[2023-06-29 13:03:23,494] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:03:23,498] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:03:23,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference
[2023-06-29 13:03:24,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:03:24,724] [INFO] Task started: Prodigal
[2023-06-29 13:03:24,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg99cb42ea-f522-47ca-a114-9c48e28d0ba8/GCA_023259155.1_ASM2325915v1_genomic.fna.gz | prodigal -d GCA_023259155.1_ASM2325915v1_genomic.fna/cds.fna -a GCA_023259155.1_ASM2325915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:03:32,029] [INFO] Task succeeded: Prodigal
[2023-06-29 13:03:32,030] [INFO] Task started: HMMsearch
[2023-06-29 13:03:32,030] [INFO] Running command: hmmsearch --tblout GCA_023259155.1_ASM2325915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/reference_markers.hmm GCA_023259155.1_ASM2325915v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:03:32,276] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:03:32,278] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg99cb42ea-f522-47ca-a114-9c48e28d0ba8/GCA_023259155.1_ASM2325915v1_genomic.fna.gz]
[2023-06-29 13:03:32,314] [INFO] Query marker FASTA was written to GCA_023259155.1_ASM2325915v1_genomic.fna/markers.fasta
[2023-06-29 13:03:32,314] [INFO] Task started: Blastn
[2023-06-29 13:03:32,314] [INFO] Running command: blastn -query GCA_023259155.1_ASM2325915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/reference_markers.fasta -out GCA_023259155.1_ASM2325915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:03:33,011] [INFO] Task succeeded: Blastn
[2023-06-29 13:03:33,015] [INFO] Selected 19 target genomes.
[2023-06-29 13:03:33,016] [INFO] Target genome list was writen to GCA_023259155.1_ASM2325915v1_genomic.fna/target_genomes.txt
[2023-06-29 13:03:33,017] [INFO] Task started: fastANI
[2023-06-29 13:03:33,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cb42ea-f522-47ca-a114-9c48e28d0ba8/GCA_023259155.1_ASM2325915v1_genomic.fna.gz --refList GCA_023259155.1_ASM2325915v1_genomic.fna/target_genomes.txt --output GCA_023259155.1_ASM2325915v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:03:48,806] [INFO] Task succeeded: fastANI
[2023-06-29 13:03:48,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:03:48,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:03:48,827] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:03:48,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:03:48,827] [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_000420125.1	316997	316997	type	True	80.3496	286	596	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.2792	281	596	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.2394	281	596	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.2073	285	596	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.1471	292	596	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.8051	291	596	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.7866	292	596	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.3481	278	596	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.094	272	596	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	78.9922	289	596	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.9506	256	596	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.9178	310	596	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.8856	297	596	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.862	222	596	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.8005	299	596	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.7152	220	596	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	78.6582	241	596	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.5609	255	596	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.5234	253	596	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:03:48,830] [INFO] DFAST Taxonomy check result was written to GCA_023259155.1_ASM2325915v1_genomic.fna/tc_result.tsv
[2023-06-29 13:03:48,830] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:03:48,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:03:48,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/checkm_data
[2023-06-29 13:03:48,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:03:48,869] [INFO] Task started: CheckM
[2023-06-29 13:03:48,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023259155.1_ASM2325915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023259155.1_ASM2325915v1_genomic.fna/checkm_input GCA_023259155.1_ASM2325915v1_genomic.fna/checkm_result
[2023-06-29 13:04:15,511] [INFO] Task succeeded: CheckM
[2023-06-29 13:04:15,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:04:15,535] [INFO] ===== Completeness check finished =====
[2023-06-29 13:04:15,535] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:04:15,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023259155.1_ASM2325915v1_genomic.fna/markers.fasta)
[2023-06-29 13:04:15,536] [INFO] Task started: Blastn
[2023-06-29 13:04:15,536] [INFO] Running command: blastn -query GCA_023259155.1_ASM2325915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg763567e9-ac82-45be-9b54-0067c8016d9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_023259155.1_ASM2325915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:04:16,541] [INFO] Task succeeded: Blastn
[2023-06-29 13:04:16,546] [INFO] Selected 14 target genomes.
[2023-06-29 13:04:16,547] [INFO] Target genome list was writen to GCA_023259155.1_ASM2325915v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:04:16,553] [INFO] Task started: fastANI
[2023-06-29 13:04:16,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cb42ea-f522-47ca-a114-9c48e28d0ba8/GCA_023259155.1_ASM2325915v1_genomic.fna.gz --refList GCA_023259155.1_ASM2325915v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023259155.1_ASM2325915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:04:29,560] [INFO] Task succeeded: fastANI
[2023-06-29 13:04:29,572] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:04:29,573] [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_001425865.1	s__LMDS01 sp001425865	86.529	404	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241265.1	s__JAFEEF01 sp018241265	82.0833	360	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFEEF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	81.8871	358	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799605.1	s__Rhizobacter sp000799605	81.8533	353	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	81.7459	358	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCF_012275445.1	s__Rhizobacter sp012275445	81.6889	360	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706565.1	s__Piscinibacter sp016706565	81.5765	348	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCA_007994965.1	s__Piscinibacter aquaticus	81.5667	316	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	81.5296	334	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	81.439	358	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	81.3934	358	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882155.1	s__Albitalea sp005882155	81.1431	277	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Albitalea	95.0	98.79	98.79	0.82	0.82	2	-
GCA_905339355.1	s__Albitalea sp905339355	80.7933	274	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Albitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241055.1	s__Pelomonas depolymerans_A	78.6934	242	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:04:29,575] [INFO] GTDB search result was written to GCA_023259155.1_ASM2325915v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:04:29,575] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:04:29,584] [INFO] DFAST_QC result json was written to GCA_023259155.1_ASM2325915v1_genomic.fna/dqc_result.json
[2023-06-29 13:04:29,585] [INFO] DFAST_QC completed!
[2023-06-29 13:04:29,585] [INFO] Total running time: 0h1m6s