[2023-03-15 08:59:47,082] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,083] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,083] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference
[2023-03-15 08:59:48,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,185] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,186] [INFO] Running command: cat /var/lib/cwl/stg1b2eb9f7-60f6-4f25-821c-141afeaf73dc/OceanDNA-b17610.fa | prodigal -d OceanDNA-b17610/cds.fna -a OceanDNA-b17610/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:05,460] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:05,461] [INFO] Task started: HMMsearch
[2023-03-15 09:00:05,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b17610/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/reference_markers.hmm OceanDNA-b17610/protein.faa > /dev/null
[2023-03-15 09:00:05,685] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:05,685] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1b2eb9f7-60f6-4f25-821c-141afeaf73dc/OceanDNA-b17610.fa]
[2023-03-15 09:00:05,715] [INFO] Query marker FASTA was written to OceanDNA-b17610/markers.fasta
[2023-03-15 09:00:05,716] [INFO] Task started: Blastn
[2023-03-15 09:00:05,716] [INFO] Running command: blastn -query OceanDNA-b17610/markers.fasta -db /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/reference_markers.fasta -out OceanDNA-b17610/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:06,321] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:06,322] [INFO] Selected 30 target genomes.
[2023-03-15 09:00:06,322] [INFO] Target genome list was writen to OceanDNA-b17610/target_genomes.txt
[2023-03-15 09:00:06,346] [INFO] Task started: fastANI
[2023-03-15 09:00:06,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2eb9f7-60f6-4f25-821c-141afeaf73dc/OceanDNA-b17610.fa --refList OceanDNA-b17610/target_genomes.txt --output OceanDNA-b17610/fastani_result.tsv --threads 1
[2023-03-15 09:00:26,986] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:26,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:26,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:26,991] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:26,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:26,991] [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=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.6724	68	835	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.6724	68	835	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	74.5582	52	835	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:26,991] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17610/tc_result.tsv
[2023-03-15 09:00:26,991] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:26,991] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:26,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/checkm_data
[2023-03-15 09:00:26,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:26,999] [INFO] Task started: CheckM
[2023-03-15 09:00:26,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17610/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17610/checkm_input OceanDNA-b17610/checkm_result
[2023-03-15 09:01:11,639] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:11,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.82%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:11,643] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:11,643] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:11,643] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17610/markers.fasta)
[2023-03-15 09:01:11,644] [INFO] Task started: Blastn
[2023-03-15 09:01:11,644] [INFO] Running command: blastn -query OceanDNA-b17610/markers.fasta -db /var/lib/cwl/stgf4e5cff3-8eeb-41bf-b8fc-2bc2ec1d01d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17610/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:12,531] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:12,532] [INFO] Selected 26 target genomes.
[2023-03-15 09:01:12,532] [INFO] Target genome list was writen to OceanDNA-b17610/target_genomes_gtdb.txt
[2023-03-15 09:01:12,602] [INFO] Task started: fastANI
[2023-03-15 09:01:12,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b2eb9f7-60f6-4f25-821c-141afeaf73dc/OceanDNA-b17610.fa --refList OceanDNA-b17610/target_genomes_gtdb.txt --output OceanDNA-b17610/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:30,095] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:30,100] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:01:30,100] [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_016187725.1	s__SICG01 sp016187725	76.5822	106	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725915.1	s__GCA-2725915 sp002725915	76.2892	66	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	76.2319	100	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841115.1	s__GCA-2724215 sp009841115	75.9637	66	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.5256	61	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
GCA_009840005.1	s__GCA-2724215 sp009840005	75.5142	77	835	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:30,100] [INFO] GTDB search result was written to OceanDNA-b17610/result_gtdb.tsv
[2023-03-15 09:01:30,100] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:30,101] [INFO] DFAST_QC result json was written to OceanDNA-b17610/dqc_result.json
[2023-03-15 09:01:30,101] [INFO] DFAST_QC completed!
[2023-03-15 09:01:30,101] [INFO] Total running time: 0h1m43s