[2023-03-18 21:37:49,967] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:37:49,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:37:49,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference
[2023-03-18 21:37:51,085] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:37:51,086] [INFO] Task started: Prodigal
[2023-03-18 21:37:51,087] [INFO] Running command: cat /var/lib/cwl/stg7e020265-fd8a-47d7-9d07-a69ab86761ea/OceanDNA-b32879.fa | prodigal -d OceanDNA-b32879/cds.fna -a OceanDNA-b32879/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:38:03,434] [INFO] Task succeeded: Prodigal
[2023-03-18 21:38:03,434] [INFO] Task started: HMMsearch
[2023-03-18 21:38:03,435] [INFO] Running command: hmmsearch --tblout OceanDNA-b32879/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/reference_markers.hmm OceanDNA-b32879/protein.faa > /dev/null
[2023-03-18 21:38:03,614] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:38:03,614] [INFO] Found 6/6 markers.
[2023-03-18 21:38:03,636] [INFO] Query marker FASTA was written to OceanDNA-b32879/markers.fasta
[2023-03-18 21:38:03,637] [INFO] Task started: Blastn
[2023-03-18 21:38:03,637] [INFO] Running command: blastn -query OceanDNA-b32879/markers.fasta -db /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/reference_markers.fasta -out OceanDNA-b32879/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:38:04,284] [INFO] Task succeeded: Blastn
[2023-03-18 21:38:04,287] [INFO] Selected 35 target genomes.
[2023-03-18 21:38:04,287] [INFO] Target genome list was writen to OceanDNA-b32879/target_genomes.txt
[2023-03-18 21:38:04,309] [INFO] Task started: fastANI
[2023-03-18 21:38:04,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e020265-fd8a-47d7-9d07-a69ab86761ea/OceanDNA-b32879.fa --refList OceanDNA-b32879/target_genomes.txt --output OceanDNA-b32879/fastani_result.tsv --threads 1
[2023-03-18 21:38:37,618] [INFO] Task succeeded: fastANI
[2023-03-18 21:38:37,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:38:37,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:38:37,619] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:38:37,619] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:38:37,619] [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 21:38:37,620] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32879/tc_result.tsv
[2023-03-18 21:38:37,625] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:38:37,625] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:38:37,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/checkm_data
[2023-03-18 21:38:37,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:38:37,642] [INFO] Task started: CheckM
[2023-03-18 21:38:37,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32879/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32879/checkm_input OceanDNA-b32879/checkm_result
[2023-03-18 21:39:12,551] [INFO] Task succeeded: CheckM
[2023-03-18 21:39:12,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:39:12,647] [INFO] ===== Completeness check finished =====
[2023-03-18 21:39:12,647] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:39:12,647] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32879/markers.fasta)
[2023-03-18 21:39:12,649] [INFO] Task started: Blastn
[2023-03-18 21:39:12,649] [INFO] Running command: blastn -query OceanDNA-b32879/markers.fasta -db /var/lib/cwl/stgbf07c2b7-f0cf-4989-995f-d165e12ad887/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32879/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:39:13,765] [INFO] Task succeeded: Blastn
[2023-03-18 21:39:13,771] [INFO] Selected 20 target genomes.
[2023-03-18 21:39:13,771] [INFO] Target genome list was writen to OceanDNA-b32879/target_genomes_gtdb.txt
[2023-03-18 21:39:13,788] [INFO] Task started: fastANI
[2023-03-18 21:39:13,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e020265-fd8a-47d7-9d07-a69ab86761ea/OceanDNA-b32879.fa --refList OceanDNA-b32879/target_genomes_gtdb.txt --output OceanDNA-b32879/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:39:28,176] [INFO] Task succeeded: fastANI
[2023-03-18 21:39:28,180] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:39:28,180] [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_002690455.1	s__UBA7985 sp002690455	99.5853	430	666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002708995.1	s__UBA7985 sp002708995	80.8073	425	666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	95.44	95.44	0.84	0.83	3	-
GCA_002711265.1	s__UBA7985 sp002711265	80.4559	378	666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.38	98.76	0.89	0.83	3	-
GCA_002700865.1	s__UBA7985 sp002700865	80.2532	115	666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.96	99.96	0.93	0.93	2	-
GCA_002705565.1	s__UBA7985 sp002705565	77.0883	125	666	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.09	99.09	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:39:28,183] [INFO] GTDB search result was written to OceanDNA-b32879/result_gtdb.tsv
[2023-03-18 21:39:28,186] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:39:28,190] [INFO] DFAST_QC result json was written to OceanDNA-b32879/dqc_result.json
[2023-03-18 21:39:28,190] [INFO] DFAST_QC completed!
[2023-03-18 21:39:28,190] [INFO] Total running time: 0h1m38s