[2023-03-15 17:46:31,525] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,525] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference
[2023-03-15 17:46:32,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,688] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,688] [INFO] Running command: cat /var/lib/cwl/stg0127a9d2-0740-4623-8439-b15b6b6e35e9/OceanDNA-b24894.fa | prodigal -d OceanDNA-b24894/cds.fna -a OceanDNA-b24894/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:53,228] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:53,228] [INFO] Task started: HMMsearch
[2023-03-15 17:46:53,228] [INFO] Running command: hmmsearch --tblout OceanDNA-b24894/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/reference_markers.hmm OceanDNA-b24894/protein.faa > /dev/null
[2023-03-15 17:46:53,472] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:53,472] [INFO] Found 6/6 markers.
[2023-03-15 17:46:53,496] [INFO] Query marker FASTA was written to OceanDNA-b24894/markers.fasta
[2023-03-15 17:46:53,497] [INFO] Task started: Blastn
[2023-03-15 17:46:53,497] [INFO] Running command: blastn -query OceanDNA-b24894/markers.fasta -db /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/reference_markers.fasta -out OceanDNA-b24894/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:54,168] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:54,171] [INFO] Selected 30 target genomes.
[2023-03-15 17:46:54,171] [INFO] Target genome list was writen to OceanDNA-b24894/target_genomes.txt
[2023-03-15 17:46:54,194] [INFO] Task started: fastANI
[2023-03-15 17:46:54,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg0127a9d2-0740-4623-8439-b15b6b6e35e9/OceanDNA-b24894.fa --refList OceanDNA-b24894/target_genomes.txt --output OceanDNA-b24894/fastani_result.tsv --threads 1
[2023-03-15 17:47:14,935] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:14,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:14,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:14,941] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:14,941] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:14,941] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.2554	70	1050	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.0901	53	1050	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.0523	99	1050	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.0396	52	1050	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	75.9382	118	1050	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:14,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24894/tc_result.tsv
[2023-03-15 17:47:14,943] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:14,944] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:14,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/checkm_data
[2023-03-15 17:47:14,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:14,950] [INFO] Task started: CheckM
[2023-03-15 17:47:14,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24894/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24894/checkm_input OceanDNA-b24894/checkm_result
[2023-03-15 17:48:05,833] [INFO] Task succeeded: CheckM
[2023-03-15 17:48:05,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:48:05,840] [INFO] ===== Completeness check finished =====
[2023-03-15 17:48:05,841] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:48:05,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24894/markers.fasta)
[2023-03-15 17:48:05,842] [INFO] Task started: Blastn
[2023-03-15 17:48:05,842] [INFO] Running command: blastn -query OceanDNA-b24894/markers.fasta -db /var/lib/cwl/stgc9243a2e-e1e3-4d84-963c-11278125215b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24894/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:48:06,973] [INFO] Task succeeded: Blastn
[2023-03-15 17:48:07,088] [INFO] Selected 13 target genomes.
[2023-03-15 17:48:07,088] [INFO] Target genome list was writen to OceanDNA-b24894/target_genomes_gtdb.txt
[2023-03-15 17:48:07,108] [INFO] Task started: fastANI
[2023-03-15 17:48:07,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg0127a9d2-0740-4623-8439-b15b6b6e35e9/OceanDNA-b24894.fa --refList OceanDNA-b24894/target_genomes_gtdb.txt --output OceanDNA-b24894/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:48:15,449] [INFO] Task succeeded: fastANI
[2023-03-15 17:48:15,455] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:48:15,455] [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_002695905.1	s__Mf105b01 sp002695905	99.8703	932	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.79	99.79	0.82	0.82	2	conclusive
GCA_003330885.1	s__Mf105b01 sp003330885	85.6554	969	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000509225.1	s__Mf105b01 sp000509225	85.1909	946	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	98.75	98.75	0.94	0.94	2	-
GCA_002715765.1	s__Mf105b01 sp002715765	77.5315	182	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.04	98.86	0.91	0.89	5	-
GCA_002746275.1	s__Mf105b01 sp002746275	76.993	210	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	76.1727	78	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.0483	98	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739695.1	s__Tepidicaulis marinus	75.9382	118	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	98.55	98.55	0.94	0.94	2	-
GCA_002841195.1	s__Parvibaculum sp002841195	75.793	54	1050	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 17:48:15,457] [INFO] GTDB search result was written to OceanDNA-b24894/result_gtdb.tsv
[2023-03-15 17:48:15,457] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:48:15,459] [INFO] DFAST_QC result json was written to OceanDNA-b24894/dqc_result.json
[2023-03-15 17:48:15,460] [INFO] DFAST_QC completed!
[2023-03-15 17:48:15,460] [INFO] Total running time: 0h1m44s