[2023-03-18 07:29:32,031] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:32,031] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:32,031] [INFO] DQC Reference Directory: /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference
[2023-03-18 07:29:33,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:33,222] [INFO] Task started: Prodigal
[2023-03-18 07:29:33,222] [INFO] Running command: cat /var/lib/cwl/stg3c713d4e-4f17-4156-a4b5-053289dd1354/OceanDNA-b2837.fa | prodigal -d OceanDNA-b2837/cds.fna -a OceanDNA-b2837/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:54,385] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:54,386] [INFO] Task started: HMMsearch
[2023-03-18 07:29:54,386] [INFO] Running command: hmmsearch --tblout OceanDNA-b2837/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/reference_markers.hmm OceanDNA-b2837/protein.faa > /dev/null
[2023-03-18 07:29:54,566] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:54,566] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3c713d4e-4f17-4156-a4b5-053289dd1354/OceanDNA-b2837.fa]
[2023-03-18 07:29:54,587] [INFO] Query marker FASTA was written to OceanDNA-b2837/markers.fasta
[2023-03-18 07:29:54,588] [INFO] Task started: Blastn
[2023-03-18 07:29:54,588] [INFO] Running command: blastn -query OceanDNA-b2837/markers.fasta -db /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/reference_markers.fasta -out OceanDNA-b2837/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:55,346] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:55,347] [INFO] Selected 9 target genomes.
[2023-03-18 07:29:55,347] [INFO] Target genome list was writen to OceanDNA-b2837/target_genomes.txt
[2023-03-18 07:29:55,352] [INFO] Task started: fastANI
[2023-03-18 07:29:55,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c713d4e-4f17-4156-a4b5-053289dd1354/OceanDNA-b2837.fa --refList OceanDNA-b2837/target_genomes.txt --output OceanDNA-b2837/fastani_result.tsv --threads 1
[2023-03-18 07:30:01,929] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:01,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:01,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:01,936] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2023-03-18 07:30:01,937] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 07:30:01,937] [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
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	97.1078	1022	1130	95	inconclusive
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	97.0883	1009	1130	95	inconclusive
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	96.6582	649	1130	95	inconclusive
Dietzia maris	strain=IMV 195	GCA_009806365.1	37915	37915	suspected-type	True	96.6274	648	1130	95	inconclusive
Dietzia maris	strain=IMV 195T	GCA_014144855.1	37915	37915	suspected-type	True	96.6078	626	1130	95	inconclusive
Dietzia kunjamensis subsp. schimae	strain=YIM 65001T	GCA_014144975.1	498198	322509	type	True	96.2126	515	1130	95	inconclusive
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	86.3974	863	1130	95	below_threshold
Dietzia cinnamea	strain=NBRC 102147	GCA_001571065.1	321318	321318	type	True	86.3356	878	1130	95	below_threshold
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	85.9274	927	1130	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:01,937] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2837/tc_result.tsv
[2023-03-18 07:30:01,937] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:01,937] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:01,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/checkm_data
[2023-03-18 07:30:01,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:01,943] [INFO] Task started: CheckM
[2023-03-18 07:30:01,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2837/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2837/checkm_input OceanDNA-b2837/checkm_result
[2023-03-18 07:30:58,408] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:58,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:58,461] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:58,461] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:58,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2837/markers.fasta)
[2023-03-18 07:30:58,461] [INFO] Task started: Blastn
[2023-03-18 07:30:58,461] [INFO] Running command: blastn -query OceanDNA-b2837/markers.fasta -db /var/lib/cwl/stge7d710fe-5c15-4305-9858-0dc294d8e6c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2837/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:59,526] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:59,527] [INFO] Selected 6 target genomes.
[2023-03-18 07:30:59,527] [INFO] Target genome list was writen to OceanDNA-b2837/target_genomes_gtdb.txt
[2023-03-18 07:30:59,549] [INFO] Task started: fastANI
[2023-03-18 07:30:59,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c713d4e-4f17-4156-a4b5-053289dd1354/OceanDNA-b2837.fa --refList OceanDNA-b2837/target_genomes_gtdb.txt --output OceanDNA-b2837/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:04,581] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:04,585] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:04,586] [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_014144855.1	s__Dietzia maris	96.6078	626	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	conclusive
GCF_000186325.1	s__Dietzia cinnamea_A	86.6425	787	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	96.59	96.10	0.87	0.83	4	-
GCF_001571065.1	s__Dietzia cinnamea	86.3274	878	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.1735	97.27	96.55	0.88	0.84	8	-
GCF_008369165.1	s__Dietzia sp008369165	86.2533	845	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096075.1	s__Dietzia lutea	85.915	928	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002415925.1	s__Dietzia sp002415925	84.0416	723	1130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:04,586] [INFO] GTDB search result was written to OceanDNA-b2837/result_gtdb.tsv
[2023-03-18 07:31:04,586] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:04,587] [INFO] DFAST_QC result json was written to OceanDNA-b2837/dqc_result.json
[2023-03-18 07:31:04,587] [INFO] DFAST_QC completed!
[2023-03-18 07:31:04,587] [INFO] Total running time: 0h1m33s