[2023-03-19 01:12:15,647] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:12:15,648] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:12:15,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference
[2023-03-19 01:12:16,775] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:12:16,775] [INFO] Task started: Prodigal
[2023-03-19 01:12:16,775] [INFO] Running command: cat /var/lib/cwl/stg3cedf685-739c-4176-979d-45255a332d94/OceanDNA-b22977.fa | prodigal -d OceanDNA-b22977/cds.fna -a OceanDNA-b22977/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:12:46,638] [INFO] Task succeeded: Prodigal
[2023-03-19 01:12:46,638] [INFO] Task started: HMMsearch
[2023-03-19 01:12:46,638] [INFO] Running command: hmmsearch --tblout OceanDNA-b22977/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/reference_markers.hmm OceanDNA-b22977/protein.faa > /dev/null
[2023-03-19 01:12:46,873] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:12:46,874] [INFO] Found 6/6 markers.
[2023-03-19 01:12:46,905] [INFO] Query marker FASTA was written to OceanDNA-b22977/markers.fasta
[2023-03-19 01:12:46,906] [INFO] Task started: Blastn
[2023-03-19 01:12:46,906] [INFO] Running command: blastn -query OceanDNA-b22977/markers.fasta -db /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/reference_markers.fasta -out OceanDNA-b22977/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:12:47,427] [INFO] Task succeeded: Blastn
[2023-03-19 01:12:47,429] [INFO] Selected 22 target genomes.
[2023-03-19 01:12:47,429] [INFO] Target genome list was writen to OceanDNA-b22977/target_genomes.txt
[2023-03-19 01:12:47,444] [INFO] Task started: fastANI
[2023-03-19 01:12:47,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cedf685-739c-4176-979d-45255a332d94/OceanDNA-b22977.fa --refList OceanDNA-b22977/target_genomes.txt --output OceanDNA-b22977/fastani_result.tsv --threads 1
[2023-03-19 01:13:06,223] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:06,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:13:06,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:13:06,228] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:13:06,228] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:13:06,228] [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
Rubinisphaera italica	strain=Pan54	GCA_007859715.1	2527969	2527969	type	True	94.7248	1546	1684	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	76.5209	229	1684	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	76.0906	139	1684	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:13:06,229] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22977/tc_result.tsv
[2023-03-19 01:13:06,229] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:13:06,229] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:06,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/checkm_data
[2023-03-19 01:13:06,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:06,236] [INFO] Task started: CheckM
[2023-03-19 01:13:06,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22977/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22977/checkm_input OceanDNA-b22977/checkm_result
[2023-03-19 01:14:21,116] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:21,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:21,121] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:21,121] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:21,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22977/markers.fasta)
[2023-03-19 01:14:21,122] [INFO] Task started: Blastn
[2023-03-19 01:14:21,122] [INFO] Running command: blastn -query OceanDNA-b22977/markers.fasta -db /var/lib/cwl/stg85eb2884-76da-4e15-95a8-a4953473b07d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22977/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:21,839] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:21,842] [INFO] Selected 19 target genomes.
[2023-03-19 01:14:21,842] [INFO] Target genome list was writen to OceanDNA-b22977/target_genomes_gtdb.txt
[2023-03-19 01:14:21,861] [INFO] Task started: fastANI
[2023-03-19 01:14:21,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cedf685-739c-4176-979d-45255a332d94/OceanDNA-b22977.fa --refList OceanDNA-b22977/target_genomes_gtdb.txt --output OceanDNA-b22977/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:39,266] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:39,270] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:39,270] [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_007859715.1	s__Rubinisphaera italica	94.7466	1543	1684	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359185.1	s__Rubinisphaera sp002359185	86.4685	1353	1684	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	99.90	99.90	0.94	0.94	2	-
GCA_017795105.1	s__Rubinisphaera sp017795105	76.2801	224	1684	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	76.0908	139	1684	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765335.1	s__Rubinisphaera sp016765335	75.2835	50	1684	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:39,270] [INFO] GTDB search result was written to OceanDNA-b22977/result_gtdb.tsv
[2023-03-19 01:14:39,271] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:39,272] [INFO] DFAST_QC result json was written to OceanDNA-b22977/dqc_result.json
[2023-03-19 01:14:39,272] [INFO] DFAST_QC completed!
[2023-03-19 01:14:39,272] [INFO] Total running time: 0h2m24s