[2023-06-28 01:43:29,192] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:43:29,194] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:43:29,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference
[2023-06-28 01:43:30,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:43:30,444] [INFO] Task started: Prodigal
[2023-06-28 01:43:30,444] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9031f1e-9f8f-4d98-8358-0d28fb5dceaf/GCA_026647635.1_ASM2664763v1_genomic.fna.gz | prodigal -d GCA_026647635.1_ASM2664763v1_genomic.fna/cds.fna -a GCA_026647635.1_ASM2664763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:40,249] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:40,249] [INFO] Task started: HMMsearch
[2023-06-28 01:43:40,250] [INFO] Running command: hmmsearch --tblout GCA_026647635.1_ASM2664763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/reference_markers.hmm GCA_026647635.1_ASM2664763v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:40,561] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:40,562] [INFO] Found 6/6 markers.
[2023-06-28 01:43:40,602] [INFO] Query marker FASTA was written to GCA_026647635.1_ASM2664763v1_genomic.fna/markers.fasta
[2023-06-28 01:43:40,603] [INFO] Task started: Blastn
[2023-06-28 01:43:40,603] [INFO] Running command: blastn -query GCA_026647635.1_ASM2664763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/reference_markers.fasta -out GCA_026647635.1_ASM2664763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:41,268] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:41,272] [INFO] Selected 30 target genomes.
[2023-06-28 01:43:41,272] [INFO] Target genome list was writen to GCA_026647635.1_ASM2664763v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:41,276] [INFO] Task started: fastANI
[2023-06-28 01:43:41,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9031f1e-9f8f-4d98-8358-0d28fb5dceaf/GCA_026647635.1_ASM2664763v1_genomic.fna.gz --refList GCA_026647635.1_ASM2664763v1_genomic.fna/target_genomes.txt --output GCA_026647635.1_ASM2664763v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:44:08,325] [INFO] Task succeeded: fastANI
[2023-06-28 01:44:08,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:44:08,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:44:08,337] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:44:08,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:44:08,338] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.1401	50	1283	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	74.9227	99	1283	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8675	158	1283	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.7877	73	1283	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	74.7679	108	1283	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	74.7646	109	1283	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	74.7168	61	1283	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	74.6646	71	1283	95	below_threshold
Nocardioides insulae	strain=DSM 17944	GCA_000422825.1	394734	394734	type	True	74.6625	50	1283	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	74.6594	73	1283	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	74.658	73	1283	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	74.6458	79	1283	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	74.6428	163	1283	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	74.6075	84	1283	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:44:08,340] [INFO] DFAST Taxonomy check result was written to GCA_026647635.1_ASM2664763v1_genomic.fna/tc_result.tsv
[2023-06-28 01:44:08,340] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:44:08,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:44:08,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/checkm_data
[2023-06-28 01:44:08,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:44:08,391] [INFO] Task started: CheckM
[2023-06-28 01:44:08,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647635.1_ASM2664763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647635.1_ASM2664763v1_genomic.fna/checkm_input GCA_026647635.1_ASM2664763v1_genomic.fna/checkm_result
[2023-06-28 01:44:55,405] [INFO] Task succeeded: CheckM
[2023-06-28 01:44:55,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:44:55,428] [INFO] ===== Completeness check finished =====
[2023-06-28 01:44:55,428] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:44:55,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647635.1_ASM2664763v1_genomic.fna/markers.fasta)
[2023-06-28 01:44:55,429] [INFO] Task started: Blastn
[2023-06-28 01:44:55,429] [INFO] Running command: blastn -query GCA_026647635.1_ASM2664763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37da8946-dcd5-4091-8885-88dc829410f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647635.1_ASM2664763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:44:56,237] [INFO] Task succeeded: Blastn
[2023-06-28 01:44:56,242] [INFO] Selected 20 target genomes.
[2023-06-28 01:44:56,243] [INFO] Target genome list was writen to GCA_026647635.1_ASM2664763v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:44:56,255] [INFO] Task started: fastANI
[2023-06-28 01:44:56,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9031f1e-9f8f-4d98-8358-0d28fb5dceaf/GCA_026647635.1_ASM2664763v1_genomic.fna.gz --refList GCA_026647635.1_ASM2664763v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647635.1_ASM2664763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:45:13,521] [INFO] Task succeeded: fastANI
[2023-06-28 01:45:13,534] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:45:13,535] [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_013360825.1	s__WSZJ01 sp013360825	99.3729	948	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__WSZJ01;g__WSZJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016190145.1	s__WSZJ01 sp016190145	77.8854	456	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__WSZJ01;g__WSZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773755.1	s__WSZJ01 sp009773755	77.498	453	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__WSZJ01;g__WSZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190175.1	s__JACPRC01 sp016190175	75.1927	78	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__MHYJ01;f__JACPRB01;g__JACPRC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220045.1	s__JACRIP01 sp016220045	75.187	138	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACRIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197205.1	s__JACPWG01 sp016197205	75.0842	170	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACPWG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011327745.1	s__DSWA01 sp011327745	74.8389	105	1283	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__DSWA01;f__DSWA01;g__DSWA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692555.1	s__SHYY01 sp009692555	74.765	109	1283	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__SHYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881315.1	s__JADGRB01 sp017881315	74.7413	81	1283	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104_A;f__Fen-1088;g__JADGRB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016188005.1	s__UBA12499 sp016188005	74.7335	69	1283	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	74.6475	88	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	74.6053	86	1283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:45:13,537] [INFO] GTDB search result was written to GCA_026647635.1_ASM2664763v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:45:13,537] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:45:13,541] [INFO] DFAST_QC result json was written to GCA_026647635.1_ASM2664763v1_genomic.fna/dqc_result.json
[2023-06-28 01:45:13,541] [INFO] DFAST_QC completed!
[2023-06-28 01:45:13,541] [INFO] Total running time: 0h1m44s