[2023-03-19 00:33:19,091] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,091] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,091] [INFO] DQC Reference Directory: /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference
[2023-03-19 00:33:20,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,361] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,361] [INFO] Running command: cat /var/lib/cwl/stgdb99acba-98e2-46bf-a350-963b642ecefe/OceanDNA-b3313.fa | prodigal -d OceanDNA-b3313/cds.fna -a OceanDNA-b3313/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:32,818] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:32,819] [INFO] Task started: HMMsearch
[2023-03-19 00:33:32,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b3313/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/reference_markers.hmm OceanDNA-b3313/protein.faa > /dev/null
[2023-03-19 00:33:33,051] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:33,051] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb99acba-98e2-46bf-a350-963b642ecefe/OceanDNA-b3313.fa]
[2023-03-19 00:33:33,074] [INFO] Query marker FASTA was written to OceanDNA-b3313/markers.fasta
[2023-03-19 00:33:33,076] [INFO] Task started: Blastn
[2023-03-19 00:33:33,076] [INFO] Running command: blastn -query OceanDNA-b3313/markers.fasta -db /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/reference_markers.fasta -out OceanDNA-b3313/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:33,811] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:33,813] [INFO] Selected 14 target genomes.
[2023-03-19 00:33:33,813] [INFO] Target genome list was writen to OceanDNA-b3313/target_genomes.txt
[2023-03-19 00:33:33,824] [INFO] Task started: fastANI
[2023-03-19 00:33:33,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb99acba-98e2-46bf-a350-963b642ecefe/OceanDNA-b3313.fa --refList OceanDNA-b3313/target_genomes.txt --output OceanDNA-b3313/fastani_result.tsv --threads 1
[2023-03-19 00:33:46,700] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:46,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:46,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:46,710] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:46,710] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:33:46,710] [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
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	93.3106	583	622	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	93.0758	570	622	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	86.1126	532	622	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.8995	537	622	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	85.8841	539	622	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	85.6228	535	622	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	85.5307	511	622	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.3766	521	622	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.273	521	622	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.2621	514	622	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.2048	508	622	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.2014	513	622	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	84.7776	517	622	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	84.5326	517	622	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:33:46,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3313/tc_result.tsv
[2023-03-19 00:33:46,711] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:46,712] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:46,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/checkm_data
[2023-03-19 00:33:46,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:46,722] [INFO] Task started: CheckM
[2023-03-19 00:33:46,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3313/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3313/checkm_input OceanDNA-b3313/checkm_result
[2023-03-19 00:34:20,844] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:20,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.12%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:34:20,853] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:20,854] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:20,854] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3313/markers.fasta)
[2023-03-19 00:34:20,855] [INFO] Task started: Blastn
[2023-03-19 00:34:20,855] [INFO] Running command: blastn -query OceanDNA-b3313/markers.fasta -db /var/lib/cwl/stgefab7e68-823c-433b-b845-b02f6df027e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3313/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:21,912] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:21,915] [INFO] Selected 13 target genomes.
[2023-03-19 00:34:21,915] [INFO] Target genome list was writen to OceanDNA-b3313/target_genomes_gtdb.txt
[2023-03-19 00:34:22,043] [INFO] Task started: fastANI
[2023-03-19 00:34:22,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb99acba-98e2-46bf-a350-963b642ecefe/OceanDNA-b3313.fa --refList OceanDNA-b3313/target_genomes_gtdb.txt --output OceanDNA-b3313/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:32,585] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:32,592] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:34:32,593] [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_009699265.1	s__Nocardioides sp009699265	93.3274	566	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	92.7369	576	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	86.4653	513	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	86.1209	532	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112035.1	s__Nocardioides alpinus	85.9104	536	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004785795.1	s__Nocardioides eburneiflavus	85.6268	535	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	85.4386	512	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	85.4227	517	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	85.2938	520	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	85.0411	520	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	84.8372	514	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	84.7987	520	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779665.1	s__Nocardioides hwasunensis	84.552	516	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:32,593] [INFO] GTDB search result was written to OceanDNA-b3313/result_gtdb.tsv
[2023-03-19 00:34:32,594] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:32,596] [INFO] DFAST_QC result json was written to OceanDNA-b3313/dqc_result.json
[2023-03-19 00:34:32,596] [INFO] DFAST_QC completed!
[2023-03-19 00:34:32,596] [INFO] Total running time: 0h1m14s