[2023-03-18 23:03:14,060] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:03:14,060] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:03:14,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference
[2023-03-18 23:03:15,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:03:15,189] [INFO] Task started: Prodigal
[2023-03-18 23:03:15,189] [INFO] Running command: cat /var/lib/cwl/stgbdad16a1-a66b-4620-b4f5-88341db62955/OceanDNA-b40892.fa | prodigal -d OceanDNA-b40892/cds.fna -a OceanDNA-b40892/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:03:33,572] [INFO] Task succeeded: Prodigal
[2023-03-18 23:03:33,573] [INFO] Task started: HMMsearch
[2023-03-18 23:03:33,573] [INFO] Running command: hmmsearch --tblout OceanDNA-b40892/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/reference_markers.hmm OceanDNA-b40892/protein.faa > /dev/null
[2023-03-18 23:03:33,775] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:03:33,776] [INFO] Found 6/6 markers.
[2023-03-18 23:03:33,797] [INFO] Query marker FASTA was written to OceanDNA-b40892/markers.fasta
[2023-03-18 23:03:33,798] [INFO] Task started: Blastn
[2023-03-18 23:03:33,799] [INFO] Running command: blastn -query OceanDNA-b40892/markers.fasta -db /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/reference_markers.fasta -out OceanDNA-b40892/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:34,382] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:34,384] [INFO] Selected 31 target genomes.
[2023-03-18 23:03:34,384] [INFO] Target genome list was writen to OceanDNA-b40892/target_genomes.txt
[2023-03-18 23:03:34,400] [INFO] Task started: fastANI
[2023-03-18 23:03:34,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdad16a1-a66b-4620-b4f5-88341db62955/OceanDNA-b40892.fa --refList OceanDNA-b40892/target_genomes.txt --output OceanDNA-b40892/fastani_result.tsv --threads 1
[2023-03-18 23:03:53,296] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:53,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:03:53,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:03:53,297] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:03:53,297] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:03:53,297] [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
--------------------------------------------------------------------------------
[2023-03-18 23:03:53,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40892/tc_result.tsv
[2023-03-18 23:03:53,298] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:03:53,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:03:53,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/checkm_data
[2023-03-18 23:03:53,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:03:53,306] [INFO] Task started: CheckM
[2023-03-18 23:03:53,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40892/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40892/checkm_input OceanDNA-b40892/checkm_result
[2023-03-18 23:04:40,666] [INFO] Task succeeded: CheckM
[2023-03-18 23:04:40,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:04:40,669] [INFO] ===== Completeness check finished =====
[2023-03-18 23:04:40,670] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:04:40,670] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40892/markers.fasta)
[2023-03-18 23:04:40,671] [INFO] Task started: Blastn
[2023-03-18 23:04:40,671] [INFO] Running command: blastn -query OceanDNA-b40892/markers.fasta -db /var/lib/cwl/stg79e11b79-5267-4370-8311-1ac6d924bce5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40892/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:04:41,634] [INFO] Task succeeded: Blastn
[2023-03-18 23:04:41,635] [INFO] Selected 27 target genomes.
[2023-03-18 23:04:41,635] [INFO] Target genome list was writen to OceanDNA-b40892/target_genomes_gtdb.txt
[2023-03-18 23:04:41,655] [INFO] Task started: fastANI
[2023-03-18 23:04:41,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdad16a1-a66b-4620-b4f5-88341db62955/OceanDNA-b40892.fa --refList OceanDNA-b40892/target_genomes_gtdb.txt --output OceanDNA-b40892/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:04:56,669] [INFO] Task succeeded: fastANI
[2023-03-18 23:04:56,673] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:04:56,673] [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_002726595.1	s__UBA9145 sp002726595	99.6602	807	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002730035.1	s__UBA9145 sp002730035	78.3136	115	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
GCA_013204155.1	s__UBA9145 sp013204155	76.4418	79	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018661465.1	s__UBA9145 sp018661465	75.9581	57	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.99	99.98	0.99	0.97	14	-
GCA_009692305.1	s__UBA9145 sp009692305	75.847	50	1047	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:04:56,673] [INFO] GTDB search result was written to OceanDNA-b40892/result_gtdb.tsv
[2023-03-18 23:04:56,673] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:04:56,674] [INFO] DFAST_QC result json was written to OceanDNA-b40892/dqc_result.json
[2023-03-18 23:04:56,674] [INFO] DFAST_QC completed!
[2023-03-18 23:04:56,674] [INFO] Total running time: 0h1m43s