[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference
[2023-03-16 04:05:22,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,126] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,126] [INFO] Running command: cat /var/lib/cwl/stg4ec613a0-ae94-4752-a550-2b0f5640df30/OceanDNA-b2829.fa | prodigal -d OceanDNA-b2829/cds.fna -a OceanDNA-b2829/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:42,962] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:42,963] [INFO] Task started: HMMsearch
[2023-03-16 04:05:42,963] [INFO] Running command: hmmsearch --tblout OceanDNA-b2829/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/reference_markers.hmm OceanDNA-b2829/protein.faa > /dev/null
[2023-03-16 04:05:43,145] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:43,145] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4ec613a0-ae94-4752-a550-2b0f5640df30/OceanDNA-b2829.fa]
[2023-03-16 04:05:43,166] [INFO] Query marker FASTA was written to OceanDNA-b2829/markers.fasta
[2023-03-16 04:05:43,167] [INFO] Task started: Blastn
[2023-03-16 04:05:43,167] [INFO] Running command: blastn -query OceanDNA-b2829/markers.fasta -db /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/reference_markers.fasta -out OceanDNA-b2829/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:43,715] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:43,716] [INFO] Selected 16 target genomes.
[2023-03-16 04:05:43,716] [INFO] Target genome list was writen to OceanDNA-b2829/target_genomes.txt
[2023-03-16 04:05:43,724] [INFO] Task started: fastANI
[2023-03-16 04:05:43,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec613a0-ae94-4752-a550-2b0f5640df30/OceanDNA-b2829.fa --refList OceanDNA-b2829/target_genomes.txt --output OceanDNA-b2829/fastani_result.tsv --threads 1
[2023-03-16 04:05:56,388] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:56,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:56,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:56,399] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:56,399] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:56,399] [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
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	80.7028	588	1131	95	below_threshold
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	80.5745	610	1131	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	80.4632	596	1131	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	80.4346	581	1131	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	80.3783	613	1131	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	80.181	532	1131	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	79.9456	557	1131	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	79.9326	514	1131	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	79.9111	561	1131	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	79.8206	524	1131	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	79.7526	527	1131	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.9484	426	1131	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	78.9404	434	1131	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.0551	340	1131	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.9172	265	1131	95	below_threshold
Arthrobacter terrae	strain=Z1-20	GCA_015708085.1	2935737	2935737	type	True	77.1366	183	1131	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:56,399] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2829/tc_result.tsv
[2023-03-16 04:05:56,399] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:56,400] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:56,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/checkm_data
[2023-03-16 04:05:56,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:56,406] [INFO] Task started: CheckM
[2023-03-16 04:05:56,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2829/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2829/checkm_input OceanDNA-b2829/checkm_result
[2023-03-16 04:06:48,625] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:48,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:48,628] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:48,629] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:48,629] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2829/markers.fasta)
[2023-03-16 04:06:48,629] [INFO] Task started: Blastn
[2023-03-16 04:06:48,629] [INFO] Running command: blastn -query OceanDNA-b2829/markers.fasta -db /var/lib/cwl/stgef365f42-18fe-4688-afb5-c7758a1503ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2829/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:49,376] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:49,376] [INFO] Selected 7 target genomes.
[2023-03-16 04:06:49,377] [INFO] Target genome list was writen to OceanDNA-b2829/target_genomes_gtdb.txt
[2023-03-16 04:06:49,381] [INFO] Task started: fastANI
[2023-03-16 04:06:49,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec613a0-ae94-4752-a550-2b0f5640df30/OceanDNA-b2829.fa --refList OceanDNA-b2829/target_genomes_gtdb.txt --output OceanDNA-b2829/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:55,928] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:55,933] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:06:55,934] [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_000427315.1	s__Arthrobacter_I sp000427315	98.652	833	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009928425.1	s__Arthrobacter_I sp009928425	94.3521	964	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750145.1	s__Arthrobacter_I sp001750145	88.2559	896	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422645.1	s__Arthrobacter_I sp001422645	87.7347	863	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679325.1	s__Arthrobacter_I sp007679325	87.3358	854	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001512305.1	s__Arthrobacter_I sp001512305	86.0979	837	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097355.1	s__Arthrobacter_I sp003097355	83.3807	785	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.72	95.72	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:55,934] [INFO] GTDB search result was written to OceanDNA-b2829/result_gtdb.tsv
[2023-03-16 04:06:55,934] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:55,935] [INFO] DFAST_QC result json was written to OceanDNA-b2829/dqc_result.json
[2023-03-16 04:06:55,935] [INFO] DFAST_QC completed!
[2023-03-16 04:06:55,936] [INFO] Total running time: 0h1m36s