[2023-03-15 10:09:49,679] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,679] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference
[2023-03-15 10:09:51,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stgb91b6f91-5a1c-484f-8f71-40a01e1d3247/OceanDNA-b22830.fa | prodigal -d OceanDNA-b22830/cds.fna -a OceanDNA-b22830/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:41,260] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:41,260] [INFO] Task started: HMMsearch
[2023-03-15 10:10:41,260] [INFO] Running command: hmmsearch --tblout OceanDNA-b22830/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/reference_markers.hmm OceanDNA-b22830/protein.faa > /dev/null
[2023-03-15 10:10:41,586] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:41,586] [INFO] Found 6/6 markers.
[2023-03-15 10:10:41,638] [INFO] Query marker FASTA was written to OceanDNA-b22830/markers.fasta
[2023-03-15 10:10:41,639] [INFO] Task started: Blastn
[2023-03-15 10:10:41,639] [INFO] Running command: blastn -query OceanDNA-b22830/markers.fasta -db /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/reference_markers.fasta -out OceanDNA-b22830/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:42,188] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:42,189] [INFO] Selected 30 target genomes.
[2023-03-15 10:10:42,190] [INFO] Target genome list was writen to OceanDNA-b22830/target_genomes.txt
[2023-03-15 10:10:42,341] [INFO] Task started: fastANI
[2023-03-15 10:10:42,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91b6f91-5a1c-484f-8f71-40a01e1d3247/OceanDNA-b22830.fa --refList OceanDNA-b22830/target_genomes.txt --output OceanDNA-b22830/fastani_result.tsv --threads 1
[2023-03-15 10:11:09,834] [INFO] Task succeeded: fastANI
[2023-03-15 10:11:09,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:11:09,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:11:09,841] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:11:09,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:11:09,842] [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 brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	75.9123	59	2666	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.7216	106	2666	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.5373	77	2666	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.2708	103	2666	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.2691	76	2666	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	75.2173	58	2666	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	75.2077	59	2666	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:11:09,843] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22830/tc_result.tsv
[2023-03-15 10:11:09,845] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:11:09,845] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:11:09,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/checkm_data
[2023-03-15 10:11:09,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:11:09,866] [INFO] Task started: CheckM
[2023-03-15 10:11:09,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22830/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22830/checkm_input OceanDNA-b22830/checkm_result
[2023-03-15 10:13:10,493] [INFO] Task succeeded: CheckM
[2023-03-15 10:13:10,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:13:10,709] [INFO] ===== Completeness check finished =====
[2023-03-15 10:13:10,709] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:13:10,710] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22830/markers.fasta)
[2023-03-15 10:13:10,711] [INFO] Task started: Blastn
[2023-03-15 10:13:10,711] [INFO] Running command: blastn -query OceanDNA-b22830/markers.fasta -db /var/lib/cwl/stgcd897d3d-98df-4bcb-ab29-269f026be7e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22830/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:13:12,104] [INFO] Task succeeded: Blastn
[2023-03-15 10:13:12,109] [INFO] Selected 35 target genomes.
[2023-03-15 10:13:12,110] [INFO] Target genome list was writen to OceanDNA-b22830/target_genomes_gtdb.txt
[2023-03-15 10:13:13,849] [INFO] Task started: fastANI
[2023-03-15 10:13:13,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91b6f91-5a1c-484f-8f71-40a01e1d3247/OceanDNA-b22830.fa --refList OceanDNA-b22830/target_genomes_gtdb.txt --output OceanDNA-b22830/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:13:41,249] [INFO] Task succeeded: fastANI
[2023-03-15 10:13:41,255] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:13:41,255] [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_013203845.1	s__JABMPE01 sp013203845	78.9129	1090	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779365.1	s__JABMPE01 sp016779365	78.8368	528	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	76.3698	335	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.4917	84	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584345.1	s__Rubinisphaera sp014584345	75.4396	50	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.2691	76	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299185.1	s__AM-0621 sp900299185	75.0923	88	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__AM-0621	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	74.9578	61	2666	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:13:41,259] [INFO] GTDB search result was written to OceanDNA-b22830/result_gtdb.tsv
[2023-03-15 10:13:41,265] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:13:41,271] [INFO] DFAST_QC result json was written to OceanDNA-b22830/dqc_result.json
[2023-03-15 10:13:41,272] [INFO] DFAST_QC completed!
[2023-03-15 10:13:41,272] [INFO] Total running time: 0h3m52s