[2023-03-16 09:58:17,576] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:58:17,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:58:17,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference
[2023-03-16 09:58:18,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:58:18,665] [INFO] Task started: Prodigal
[2023-03-16 09:58:18,665] [INFO] Running command: cat /var/lib/cwl/stgcbb1fc0a-947e-4118-b93d-20df0be2b7f2/OceanDNA-b32887.fa | prodigal -d OceanDNA-b32887/cds.fna -a OceanDNA-b32887/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:58:26,168] [INFO] Task succeeded: Prodigal
[2023-03-16 09:58:26,168] [INFO] Task started: HMMsearch
[2023-03-16 09:58:26,168] [INFO] Running command: hmmsearch --tblout OceanDNA-b32887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/reference_markers.hmm OceanDNA-b32887/protein.faa > /dev/null
[2023-03-16 09:58:26,323] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:58:26,323] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcbb1fc0a-947e-4118-b93d-20df0be2b7f2/OceanDNA-b32887.fa]
[2023-03-16 09:58:26,339] [INFO] Query marker FASTA was written to OceanDNA-b32887/markers.fasta
[2023-03-16 09:58:26,340] [INFO] Task started: Blastn
[2023-03-16 09:58:26,340] [INFO] Running command: blastn -query OceanDNA-b32887/markers.fasta -db /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/reference_markers.fasta -out OceanDNA-b32887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:58:27,047] [INFO] Task succeeded: Blastn
[2023-03-16 09:58:27,049] [INFO] Selected 29 target genomes.
[2023-03-16 09:58:27,049] [INFO] Target genome list was writen to OceanDNA-b32887/target_genomes.txt
[2023-03-16 09:58:27,069] [INFO] Task started: fastANI
[2023-03-16 09:58:27,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb1fc0a-947e-4118-b93d-20df0be2b7f2/OceanDNA-b32887.fa --refList OceanDNA-b32887/target_genomes.txt --output OceanDNA-b32887/fastani_result.tsv --threads 1
[2023-03-16 09:58:48,979] [INFO] Task succeeded: fastANI
[2023-03-16 09:58:48,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:58:48,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:58:48,983] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:58:48,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:58:48,984] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4461	53	313	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.446	53	313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:58:48,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32887/tc_result.tsv
[2023-03-16 09:58:48,984] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:58:48,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:58:48,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/checkm_data
[2023-03-16 09:58:48,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:58:48,989] [INFO] Task started: CheckM
[2023-03-16 09:58:48,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32887/checkm_input OceanDNA-b32887/checkm_result
[2023-03-16 09:59:14,213] [INFO] Task succeeded: CheckM
[2023-03-16 09:59:14,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.13%
Contamintation: 9.23%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:59:14,216] [INFO] ===== Completeness check finished =====
[2023-03-16 09:59:14,216] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:59:14,216] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32887/markers.fasta)
[2023-03-16 09:59:14,217] [INFO] Task started: Blastn
[2023-03-16 09:59:14,217] [INFO] Running command: blastn -query OceanDNA-b32887/markers.fasta -db /var/lib/cwl/stg90f71578-7d83-4fcb-bd2e-acb1f76e6bb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:59:15,336] [INFO] Task succeeded: Blastn
[2023-03-16 09:59:15,336] [INFO] Selected 11 target genomes.
[2023-03-16 09:59:15,337] [INFO] Target genome list was writen to OceanDNA-b32887/target_genomes_gtdb.txt
[2023-03-16 09:59:15,347] [INFO] Task started: fastANI
[2023-03-16 09:59:15,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbb1fc0a-947e-4118-b93d-20df0be2b7f2/OceanDNA-b32887.fa --refList OceanDNA-b32887/target_genomes_gtdb.txt --output OceanDNA-b32887/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:59:22,427] [INFO] Task succeeded: fastANI
[2023-03-16 09:59:22,432] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:59:22,432] [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_002711265.1	s__UBA7985 sp002711265	98.9494	253	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.38	98.76	0.89	0.83	3	conclusive
GCA_002708995.1	s__UBA7985 sp002708995	93.6604	287	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	95.44	95.44	0.84	0.83	3	-
GCA_002690455.1	s__UBA7985 sp002690455	81.2187	157	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479265.1	s__UBA7985 sp905479265	77.8479	104	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705565.1	s__UBA7985 sp002705565	77.8082	118	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.09	99.09	0.80	0.80	2	-
GCA_002700865.1	s__UBA7985 sp002700865	77.749	100	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.96	99.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:59:22,433] [INFO] GTDB search result was written to OceanDNA-b32887/result_gtdb.tsv
[2023-03-16 09:59:22,433] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:59:22,434] [INFO] DFAST_QC result json was written to OceanDNA-b32887/dqc_result.json
[2023-03-16 09:59:22,434] [INFO] DFAST_QC completed!
[2023-03-16 09:59:22,434] [INFO] Total running time: 0h1m5s