[2023-06-27 22:32:03,852] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:32:03,854] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:32:03,854] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference
[2023-06-27 22:32:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:32:05,096] [INFO] Task started: Prodigal
[2023-06-27 22:32:05,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg038dc23d-494b-45e0-818c-e8c9a4263163/GCA_026647055.1_ASM2664705v1_genomic.fna.gz | prodigal -d GCA_026647055.1_ASM2664705v1_genomic.fna/cds.fna -a GCA_026647055.1_ASM2664705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:32:20,390] [INFO] Task succeeded: Prodigal
[2023-06-27 22:32:20,391] [INFO] Task started: HMMsearch
[2023-06-27 22:32:20,391] [INFO] Running command: hmmsearch --tblout GCA_026647055.1_ASM2664705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/reference_markers.hmm GCA_026647055.1_ASM2664705v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:32:20,703] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:32:20,705] [INFO] Found 6/6 markers.
[2023-06-27 22:32:20,748] [INFO] Query marker FASTA was written to GCA_026647055.1_ASM2664705v1_genomic.fna/markers.fasta
[2023-06-27 22:32:20,749] [INFO] Task started: Blastn
[2023-06-27 22:32:20,749] [INFO] Running command: blastn -query GCA_026647055.1_ASM2664705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/reference_markers.fasta -out GCA_026647055.1_ASM2664705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:32:21,961] [INFO] Task succeeded: Blastn
[2023-06-27 22:32:21,965] [INFO] Selected 25 target genomes.
[2023-06-27 22:32:21,965] [INFO] Target genome list was writen to GCA_026647055.1_ASM2664705v1_genomic.fna/target_genomes.txt
[2023-06-27 22:32:21,973] [INFO] Task started: fastANI
[2023-06-27 22:32:21,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg038dc23d-494b-45e0-818c-e8c9a4263163/GCA_026647055.1_ASM2664705v1_genomic.fna.gz --refList GCA_026647055.1_ASM2664705v1_genomic.fna/target_genomes.txt --output GCA_026647055.1_ASM2664705v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:32:46,604] [INFO] Task succeeded: fastANI
[2023-06-27 22:32:46,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:32:46,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:32:46,625] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:32:46,625] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:32:46,625] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.6954	534	1491	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	79.6912	556	1491	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.559	514	1491	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.5041	515	1491	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.3644	497	1491	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	79.3164	517	1491	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.272	534	1491	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.255	613	1491	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.1469	490	1491	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.121	603	1491	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.1087	600	1491	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.0947	634	1491	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.9585	531	1491	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.8709	550	1491	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	78.8679	524	1491	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	78.8585	536	1491	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	78.6649	504	1491	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.5048	539	1491	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	78.4104	414	1491	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	78.4069	336	1491	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	78.4065	510	1491	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	78.397	512	1491	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.3832	406	1491	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	78.2942	394	1491	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.115	451	1491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:32:46,627] [INFO] DFAST Taxonomy check result was written to GCA_026647055.1_ASM2664705v1_genomic.fna/tc_result.tsv
[2023-06-27 22:32:46,628] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:32:46,628] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:32:46,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/checkm_data
[2023-06-27 22:32:46,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:32:46,695] [INFO] Task started: CheckM
[2023-06-27 22:32:46,695] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026647055.1_ASM2664705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026647055.1_ASM2664705v1_genomic.fna/checkm_input GCA_026647055.1_ASM2664705v1_genomic.fna/checkm_result
[2023-06-27 22:34:04,215] [INFO] Task succeeded: CheckM
[2023-06-27 22:34:04,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:34:04,248] [INFO] ===== Completeness check finished =====
[2023-06-27 22:34:04,249] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:34:04,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026647055.1_ASM2664705v1_genomic.fna/markers.fasta)
[2023-06-27 22:34:04,249] [INFO] Task started: Blastn
[2023-06-27 22:34:04,250] [INFO] Running command: blastn -query GCA_026647055.1_ASM2664705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f084f6-c137-40ca-884d-ab73055631a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026647055.1_ASM2664705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:34:06,220] [INFO] Task succeeded: Blastn
[2023-06-27 22:34:06,226] [INFO] Selected 16 target genomes.
[2023-06-27 22:34:06,226] [INFO] Target genome list was writen to GCA_026647055.1_ASM2664705v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:34:06,258] [INFO] Task started: fastANI
[2023-06-27 22:34:06,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg038dc23d-494b-45e0-818c-e8c9a4263163/GCA_026647055.1_ASM2664705v1_genomic.fna.gz --refList GCA_026647055.1_ASM2664705v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026647055.1_ASM2664705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:34:23,884] [INFO] Task succeeded: fastANI
[2023-06-27 22:34:23,902] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:34:23,903] [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_013360485.1	s__Aquabacterium_A sp013360485	99.4333	1036	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016213205.1	s__Aquabacterium_A sp016213205	81.1401	801	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.4173	784	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	80.3523	813	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.2596	626	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	80.2281	692	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.1357	758	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	79.9299	500	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	79.8957	612	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	79.779	606	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240325.1	s__Rubrivivax sp018240325	79.7474	535	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	79.7065	714	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721465.1	s__Aquabacterium_A sp016721465	79.6347	671	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	98.92	98.92	0.93	0.93	2	-
GCA_003265685.1	s__Piscinibacter caeni	79.5849	671	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706565.1	s__Piscinibacter sp016706565	79.5532	645	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCA_016213265.1	s__Ideonella sp016213265	79.5208	586	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:34:23,911] [INFO] GTDB search result was written to GCA_026647055.1_ASM2664705v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:34:23,916] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:34:23,924] [INFO] DFAST_QC result json was written to GCA_026647055.1_ASM2664705v1_genomic.fna/dqc_result.json
[2023-06-27 22:34:23,924] [INFO] DFAST_QC completed!
[2023-06-27 22:34:23,925] [INFO] Total running time: 0h2m20s