[2023-03-18 23:44:32,870] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:32,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:32,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:32,873] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:32,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:32,873] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.2459	59	284	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:32,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16273/tc_result.tsv
[2023-03-18 23:44:32,873] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:32,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:32,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/checkm_data
[2023-03-18 23:44:32,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:32,889] [INFO] Task started: CheckM
[2023-03-18 23:44:32,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16273/checkm_input OceanDNA-b16273/checkm_result
[2023-03-18 23:45:06,105] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:06,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.69%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:06,111] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:06,111] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:06,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16273/markers.fasta)
[2023-03-18 23:45:06,112] [INFO] Task started: Blastn
[2023-03-18 23:45:06,112] [INFO] Running command: blastn -query OceanDNA-b16273/markers.fasta -db /var/lib/cwl/stgc0a4cb69-ffa1-4ee8-adea-df15316716d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:07,129] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:07,130] [INFO] Selected 16 target genomes.
[2023-03-18 23:45:07,130] [INFO] Target genome list was writen to OceanDNA-b16273/target_genomes_gtdb.txt
[2023-03-18 23:45:07,145] [INFO] Task started: fastANI
[2023-03-18 23:45:07,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc1196f6-9b50-4309-bfae-4f03fe168af3/OceanDNA-b16273.fa --refList OceanDNA-b16273/target_genomes_gtdb.txt --output OceanDNA-b16273/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:13,868] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:13,877] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:45:13,878] [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_903928835.1	s__Cyanobium_A sp903928835	91.4463	215	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	79.7541	194	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252665.1	s__Cyanobium_A sp002252665	79.6628	178	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	79.6249	147	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399015.1	s__NIES-981 sp018399015	78.8042	162	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280235.1	s__NIES-981 sp014280235	78.7608	158	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	97.33	97.33	0.87	0.87	2	-
GCA_016882525.1	s__NIES-981 sp016882525	78.7211	154	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316515.1	s__Cyanobium gracile	78.7199	136	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205255.1	s__Cyanobium_A sp013205255	78.5153	106	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003925.1	s__Cyanobium minutissimum	78.4007	137	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCF_900088535.1	s__NIES-981 sp900088535	78.3578	158	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038415.1	s__Cyanobium sp019038415	78.3499	143	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029175.1	s__Vulcanococcus sp010029175	78.3171	124	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698445.1	s__Cyanobium elabens	78.0642	140	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882285.1	s__Cyanobium sp903882285	77.9063	118	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
GCA_010027605.1	s__RGUW01 sp010027605	77.6274	87	284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RGUW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:13,880] [INFO] GTDB search result was written to OceanDNA-b16273/result_gtdb.tsv
[2023-03-18 23:45:13,881] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:13,885] [INFO] DFAST_QC result json was written to OceanDNA-b16273/dqc_result.json
[2023-03-18 23:45:13,885] [INFO] DFAST_QC completed!
[2023-03-18 23:45:13,885] [INFO] Total running time: 0h1m8s