[2023-03-17 23:09:11,943] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:09:11,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:09:11,945] [INFO] DQC Reference Directory: /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference
[2023-03-17 23:09:13,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:09:13,105] [INFO] Task started: Prodigal
[2023-03-17 23:09:13,105] [INFO] Running command: cat /var/lib/cwl/stg7c77977d-6298-495e-b80c-f8657a6bb9b5/OceanDNA-b15511.fa | prodigal -d OceanDNA-b15511/cds.fna -a OceanDNA-b15511/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:09:28,363] [INFO] Task succeeded: Prodigal
[2023-03-17 23:09:28,364] [INFO] Task started: HMMsearch
[2023-03-17 23:09:28,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b15511/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/reference_markers.hmm OceanDNA-b15511/protein.faa > /dev/null
[2023-03-17 23:09:28,567] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:09:28,568] [INFO] Found 6/6 markers.
[2023-03-17 23:09:28,603] [INFO] Query marker FASTA was written to OceanDNA-b15511/markers.fasta
[2023-03-17 23:09:28,604] [INFO] Task started: Blastn
[2023-03-17 23:09:28,604] [INFO] Running command: blastn -query OceanDNA-b15511/markers.fasta -db /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/reference_markers.fasta -out OceanDNA-b15511/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:29,132] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:29,136] [INFO] Selected 16 target genomes.
[2023-03-17 23:09:29,136] [INFO] Target genome list was writen to OceanDNA-b15511/target_genomes.txt
[2023-03-17 23:09:29,144] [INFO] Task started: fastANI
[2023-03-17 23:09:29,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c77977d-6298-495e-b80c-f8657a6bb9b5/OceanDNA-b15511.fa --refList OceanDNA-b15511/target_genomes.txt --output OceanDNA-b15511/fastani_result.tsv --threads 1
[2023-03-17 23:09:41,446] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:41,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:41,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:41,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:41,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:09:41,447] [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
--------------------------------------------------------------------------------
[2023-03-17 23:09:41,449] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15511/tc_result.tsv
[2023-03-17 23:09:41,449] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:41,449] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:41,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/checkm_data
[2023-03-17 23:09:41,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:41,463] [INFO] Task started: CheckM
[2023-03-17 23:09:41,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15511/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15511/checkm_input OceanDNA-b15511/checkm_result
[2023-03-17 23:10:22,214] [INFO] Task succeeded: CheckM
[2023-03-17 23:10:22,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:10:22,232] [INFO] ===== Completeness check finished =====
[2023-03-17 23:10:22,232] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:10:22,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15511/markers.fasta)
[2023-03-17 23:10:22,233] [INFO] Task started: Blastn
[2023-03-17 23:10:22,234] [INFO] Running command: blastn -query OceanDNA-b15511/markers.fasta -db /var/lib/cwl/stgca46a8db-edd5-4aac-aaad-d036ecfa7265/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15511/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:22,982] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:22,985] [INFO] Selected 18 target genomes.
[2023-03-17 23:10:22,985] [INFO] Target genome list was writen to OceanDNA-b15511/target_genomes_gtdb.txt
[2023-03-17 23:10:22,999] [INFO] Task started: fastANI
[2023-03-17 23:10:22,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c77977d-6298-495e-b80c-f8657a6bb9b5/OceanDNA-b15511.fa --refList OceanDNA-b15511/target_genomes_gtdb.txt --output OceanDNA-b15511/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:32,662] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:32,668] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:10:32,668] [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_002816875.1	s__Io17-Chloro-G2 sp002816875	79.0177	220	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Io17-Chloro-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721995.1	s__UBA9611 sp002721995	76.5988	98	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002401285.1	s__UBA11650 sp002401285	76.4102	88	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	-
GCA_009692925.1	s__SHYG01 sp009692925	76.1572	82	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002328185.1	s__UBA9611 sp002328185	76.1217	99	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_016872385.1	s__SHYG01 sp016872385	76.097	75	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002816575.1	s__UBA9611 sp002816575	76.0405	81	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204585.1	s__UBA9611 sp013204585	75.7057	68	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698265.1	s__UBA9611 sp002698265	75.6814	62	813	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
--------------------------------------------------------------------------------
[2023-03-17 23:10:32,672] [INFO] GTDB search result was written to OceanDNA-b15511/result_gtdb.tsv
[2023-03-17 23:10:32,677] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:32,682] [INFO] DFAST_QC result json was written to OceanDNA-b15511/dqc_result.json
[2023-03-17 23:10:32,682] [INFO] DFAST_QC completed!
[2023-03-17 23:10:32,682] [INFO] Total running time: 0h1m21s