[2023-03-16 21:45:15,322] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,323] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference
[2023-03-16 21:45:16,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,479] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,480] [INFO] Running command: cat /var/lib/cwl/stg7dc8a9aa-9990-4b69-aea1-afdf98ced854/OceanDNA-b22806.fa | prodigal -d OceanDNA-b22806/cds.fna -a OceanDNA-b22806/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:46:05,612] [INFO] Task succeeded: Prodigal
[2023-03-16 21:46:05,612] [INFO] Task started: HMMsearch
[2023-03-16 21:46:05,612] [INFO] Running command: hmmsearch --tblout OceanDNA-b22806/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/reference_markers.hmm OceanDNA-b22806/protein.faa > /dev/null
[2023-03-16 21:46:05,912] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:46:05,912] [INFO] Found 6/6 markers.
[2023-03-16 21:46:05,954] [INFO] Query marker FASTA was written to OceanDNA-b22806/markers.fasta
[2023-03-16 21:46:05,954] [INFO] Task started: Blastn
[2023-03-16 21:46:05,954] [INFO] Running command: blastn -query OceanDNA-b22806/markers.fasta -db /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/reference_markers.fasta -out OceanDNA-b22806/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:06,477] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:06,478] [INFO] Selected 26 target genomes.
[2023-03-16 21:46:06,478] [INFO] Target genome list was writen to OceanDNA-b22806/target_genomes.txt
[2023-03-16 21:46:06,495] [INFO] Task started: fastANI
[2023-03-16 21:46:06,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc8a9aa-9990-4b69-aea1-afdf98ced854/OceanDNA-b22806.fa --refList OceanDNA-b22806/target_genomes.txt --output OceanDNA-b22806/fastani_result.tsv --threads 1
[2023-03-16 21:46:29,743] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:29,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:46:29,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:46:29,748] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:46:29,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:46:29,748] [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
Symmachiella macrocystis	strain=CA54	GCA_007860075.1	2527985	2527985	type	True	75.2016	52	2502	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.1867	51	2502	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:46:29,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22806/tc_result.tsv
[2023-03-16 21:46:29,748] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:46:29,748] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:46:29,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/checkm_data
[2023-03-16 21:46:29,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:46:29,757] [INFO] Task started: CheckM
[2023-03-16 21:46:29,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22806/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22806/checkm_input OceanDNA-b22806/checkm_result
[2023-03-16 21:48:26,605] [INFO] Task succeeded: CheckM
[2023-03-16 21:48:26,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:48:26,610] [INFO] ===== Completeness check finished =====
[2023-03-16 21:48:26,610] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:48:26,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22806/markers.fasta)
[2023-03-16 21:48:26,611] [INFO] Task started: Blastn
[2023-03-16 21:48:26,611] [INFO] Running command: blastn -query OceanDNA-b22806/markers.fasta -db /var/lib/cwl/stg23d4ad74-a329-43c9-9a41-3c6cb405108b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22806/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:48:27,327] [INFO] Task succeeded: Blastn
[2023-03-16 21:48:27,328] [INFO] Selected 32 target genomes.
[2023-03-16 21:48:27,328] [INFO] Target genome list was writen to OceanDNA-b22806/target_genomes_gtdb.txt
[2023-03-16 21:48:27,664] [INFO] Task started: fastANI
[2023-03-16 21:48:27,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc8a9aa-9990-4b69-aea1-afdf98ced854/OceanDNA-b22806.fa --refList OceanDNA-b22806/target_genomes_gtdb.txt --output OceanDNA-b22806/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:48:53,289] [INFO] Task succeeded: fastANI
[2023-03-16 21:48:53,293] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:48:53,293] [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_003388505.1	s__MB-PLM-1 sp003388505	75.3711	63	2502	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCF_007860075.1	s__Symmachiella macrocystis	75.2016	52	2502	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.1536	50	2502	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.1188	67	2502	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 21:48:53,293] [INFO] GTDB search result was written to OceanDNA-b22806/result_gtdb.tsv
[2023-03-16 21:48:53,293] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:48:53,294] [INFO] DFAST_QC result json was written to OceanDNA-b22806/dqc_result.json
[2023-03-16 21:48:53,294] [INFO] DFAST_QC completed!
[2023-03-16 21:48:53,294] [INFO] Total running time: 0h3m38s