[2023-03-19 04:43:18,651] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,651] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference
[2023-03-19 04:43:19,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,795] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,796] [INFO] Running command: cat /var/lib/cwl/stgc85d78f9-6cee-42b9-9e98-647456587ecf/OceanDNA-b24900.fa | prodigal -d OceanDNA-b24900/cds.fna -a OceanDNA-b24900/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:41,637] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:41,638] [INFO] Task started: HMMsearch
[2023-03-19 04:43:41,638] [INFO] Running command: hmmsearch --tblout OceanDNA-b24900/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/reference_markers.hmm OceanDNA-b24900/protein.faa > /dev/null
[2023-03-19 04:43:41,848] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:41,849] [INFO] Found 6/6 markers.
[2023-03-19 04:43:41,870] [INFO] Query marker FASTA was written to OceanDNA-b24900/markers.fasta
[2023-03-19 04:43:41,870] [INFO] Task started: Blastn
[2023-03-19 04:43:41,871] [INFO] Running command: blastn -query OceanDNA-b24900/markers.fasta -db /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/reference_markers.fasta -out OceanDNA-b24900/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:42,518] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:42,519] [INFO] Selected 30 target genomes.
[2023-03-19 04:43:42,519] [INFO] Target genome list was writen to OceanDNA-b24900/target_genomes.txt
[2023-03-19 04:43:42,549] [INFO] Task started: fastANI
[2023-03-19 04:43:42,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85d78f9-6cee-42b9-9e98-647456587ecf/OceanDNA-b24900.fa --refList OceanDNA-b24900/target_genomes.txt --output OceanDNA-b24900/fastani_result.tsv --threads 1
[2023-03-19 04:44:01,324] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:01,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:44:01,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:44:01,329] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:44:01,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:44:01,329] [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
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	76.4631	121	1134	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	75.9703	106	1134	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	75.7184	80	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:44:01,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24900/tc_result.tsv
[2023-03-19 04:44:01,329] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:44:01,329] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:44:01,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/checkm_data
[2023-03-19 04:44:01,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:44:01,473] [INFO] Task started: CheckM
[2023-03-19 04:44:01,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24900/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24900/checkm_input OceanDNA-b24900/checkm_result
[2023-03-19 04:44:57,057] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:57,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:57,061] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:57,061] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:57,061] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24900/markers.fasta)
[2023-03-19 04:44:57,062] [INFO] Task started: Blastn
[2023-03-19 04:44:57,062] [INFO] Running command: blastn -query OceanDNA-b24900/markers.fasta -db /var/lib/cwl/stgda3c6874-13ba-4af0-ac22-b5f3722837b9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24900/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:58,158] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:58,159] [INFO] Selected 23 target genomes.
[2023-03-19 04:44:58,159] [INFO] Target genome list was writen to OceanDNA-b24900/target_genomes_gtdb.txt
[2023-03-19 04:44:58,198] [INFO] Task started: fastANI
[2023-03-19 04:44:58,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgc85d78f9-6cee-42b9-9e98-647456587ecf/OceanDNA-b24900.fa --refList OceanDNA-b24900/target_genomes_gtdb.txt --output OceanDNA-b24900/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:45:12,831] [INFO] Task succeeded: fastANI
[2023-03-19 04:45:12,838] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:45:12,839] [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_002715765.1	s__Mf105b01 sp002715765	99.0502	1037	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.04	98.86	0.91	0.89	5	conclusive
GCA_000509225.1	s__Mf105b01 sp000509225	77.8666	220	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	98.75	98.75	0.94	0.94	2	-
GCA_002695905.1	s__Mf105b01 sp002695905	77.5897	181	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	99.79	99.79	0.82	0.82	2	-
GCA_003330885.1	s__Mf105b01 sp003330885	77.101	203	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746275.1	s__Mf105b01 sp002746275	76.6213	199	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Mf105b01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739695.1	s__Tepidicaulis marinus	76.4631	121	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	98.55	98.55	0.94	0.94	2	-
GCA_002389665.1	s__Tepidicaulis sp002389665	76.2417	118	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124805.1	s__Parvibaculum sp016124805	76.1181	89	1134	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	75.9703	106	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	75.8445	96	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	75.5066	70	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:45:12,839] [INFO] GTDB search result was written to OceanDNA-b24900/result_gtdb.tsv
[2023-03-19 04:45:12,839] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:45:12,840] [INFO] DFAST_QC result json was written to OceanDNA-b24900/dqc_result.json
[2023-03-19 04:45:12,840] [INFO] DFAST_QC completed!
[2023-03-19 04:45:12,840] [INFO] Total running time: 0h1m54s