[2023-03-16 09:13:21,596] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:13:21,596] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:13:21,596] [INFO] DQC Reference Directory: /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference
[2023-03-16 09:13:22,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:13:22,744] [INFO] Task started: Prodigal
[2023-03-16 09:13:22,744] [INFO] Running command: cat /var/lib/cwl/stgad8870b5-eddc-41f1-9496-89b8be7027a0/OceanDNA-b2836.fa | prodigal -d OceanDNA-b2836/cds.fna -a OceanDNA-b2836/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:13:39,363] [INFO] Task succeeded: Prodigal
[2023-03-16 09:13:39,364] [INFO] Task started: HMMsearch
[2023-03-16 09:13:39,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b2836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/reference_markers.hmm OceanDNA-b2836/protein.faa > /dev/null
[2023-03-16 09:13:39,535] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:13:39,535] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgad8870b5-eddc-41f1-9496-89b8be7027a0/OceanDNA-b2836.fa]
[2023-03-16 09:13:39,558] [INFO] Query marker FASTA was written to OceanDNA-b2836/markers.fasta
[2023-03-16 09:13:39,560] [INFO] Task started: Blastn
[2023-03-16 09:13:39,560] [INFO] Running command: blastn -query OceanDNA-b2836/markers.fasta -db /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/reference_markers.fasta -out OceanDNA-b2836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:13:40,249] [INFO] Task succeeded: Blastn
[2023-03-16 09:13:40,254] [INFO] Selected 11 target genomes.
[2023-03-16 09:13:40,254] [INFO] Target genome list was writen to OceanDNA-b2836/target_genomes.txt
[2023-03-16 09:13:40,260] [INFO] Task started: fastANI
[2023-03-16 09:13:40,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8870b5-eddc-41f1-9496-89b8be7027a0/OceanDNA-b2836.fa --refList OceanDNA-b2836/target_genomes.txt --output OceanDNA-b2836/fastani_result.tsv --threads 1
[2023-03-16 09:13:47,435] [INFO] Task succeeded: fastANI
[2023-03-16 09:13:47,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:13:47,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:13:47,443] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:13:47,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:13:47,443] [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 psychralcaliphila	strain=DSM 44820	GCA_003046525.1	139021	139021	type	True	87.8736	802	901	95	below_threshold
Dietzia psychralcaliphila	strain=ILA-1	GCA_003096095.1	139021	139021	type	True	87.8636	812	901	95	below_threshold
Dietzia psychralcaliphila	strain=ILA-1	GCA_009806395.1	139021	139021	type	True	87.5855	710	901	95	below_threshold
Dietzia cercidiphylli	strain=YIM 65002T	GCA_014145145.1	498199	498199	type	True	86.5937	528	901	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=YIM 65001T	GCA_014144975.1	498198	322509	type	True	83.4444	376	901	95	below_threshold
Dietzia kunjamensis	strain=K30-10T	GCA_014144965.1	322509	322509	type	True	83.4383	483	901	95	below_threshold
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	83.2746	685	901	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	83.2553	684	901	95	below_threshold
Dietzia lutea	strain=YIM 80766	GCA_003096075.1	546160	546160	type	True	82.7523	676	901	95	below_threshold
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	82.7097	630	901	95	below_threshold
Dietzia cinnamea	strain=NBRC 102147	GCA_001571065.1	321318	321318	type	True	82.6254	631	901	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:13:47,445] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2836/tc_result.tsv
[2023-03-16 09:13:47,445] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:13:47,445] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:13:47,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/checkm_data
[2023-03-16 09:13:47,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:13:47,463] [INFO] Task started: CheckM
[2023-03-16 09:13:47,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2836/checkm_input OceanDNA-b2836/checkm_result
[2023-03-16 09:14:31,013] [INFO] Task succeeded: CheckM
[2023-03-16 09:14:31,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:14:31,080] [INFO] ===== Completeness check finished =====
[2023-03-16 09:14:31,080] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:14:31,080] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2836/markers.fasta)
[2023-03-16 09:14:31,081] [INFO] Task started: Blastn
[2023-03-16 09:14:31,081] [INFO] Running command: blastn -query OceanDNA-b2836/markers.fasta -db /var/lib/cwl/stga6cffbae-2854-4e13-bd88-42d9bda643ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:14:31,899] [INFO] Task succeeded: Blastn
[2023-03-16 09:14:31,902] [INFO] Selected 9 target genomes.
[2023-03-16 09:14:31,902] [INFO] Target genome list was writen to OceanDNA-b2836/target_genomes_gtdb.txt
[2023-03-16 09:14:31,930] [INFO] Task started: fastANI
[2023-03-16 09:14:31,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgad8870b5-eddc-41f1-9496-89b8be7027a0/OceanDNA-b2836.fa --refList OceanDNA-b2836/target_genomes_gtdb.txt --output OceanDNA-b2836/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:14:38,130] [INFO] Task succeeded: fastANI
[2023-03-16 09:14:38,136] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:14:38,136] [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_003096095.1	s__Dietzia psychralcaliphila	87.8636	812	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.31	97.95	0.96	0.91	4	-
GCF_014145095.1	s__Dietzia sp014145095	86.801	537	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145145.1	s__Dietzia cercidiphylli	86.5815	529	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.02	96.60	0.78	0.68	10	-
GCF_002289575.1	s__Dietzia natronolimnaea_A	85.3847	738	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	96.66	96.66	0.87	0.87	2	-
GCF_003052165.1	s__Dietzia sp003052165	84.9417	770	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	99.11	98.77	0.94	0.92	5	-
GCA_002415925.1	s__Dietzia sp002415925	84.2257	604	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014144855.1	s__Dietzia maris	83.444	467	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.49	96.42	0.87	0.74	16	-
GCF_001571065.1	s__Dietzia cinnamea	82.6253	631	901	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	81.8313	593	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:14:38,139] [INFO] GTDB search result was written to OceanDNA-b2836/result_gtdb.tsv
[2023-03-16 09:14:38,141] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:14:38,146] [INFO] DFAST_QC result json was written to OceanDNA-b2836/dqc_result.json
[2023-03-16 09:14:38,146] [INFO] DFAST_QC completed!
[2023-03-16 09:14:38,146] [INFO] Total running time: 0h1m17s