[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,210] [INFO] Running command: cat /var/lib/cwl/stge25f40cf-ff74-46ca-8d9b-7cd3df84a3a7/OceanDNA-b5484.fa | prodigal -d OceanDNA-b5484/cds.fna -a OceanDNA-b5484/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:55,635] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:55,635] [INFO] Task started: HMMsearch
[2023-03-18 20:40:55,636] [INFO] Running command: hmmsearch --tblout OceanDNA-b5484/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/reference_markers.hmm OceanDNA-b5484/protein.faa > /dev/null
[2023-03-18 20:40:55,875] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:55,875] [INFO] Found 6/6 markers.
[2023-03-18 20:40:55,893] [INFO] Query marker FASTA was written to OceanDNA-b5484/markers.fasta
[2023-03-18 20:40:55,894] [INFO] Task started: Blastn
[2023-03-18 20:40:55,894] [INFO] Running command: blastn -query OceanDNA-b5484/markers.fasta -db /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/reference_markers.fasta -out OceanDNA-b5484/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:56,452] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:56,453] [INFO] Selected 28 target genomes.
[2023-03-18 20:40:56,453] [INFO] Target genome list was writen to OceanDNA-b5484/target_genomes.txt
[2023-03-18 20:40:56,465] [INFO] Task started: fastANI
[2023-03-18 20:40:56,465] [INFO] Running command: fastANI --query /var/lib/cwl/stge25f40cf-ff74-46ca-8d9b-7cd3df84a3a7/OceanDNA-b5484.fa --refList OceanDNA-b5484/target_genomes.txt --output OceanDNA-b5484/fastani_result.tsv --threads 1
[2023-03-18 20:41:12,253] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:12,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:12,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:12,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:12,253] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:41:12,254] [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
--------------------------------------------------------------------------------
[2023-03-18 20:41:12,254] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5484/tc_result.tsv
[2023-03-18 20:41:12,254] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:12,254] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:12,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/checkm_data
[2023-03-18 20:41:12,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:12,260] [INFO] Task started: CheckM
[2023-03-18 20:41:12,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5484/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5484/checkm_input OceanDNA-b5484/checkm_result
[2023-03-18 20:41:52,371] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:52,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:52,374] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:52,374] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:52,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5484/markers.fasta)
[2023-03-18 20:41:52,374] [INFO] Task started: Blastn
[2023-03-18 20:41:52,374] [INFO] Running command: blastn -query OceanDNA-b5484/markers.fasta -db /var/lib/cwl/stgf94d2266-50a0-488c-a603-825b84c19800/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5484/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:53,107] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:53,107] [INFO] Selected 21 target genomes.
[2023-03-18 20:41:53,108] [INFO] Target genome list was writen to OceanDNA-b5484/target_genomes_gtdb.txt
[2023-03-18 20:41:53,147] [INFO] Task started: fastANI
[2023-03-18 20:41:53,147] [INFO] Running command: fastANI --query /var/lib/cwl/stge25f40cf-ff74-46ca-8d9b-7cd3df84a3a7/OceanDNA-b5484.fa --refList OceanDNA-b5484/target_genomes_gtdb.txt --output OceanDNA-b5484/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:01,612] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:01,617] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:01,617] [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_002480215.1	s__UBA952 sp002480215	81.9513	411	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_002167775.1	s__UBA952 sp002167775	81.2371	480	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
GCA_002683585.1	s__UBA952 sp002683585	81.1775	259	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182495.1	s__UBA952 sp905182495	77.0088	130	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331365.1	s__UBA952 sp003331365	76.1767	51	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:01,617] [INFO] GTDB search result was written to OceanDNA-b5484/result_gtdb.tsv
[2023-03-18 20:42:01,617] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:01,618] [INFO] DFAST_QC result json was written to OceanDNA-b5484/dqc_result.json
[2023-03-18 20:42:01,618] [INFO] DFAST_QC completed!
[2023-03-18 20:42:01,618] [INFO] Total running time: 0h1m22s