[2023-03-15 07:03:38,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference
[2023-03-15 07:03:39,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,969] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,969] [INFO] Running command: cat /var/lib/cwl/stg176d6c87-9488-4450-a53a-7555f972138c/OceanDNA-b24968.fa | prodigal -d OceanDNA-b24968/cds.fna -a OceanDNA-b24968/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:54,652] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:54,653] [INFO] Task started: HMMsearch
[2023-03-15 07:03:54,653] [INFO] Running command: hmmsearch --tblout OceanDNA-b24968/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/reference_markers.hmm OceanDNA-b24968/protein.faa > /dev/null
[2023-03-15 07:03:54,837] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:54,838] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg176d6c87-9488-4450-a53a-7555f972138c/OceanDNA-b24968.fa]
[2023-03-15 07:03:54,867] [INFO] Query marker FASTA was written to OceanDNA-b24968/markers.fasta
[2023-03-15 07:03:54,867] [INFO] Task started: Blastn
[2023-03-15 07:03:54,867] [INFO] Running command: blastn -query OceanDNA-b24968/markers.fasta -db /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/reference_markers.fasta -out OceanDNA-b24968/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:55,464] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:55,466] [INFO] Selected 24 target genomes.
[2023-03-15 07:03:55,467] [INFO] Target genome list was writen to OceanDNA-b24968/target_genomes.txt
[2023-03-15 07:03:55,482] [INFO] Task started: fastANI
[2023-03-15 07:03:55,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg176d6c87-9488-4450-a53a-7555f972138c/OceanDNA-b24968.fa --refList OceanDNA-b24968/target_genomes.txt --output OceanDNA-b24968/fastani_result.tsv --threads 1
[2023-03-15 07:04:09,587] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:09,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:09,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:09,593] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:09,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:04:09,593] [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
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	78.7596	332	695	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	78.7417	329	695	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	78.6911	342	695	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	75.9721	60	695	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	75.8353	68	695	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:09,594] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24968/tc_result.tsv
[2023-03-15 07:04:09,595] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:09,596] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:09,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/checkm_data
[2023-03-15 07:04:09,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:09,623] [INFO] Task started: CheckM
[2023-03-15 07:04:09,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24968/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24968/checkm_input OceanDNA-b24968/checkm_result
[2023-03-15 07:04:48,621] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:48,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:48,659] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:48,659] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:48,659] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24968/markers.fasta)
[2023-03-15 07:04:48,659] [INFO] Task started: Blastn
[2023-03-15 07:04:48,659] [INFO] Running command: blastn -query OceanDNA-b24968/markers.fasta -db /var/lib/cwl/stg071c56f3-05e4-433f-8ff2-f25634d77d3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24968/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:49,515] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:49,525] [INFO] Selected 22 target genomes.
[2023-03-15 07:04:49,525] [INFO] Target genome list was writen to OceanDNA-b24968/target_genomes_gtdb.txt
[2023-03-15 07:04:49,691] [INFO] Task started: fastANI
[2023-03-15 07:04:49,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg176d6c87-9488-4450-a53a-7555f972138c/OceanDNA-b24968.fa --refList OceanDNA-b24968/target_genomes_gtdb.txt --output OceanDNA-b24968/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:05:03,145] [INFO] Task succeeded: fastANI
[2023-03-15 07:05:03,149] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:05:03,149] [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
GCF_000689395.1	s__Pyruvatibacter ectocarpi	95.5534	618	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012848855.1	s__Pyruvatibacter mobilis	78.6911	342	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000739695.1	s__Tepidicaulis marinus	75.9721	60	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	98.55	98.55	0.94	0.94	2	-
GCF_011762095.1	s__Parvibaculum indicum	75.8353	68	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124805.1	s__Parvibaculum sp016124805	75.781	61	695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:05:03,152] [INFO] GTDB search result was written to OceanDNA-b24968/result_gtdb.tsv
[2023-03-15 07:05:03,156] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:05:03,161] [INFO] DFAST_QC result json was written to OceanDNA-b24968/dqc_result.json
[2023-03-15 07:05:03,161] [INFO] DFAST_QC completed!
[2023-03-15 07:05:03,161] [INFO] Total running time: 0h1m24s