[2023-03-16 03:47:32,863] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference
[2023-03-16 03:47:34,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,481] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,481] [INFO] Running command: cat /var/lib/cwl/stg6083c16d-c8e9-495c-8443-5c48826671ad/OceanDNA-b32682.fa | prodigal -d OceanDNA-b32682/cds.fna -a OceanDNA-b32682/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:49,016] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:49,016] [INFO] Task started: HMMsearch
[2023-03-16 03:47:49,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b32682/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/reference_markers.hmm OceanDNA-b32682/protein.faa > /dev/null
[2023-03-16 03:47:49,197] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:49,198] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6083c16d-c8e9-495c-8443-5c48826671ad/OceanDNA-b32682.fa]
[2023-03-16 03:47:49,217] [INFO] Query marker FASTA was written to OceanDNA-b32682/markers.fasta
[2023-03-16 03:47:49,217] [INFO] Task started: Blastn
[2023-03-16 03:47:49,217] [INFO] Running command: blastn -query OceanDNA-b32682/markers.fasta -db /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/reference_markers.fasta -out OceanDNA-b32682/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:49,877] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:49,878] [INFO] Selected 30 target genomes.
[2023-03-16 03:47:49,878] [INFO] Target genome list was writen to OceanDNA-b32682/target_genomes.txt
[2023-03-16 03:47:49,893] [INFO] Task started: fastANI
[2023-03-16 03:47:49,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg6083c16d-c8e9-495c-8443-5c48826671ad/OceanDNA-b32682.fa --refList OceanDNA-b32682/target_genomes.txt --output OceanDNA-b32682/fastani_result.tsv --threads 1
[2023-03-16 03:48:10,804] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:10,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:10,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:10,809] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:10,809] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:10,809] [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	75.5916	68	758	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.5916	68	758	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.3175	52	758	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.0545	55	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:10,809] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32682/tc_result.tsv
[2023-03-16 03:48:10,809] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:10,809] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:10,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/checkm_data
[2023-03-16 03:48:10,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:10,814] [INFO] Task started: CheckM
[2023-03-16 03:48:10,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32682/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32682/checkm_input OceanDNA-b32682/checkm_result
[2023-03-16 03:48:49,768] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:49,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:49,771] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:49,771] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:49,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32682/markers.fasta)
[2023-03-16 03:48:49,771] [INFO] Task started: Blastn
[2023-03-16 03:48:49,771] [INFO] Running command: blastn -query OceanDNA-b32682/markers.fasta -db /var/lib/cwl/stg55daa68e-b9a2-4395-8775-8f0e7c3d11a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32682/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:50,987] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:50,988] [INFO] Selected 37 target genomes.
[2023-03-16 03:48:50,988] [INFO] Target genome list was writen to OceanDNA-b32682/target_genomes_gtdb.txt
[2023-03-16 03:48:51,222] [INFO] Task started: fastANI
[2023-03-16 03:48:51,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg6083c16d-c8e9-495c-8443-5c48826671ad/OceanDNA-b32682.fa --refList OceanDNA-b32682/target_genomes_gtdb.txt --output OceanDNA-b32682/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:17,958] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:17,964] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:49:17,964] [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_016869765.1	s__SHVP01 sp016869765	75.8177	66	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVP01;f__SHVP01;g__SHVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.5741	69	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.5293	56	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	75.4184	56	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	75.4136	58	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467395.1	s__Reyranella sp016467395	75.3024	51	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	75.0492	56	758	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:17,964] [INFO] GTDB search result was written to OceanDNA-b32682/result_gtdb.tsv
[2023-03-16 03:49:17,964] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:17,965] [INFO] DFAST_QC result json was written to OceanDNA-b32682/dqc_result.json
[2023-03-16 03:49:17,965] [INFO] DFAST_QC completed!
[2023-03-16 03:49:17,965] [INFO] Total running time: 0h1m45s