[2023-03-18 22:17:12,709] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,709] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference
[2023-03-18 22:17:13,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,842] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,843] [INFO] Running command: cat /var/lib/cwl/stga35cc605-6cc6-4524-b27a-a6bf39c7c127/OceanDNA-b23844.fa | prodigal -d OceanDNA-b23844/cds.fna -a OceanDNA-b23844/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:22,686] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:22,686] [INFO] Task started: HMMsearch
[2023-03-18 22:17:22,686] [INFO] Running command: hmmsearch --tblout OceanDNA-b23844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/reference_markers.hmm OceanDNA-b23844/protein.faa > /dev/null
[2023-03-18 22:17:22,825] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:22,826] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga35cc605-6cc6-4524-b27a-a6bf39c7c127/OceanDNA-b23844.fa]
[2023-03-18 22:17:22,841] [INFO] Query marker FASTA was written to OceanDNA-b23844/markers.fasta
[2023-03-18 22:17:22,842] [INFO] Task started: Blastn
[2023-03-18 22:17:22,842] [INFO] Running command: blastn -query OceanDNA-b23844/markers.fasta -db /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/reference_markers.fasta -out OceanDNA-b23844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:23,406] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:23,406] [INFO] Selected 15 target genomes.
[2023-03-18 22:17:23,407] [INFO] Target genome list was writen to OceanDNA-b23844/target_genomes.txt
[2023-03-18 22:17:23,415] [INFO] Task started: fastANI
[2023-03-18 22:17:23,415] [INFO] Running command: fastANI --query /var/lib/cwl/stga35cc605-6cc6-4524-b27a-a6bf39c7c127/OceanDNA-b23844.fa --refList OceanDNA-b23844/target_genomes.txt --output OceanDNA-b23844/fastani_result.tsv --threads 1
[2023-03-18 22:17:32,233] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:32,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:32,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:32,238] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:17:32,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:17:32,238] [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
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	75.7056	62	436	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	75.7056	62	436	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.553	60	436	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.3185	65	436	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	74.9493	76	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:17:32,254] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23844/tc_result.tsv
[2023-03-18 22:17:32,254] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:32,254] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:32,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/checkm_data
[2023-03-18 22:17:32,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:32,262] [INFO] Task started: CheckM
[2023-03-18 22:17:32,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23844/checkm_input OceanDNA-b23844/checkm_result
[2023-03-18 22:17:58,482] [INFO] Task succeeded: CheckM
[2023-03-18 22:17:58,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:17:58,511] [INFO] ===== Completeness check finished =====
[2023-03-18 22:17:58,511] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:17:58,511] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23844/markers.fasta)
[2023-03-18 22:17:58,512] [INFO] Task started: Blastn
[2023-03-18 22:17:58,512] [INFO] Running command: blastn -query OceanDNA-b23844/markers.fasta -db /var/lib/cwl/stgff56e40e-95cd-45d8-b908-3f12a6237afa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:59,341] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:59,342] [INFO] Selected 15 target genomes.
[2023-03-18 22:17:59,342] [INFO] Target genome list was writen to OceanDNA-b23844/target_genomes_gtdb.txt
[2023-03-18 22:17:59,356] [INFO] Task started: fastANI
[2023-03-18 22:17:59,356] [INFO] Running command: fastANI --query /var/lib/cwl/stga35cc605-6cc6-4524-b27a-a6bf39c7c127/OceanDNA-b23844.fa --refList OceanDNA-b23844/target_genomes_gtdb.txt --output OceanDNA-b23844/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:18:08,688] [INFO] Task succeeded: fastANI
[2023-03-18 22:18:08,690] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:18:08,691] [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_017161425.1	s__Marinicauda algicola	75.7056	62	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130795.1	s__Azospirillum thermophilum	75.3185	65	436	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:18:08,691] [INFO] GTDB search result was written to OceanDNA-b23844/result_gtdb.tsv
[2023-03-18 22:18:08,691] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:18:08,692] [INFO] DFAST_QC result json was written to OceanDNA-b23844/dqc_result.json
[2023-03-18 22:18:08,692] [INFO] DFAST_QC completed!
[2023-03-18 22:18:08,692] [INFO] Total running time: 0h0m56s