[2023-03-17 07:28:30,376] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,376] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,376] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stg40205b1e-4982-4e1f-905a-051e9fc989f0/OceanDNA-b40660.fa | prodigal -d OceanDNA-b40660/cds.fna -a OceanDNA-b40660/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:46,199] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:46,199] [INFO] Task started: HMMsearch
[2023-03-17 07:28:46,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b40660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/reference_markers.hmm OceanDNA-b40660/protein.faa > /dev/null
[2023-03-17 07:28:46,385] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:46,386] [INFO] Found 6/6 markers.
[2023-03-17 07:28:46,401] [INFO] Query marker FASTA was written to OceanDNA-b40660/markers.fasta
[2023-03-17 07:28:46,402] [INFO] Task started: Blastn
[2023-03-17 07:28:46,402] [INFO] Running command: blastn -query OceanDNA-b40660/markers.fasta -db /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/reference_markers.fasta -out OceanDNA-b40660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:46,989] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:46,990] [INFO] Selected 30 target genomes.
[2023-03-17 07:28:46,990] [INFO] Target genome list was writen to OceanDNA-b40660/target_genomes.txt
[2023-03-17 07:28:47,003] [INFO] Task started: fastANI
[2023-03-17 07:28:47,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg40205b1e-4982-4e1f-905a-051e9fc989f0/OceanDNA-b40660.fa --refList OceanDNA-b40660/target_genomes.txt --output OceanDNA-b40660/fastani_result.tsv --threads 1
[2023-03-17 07:29:04,344] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:04,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:04,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:04,345] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:04,345] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:29:04,345] [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 07:29:04,345] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40660/tc_result.tsv
[2023-03-17 07:29:04,345] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:04,346] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:04,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/checkm_data
[2023-03-17 07:29:04,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:04,352] [INFO] Task started: CheckM
[2023-03-17 07:29:04,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40660/checkm_input OceanDNA-b40660/checkm_result
[2023-03-17 07:29:43,804] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:43,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:43,806] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:43,806] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:43,806] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40660/markers.fasta)
[2023-03-17 07:29:43,807] [INFO] Task started: Blastn
[2023-03-17 07:29:43,807] [INFO] Running command: blastn -query OceanDNA-b40660/markers.fasta -db /var/lib/cwl/stgdbb00dfa-c074-431f-abb8-a5e67b99accb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:44,769] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:44,770] [INFO] Selected 27 target genomes.
[2023-03-17 07:29:44,770] [INFO] Target genome list was writen to OceanDNA-b40660/target_genomes_gtdb.txt
[2023-03-17 07:29:45,199] [INFO] Task started: fastANI
[2023-03-17 07:29:45,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg40205b1e-4982-4e1f-905a-051e9fc989f0/OceanDNA-b40660.fa --refList OceanDNA-b40660/target_genomes_gtdb.txt --output OceanDNA-b40660/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:58,994] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:58,999] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:58,999] [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_002731775.1	s__UBA9145 sp002731775	78.2239	377	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.77	98.59	0.87	0.85	6	-
GCA_002730035.1	s__UBA9145 sp002730035	76.9705	106	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.69	99.69	0.91	0.91	2	-
GCA_018661465.1	s__UBA9145 sp018661465	76.5418	69	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.99	99.98	0.99	0.97	14	-
GCA_905478195.1	s__UBA9145 sp003483155	76.3646	82	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_003451715.1	s__UBA9145 sp003451715	76.3485	59	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477465.1	s__UBA9145 sp002477465	75.8142	54	830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:58,999] [INFO] GTDB search result was written to OceanDNA-b40660/result_gtdb.tsv
[2023-03-17 07:29:58,999] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:59,000] [INFO] DFAST_QC result json was written to OceanDNA-b40660/dqc_result.json
[2023-03-17 07:29:59,000] [INFO] DFAST_QC completed!
[2023-03-17 07:29:59,000] [INFO] Total running time: 0h1m29s