[2023-03-18 23:40:00,430] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,430] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference
[2023-03-18 23:40:01,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,565] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,565] [INFO] Running command: cat /var/lib/cwl/stgba394c02-8f46-4f29-a222-8753538c7a95/OceanDNA-b1719.fa | prodigal -d OceanDNA-b1719/cds.fna -a OceanDNA-b1719/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:26,407] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:26,407] [INFO] Task started: HMMsearch
[2023-03-18 23:40:26,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b1719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/reference_markers.hmm OceanDNA-b1719/protein.faa > /dev/null
[2023-03-18 23:40:26,611] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:26,612] [INFO] Found 6/6 markers.
[2023-03-18 23:40:26,638] [INFO] Query marker FASTA was written to OceanDNA-b1719/markers.fasta
[2023-03-18 23:40:26,639] [INFO] Task started: Blastn
[2023-03-18 23:40:26,639] [INFO] Running command: blastn -query OceanDNA-b1719/markers.fasta -db /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/reference_markers.fasta -out OceanDNA-b1719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:27,192] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:27,193] [INFO] Selected 28 target genomes.
[2023-03-18 23:40:27,194] [INFO] Target genome list was writen to OceanDNA-b1719/target_genomes.txt
[2023-03-18 23:40:27,210] [INFO] Task started: fastANI
[2023-03-18 23:40:27,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgba394c02-8f46-4f29-a222-8753538c7a95/OceanDNA-b1719.fa --refList OceanDNA-b1719/target_genomes.txt --output OceanDNA-b1719/fastani_result.tsv --threads 1
[2023-03-18 23:40:45,825] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:45,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:45,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:45,829] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:45,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:40:45,830] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.3734	64	1267	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.2356	76	1267	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:45,830] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1719/tc_result.tsv
[2023-03-18 23:40:45,830] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:45,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:45,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/checkm_data
[2023-03-18 23:40:45,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:45,836] [INFO] Task started: CheckM
[2023-03-18 23:40:45,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1719/checkm_input OceanDNA-b1719/checkm_result
[2023-03-18 23:41:47,295] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:47,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:47,299] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:47,299] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:47,299] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1719/markers.fasta)
[2023-03-18 23:41:47,300] [INFO] Task started: Blastn
[2023-03-18 23:41:47,301] [INFO] Running command: blastn -query OceanDNA-b1719/markers.fasta -db /var/lib/cwl/stg8e98b4ec-84ae-4f07-b253-2d09f2707149/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:48,143] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:48,144] [INFO] Selected 27 target genomes.
[2023-03-18 23:41:48,144] [INFO] Target genome list was writen to OceanDNA-b1719/target_genomes_gtdb.txt
[2023-03-18 23:41:48,159] [INFO] Task started: fastANI
[2023-03-18 23:41:48,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgba394c02-8f46-4f29-a222-8753538c7a95/OceanDNA-b1719.fa --refList OceanDNA-b1719/target_genomes_gtdb.txt --output OceanDNA-b1719/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:42:01,386] [INFO] Task succeeded: fastANI
[2023-03-18 23:42:01,388] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:42:01,388] [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_003485885.1	s__UBA10347 sp003485885	96.0291	753	1267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	98.91	98.91	0.90	0.90	2	conclusive
GCA_905182135.1	s__UBA10347 sp905182135	78.2894	310	1267	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:42:01,389] [INFO] GTDB search result was written to OceanDNA-b1719/result_gtdb.tsv
[2023-03-18 23:42:01,389] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:42:01,389] [INFO] DFAST_QC result json was written to OceanDNA-b1719/dqc_result.json
[2023-03-18 23:42:01,389] [INFO] DFAST_QC completed!
[2023-03-18 23:42:01,389] [INFO] Total running time: 0h2m1s