[2023-03-16 04:35:06,151] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:35:06,151] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:35:06,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference
[2023-03-16 04:35:07,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:35:07,271] [INFO] Task started: Prodigal
[2023-03-16 04:35:07,271] [INFO] Running command: cat /var/lib/cwl/stg7f4513ed-1ee1-437b-859a-4967366ac3ff/OceanDNA-b36148.fa | prodigal -d OceanDNA-b36148/cds.fna -a OceanDNA-b36148/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:35:24,868] [INFO] Task succeeded: Prodigal
[2023-03-16 04:35:24,868] [INFO] Task started: HMMsearch
[2023-03-16 04:35:24,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b36148/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/reference_markers.hmm OceanDNA-b36148/protein.faa > /dev/null
[2023-03-16 04:35:25,068] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:35:25,068] [INFO] Found 6/6 markers.
[2023-03-16 04:35:25,120] [INFO] Query marker FASTA was written to OceanDNA-b36148/markers.fasta
[2023-03-16 04:35:25,120] [INFO] Task started: Blastn
[2023-03-16 04:35:25,120] [INFO] Running command: blastn -query OceanDNA-b36148/markers.fasta -db /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/reference_markers.fasta -out OceanDNA-b36148/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:35:25,807] [INFO] Task succeeded: Blastn
[2023-03-16 04:35:25,833] [INFO] Selected 30 target genomes.
[2023-03-16 04:35:25,833] [INFO] Target genome list was writen to OceanDNA-b36148/target_genomes.txt
[2023-03-16 04:35:25,846] [INFO] Task started: fastANI
[2023-03-16 04:35:25,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4513ed-1ee1-437b-859a-4967366ac3ff/OceanDNA-b36148.fa --refList OceanDNA-b36148/target_genomes.txt --output OceanDNA-b36148/fastani_result.tsv --threads 1
[2023-03-16 04:35:44,816] [INFO] Task succeeded: fastANI
[2023-03-16 04:35:44,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:35:44,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:35:44,825] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:35:44,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:35:44,825] [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
Oceanococcus atlanticus	strain=22II-S10r2	GCA_002088235.1	1317117	1317117	type	True	81.4577	637	909	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	75.992	91	909	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.8524	69	909	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	75.6817	53	909	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	75.6817	53	909	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.6772	61	909	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	75.6477	61	909	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	75.6202	52	909	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	75.6147	50	909	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	75.546	98	909	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	75.5242	62	909	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	75.5147	62	909	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	75.1644	66	909	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:35:44,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36148/tc_result.tsv
[2023-03-16 04:35:44,826] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:35:44,826] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:35:44,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/checkm_data
[2023-03-16 04:35:44,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:35:44,833] [INFO] Task started: CheckM
[2023-03-16 04:35:44,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36148/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36148/checkm_input OceanDNA-b36148/checkm_result
[2023-03-16 04:36:31,182] [INFO] Task succeeded: CheckM
[2023-03-16 04:36:31,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:36:31,195] [INFO] ===== Completeness check finished =====
[2023-03-16 04:36:31,196] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:36:31,196] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36148/markers.fasta)
[2023-03-16 04:36:31,197] [INFO] Task started: Blastn
[2023-03-16 04:36:31,197] [INFO] Running command: blastn -query OceanDNA-b36148/markers.fasta -db /var/lib/cwl/stg2fed0a57-a6bf-4952-964f-587493b4dfe6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36148/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:36:32,408] [INFO] Task succeeded: Blastn
[2023-03-16 04:36:32,409] [INFO] Selected 29 target genomes.
[2023-03-16 04:36:32,409] [INFO] Target genome list was writen to OceanDNA-b36148/target_genomes_gtdb.txt
[2023-03-16 04:36:32,461] [INFO] Task started: fastANI
[2023-03-16 04:36:32,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f4513ed-1ee1-437b-859a-4967366ac3ff/OceanDNA-b36148.fa --refList OceanDNA-b36148/target_genomes_gtdb.txt --output OceanDNA-b36148/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:36:49,213] [INFO] Task succeeded: fastANI
[2023-03-16 04:36:49,219] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:36:49,219] [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_002088235.1	s__Oceanococcus atlanticus	81.4577	637	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Oceanococcaceae;g__Oceanococcus	95.0	98.37	98.37	0.93	0.93	2	-
GCF_900115555.1	s__Pseudomonas_E borbori	76.0692	55	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	75.992	91	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683405.1	s__GCA-2683405 sp002683405	75.8793	63	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__GCA-2683405	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	75.7945	58	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349845.1	s__Pseudomonas sp000349845	75.7648	57	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	75.546	98	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	75.5225	72	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:36:49,219] [INFO] GTDB search result was written to OceanDNA-b36148/result_gtdb.tsv
[2023-03-16 04:36:49,219] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:36:49,221] [INFO] DFAST_QC result json was written to OceanDNA-b36148/dqc_result.json
[2023-03-16 04:36:49,221] [INFO] DFAST_QC completed!
[2023-03-16 04:36:49,221] [INFO] Total running time: 0h1m43s