[2023-03-14 11:33:34,991] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,991] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,991] [INFO] DQC Reference Directory: /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference
[2023-03-14 11:33:36,285] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,285] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,286] [INFO] Running command: cat /var/lib/cwl/stgfc5aed7f-91db-4df1-9cd1-fb0d5e6b1013/OceanDNA-b2001.fa | prodigal -d OceanDNA-b2001/cds.fna -a OceanDNA-b2001/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:43,139] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:43,139] [INFO] Task started: HMMsearch
[2023-03-14 11:33:43,139] [INFO] Running command: hmmsearch --tblout OceanDNA-b2001/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/reference_markers.hmm OceanDNA-b2001/protein.faa > /dev/null
[2023-03-14 11:33:43,312] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:43,313] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc5aed7f-91db-4df1-9cd1-fb0d5e6b1013/OceanDNA-b2001.fa]
[2023-03-14 11:33:43,327] [INFO] Query marker FASTA was written to OceanDNA-b2001/markers.fasta
[2023-03-14 11:33:43,327] [INFO] Task started: Blastn
[2023-03-14 11:33:43,327] [INFO] Running command: blastn -query OceanDNA-b2001/markers.fasta -db /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/reference_markers.fasta -out OceanDNA-b2001/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:43,826] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:43,827] [INFO] Selected 12 target genomes.
[2023-03-14 11:33:43,827] [INFO] Target genome list was writen to OceanDNA-b2001/target_genomes.txt
[2023-03-14 11:33:43,834] [INFO] Task started: fastANI
[2023-03-14 11:33:43,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5aed7f-91db-4df1-9cd1-fb0d5e6b1013/OceanDNA-b2001.fa --refList OceanDNA-b2001/target_genomes.txt --output OceanDNA-b2001/fastani_result.tsv --threads 1
[2023-03-14 11:33:48,314] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:48,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:33:48,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:33:48,315] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:33:48,315] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:33:48,315] [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
--------------------------------------------------------------------------------
[2023-03-14 11:33:48,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2001/tc_result.tsv
[2023-03-14 11:33:48,315] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:33:48,315] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:48,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/checkm_data
[2023-03-14 11:33:48,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:48,321] [INFO] Task started: CheckM
[2023-03-14 11:33:48,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2001/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2001/checkm_input OceanDNA-b2001/checkm_result
[2023-03-14 11:34:10,587] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:10,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:10,590] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:10,591] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:10,591] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2001/markers.fasta)
[2023-03-14 11:34:10,591] [INFO] Task started: Blastn
[2023-03-14 11:34:10,591] [INFO] Running command: blastn -query OceanDNA-b2001/markers.fasta -db /var/lib/cwl/stga7c5e1ff-25ea-492e-bfee-3597b4a190e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2001/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:11,232] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:11,232] [INFO] Selected 8 target genomes.
[2023-03-14 11:34:11,232] [INFO] Target genome list was writen to OceanDNA-b2001/target_genomes_gtdb.txt
[2023-03-14 11:34:11,241] [INFO] Task started: fastANI
[2023-03-14 11:34:11,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc5aed7f-91db-4df1-9cd1-fb0d5e6b1013/OceanDNA-b2001.fa --refList OceanDNA-b2001/target_genomes_gtdb.txt --output OceanDNA-b2001/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:13,717] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:13,722] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:34:13,722] [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_002720485.1	s__UBA8592 sp002720485	96.8846	279	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	96.65	96.65	0.71	0.71	2	conclusive
GCA_902565595.1	s__UBA8592 sp902565595	93.5458	227	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703045.1	s__UBA8592 sp002703045	81.1608	199	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	95.31	95.20	0.70	0.69	3	-
GCA_002724825.1	s__UBA8592 sp002724825	81.002	209	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	98.36	98.27	0.75	0.75	3	-
GCA_002722525.1	s__UBA8592 sp002722525	80.3083	154	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.15	99.15	0.66	0.66	2	-
GCA_002715425.1	s__UBA8592 sp002715425	79.8704	133	375	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:34:13,722] [INFO] GTDB search result was written to OceanDNA-b2001/result_gtdb.tsv
[2023-03-14 11:34:13,722] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:13,723] [INFO] DFAST_QC result json was written to OceanDNA-b2001/dqc_result.json
[2023-03-14 11:34:13,723] [INFO] DFAST_QC completed!
[2023-03-14 11:34:13,723] [INFO] Total running time: 0h0m39s