[2023-03-15 11:09:10,774] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,774] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,774] [INFO] DQC Reference Directory: /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference
[2023-03-15 11:09:11,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:11,939] [INFO] Task started: Prodigal
[2023-03-15 11:09:11,939] [INFO] Running command: cat /var/lib/cwl/stgdc9bca7c-3ea2-4d93-bbaa-9b89ce4486b7/OceanDNA-b20741.fa | prodigal -d OceanDNA-b20741/cds.fna -a OceanDNA-b20741/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:17,411] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:17,411] [INFO] Task started: HMMsearch
[2023-03-15 11:09:17,412] [INFO] Running command: hmmsearch --tblout OceanDNA-b20741/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/reference_markers.hmm OceanDNA-b20741/protein.faa > /dev/null
[2023-03-15 11:09:17,600] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:17,601] [INFO] Found 6/6 markers.
[2023-03-15 11:09:17,611] [INFO] Query marker FASTA was written to OceanDNA-b20741/markers.fasta
[2023-03-15 11:09:17,611] [INFO] Task started: Blastn
[2023-03-15 11:09:17,611] [INFO] Running command: blastn -query OceanDNA-b20741/markers.fasta -db /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/reference_markers.fasta -out OceanDNA-b20741/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:18,148] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:18,149] [INFO] Selected 30 target genomes.
[2023-03-15 11:09:18,149] [INFO] Target genome list was writen to OceanDNA-b20741/target_genomes.txt
[2023-03-15 11:09:18,165] [INFO] Task started: fastANI
[2023-03-15 11:09:18,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9bca7c-3ea2-4d93-bbaa-9b89ce4486b7/OceanDNA-b20741.fa --refList OceanDNA-b20741/target_genomes.txt --output OceanDNA-b20741/fastani_result.tsv --threads 1
[2023-03-15 11:09:31,817] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:31,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:31,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:31,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:31,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:09:31,818] [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
--------------------------------------------------------------------------------
[2023-03-15 11:09:31,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20741/tc_result.tsv
[2023-03-15 11:09:31,819] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:31,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:31,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/checkm_data
[2023-03-15 11:09:31,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:31,824] [INFO] Task started: CheckM
[2023-03-15 11:09:31,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20741/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20741/checkm_input OceanDNA-b20741/checkm_result
[2023-03-15 11:09:51,926] [INFO] Task succeeded: CheckM
[2023-03-15 11:09:51,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:09:51,928] [INFO] ===== Completeness check finished =====
[2023-03-15 11:09:51,929] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:09:51,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20741/markers.fasta)
[2023-03-15 11:09:51,929] [INFO] Task started: Blastn
[2023-03-15 11:09:51,929] [INFO] Running command: blastn -query OceanDNA-b20741/markers.fasta -db /var/lib/cwl/stga72076c4-7848-4efb-930a-5e09efae0fb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20741/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:52,801] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:52,802] [INFO] Selected 26 target genomes.
[2023-03-15 11:09:52,802] [INFO] Target genome list was writen to OceanDNA-b20741/target_genomes_gtdb.txt
[2023-03-15 11:09:52,826] [INFO] Task started: fastANI
[2023-03-15 11:09:52,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9bca7c-3ea2-4d93-bbaa-9b89ce4486b7/OceanDNA-b20741.fa --refList OceanDNA-b20741/target_genomes_gtdb.txt --output OceanDNA-b20741/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:00,474] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:00,478] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:10:00,478] [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_002167465.1	s__TMED6 sp002167465	98.1972	324	351	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	98.36	98.36	0.95	0.95	2	conclusive
GCA_002710085.1	s__TMED6 sp002710085	80.9856	126	351	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239355.1	s__TMED6 sp014239355	80.6858	226	351	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701185.1	s__TMED6 sp002701185	78.4222	150	351	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711465.1	s__TMED6 sp002711465	78.2919	153	351	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:00,478] [INFO] GTDB search result was written to OceanDNA-b20741/result_gtdb.tsv
[2023-03-15 11:10:00,478] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:00,479] [INFO] DFAST_QC result json was written to OceanDNA-b20741/dqc_result.json
[2023-03-15 11:10:00,479] [INFO] DFAST_QC completed!
[2023-03-15 11:10:00,479] [INFO] Total running time: 0h0m50s