[2023-06-29 21:42:34,171] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:42:34,173] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:42:34,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference
[2023-06-29 21:42:35,343] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:42:35,344] [INFO] Task started: Prodigal
[2023-06-29 21:42:35,344] [INFO] Running command: gunzip -c /var/lib/cwl/stga52f6ec9-c402-40ea-acf3-4ee28c13bada/GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna.gz | prodigal -d GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/cds.fna -a GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:42:46,293] [INFO] Task succeeded: Prodigal
[2023-06-29 21:42:46,294] [INFO] Task started: HMMsearch
[2023-06-29 21:42:46,294] [INFO] Running command: hmmsearch --tblout GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/reference_markers.hmm GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:42:46,533] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:42:46,534] [INFO] Found 6/6 markers.
[2023-06-29 21:42:46,581] [INFO] Query marker FASTA was written to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/markers.fasta
[2023-06-29 21:42:46,581] [INFO] Task started: Blastn
[2023-06-29 21:42:46,581] [INFO] Running command: blastn -query GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/markers.fasta -db /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/reference_markers.fasta -out GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:47,575] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:47,579] [INFO] Selected 21 target genomes.
[2023-06-29 21:42:47,579] [INFO] Target genome list was writen to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/target_genomes.txt
[2023-06-29 21:42:47,583] [INFO] Task started: fastANI
[2023-06-29 21:42:47,583] [INFO] Running command: fastANI --query /var/lib/cwl/stga52f6ec9-c402-40ea-acf3-4ee28c13bada/GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna.gz --refList GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/target_genomes.txt --output GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:43:04,369] [INFO] Task succeeded: fastANI
[2023-06-29 21:43:04,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:43:04,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:43:04,386] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:43:04,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:43:04,387] [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	80.491	514	1199	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.4182	549	1199	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.2097	512	1199	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	80.1746	550	1199	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.1354	509	1199	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.1316	510	1199	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	80.123	564	1199	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.5897	506	1199	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.5715	508	1199	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.3077	445	1199	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.2889	484	1199	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.2249	452	1199	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.0819	562	1199	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.0624	474	1199	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	79.0023	493	1199	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.9398	453	1199	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.9161	517	1199	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.8614	473	1199	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.698	411	1199	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	78.5262	365	1199	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.4989	360	1199	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:43:04,389] [INFO] DFAST Taxonomy check result was written to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/tc_result.tsv
[2023-06-29 21:43:04,389] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:43:04,389] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:43:04,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/checkm_data
[2023-06-29 21:43:04,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:43:04,431] [INFO] Task started: CheckM
[2023-06-29 21:43:04,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/checkm_input GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/checkm_result
[2023-06-29 21:43:41,388] [INFO] Task succeeded: CheckM
[2023-06-29 21:43:41,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:43:41,407] [INFO] ===== Completeness check finished =====
[2023-06-29 21:43:41,407] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:43:41,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/markers.fasta)
[2023-06-29 21:43:41,408] [INFO] Task started: Blastn
[2023-06-29 21:43:41,408] [INFO] Running command: blastn -query GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/markers.fasta -db /var/lib/cwl/stg1979f358-26d8-4408-8946-238cbb15292e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:43:43,476] [INFO] Task succeeded: Blastn
[2023-06-29 21:43:43,480] [INFO] Selected 21 target genomes.
[2023-06-29 21:43:43,480] [INFO] Target genome list was writen to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:43:43,491] [INFO] Task started: fastANI
[2023-06-29 21:43:43,491] [INFO] Running command: fastANI --query /var/lib/cwl/stga52f6ec9-c402-40ea-acf3-4ee28c13bada/GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna.gz --refList GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/target_genomes_gtdb.txt --output GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:44:05,564] [INFO] Task succeeded: fastANI
[2023-06-29 21:44:05,581] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:44:05,582] [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_903830565.1	s__CAIKUF01 sp903830565	100.0	1187	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016702655.1	s__CAIKUF01 sp016702655	82.9815	755	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879745.1	s__CAIKUF01 sp014879745	81.2721	560	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	81.242	635	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCA_016706565.1	s__Piscinibacter sp016706565	81.1774	620	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCA_003265685.1	s__Piscinibacter caeni	80.9671	647	1199	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	80.9209	630	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425865.1	s__LMDS01 sp001425865	80.8857	656	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	80.8639	623	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	80.8408	671	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275445.1	s__Rhizobacter sp012275445	80.7563	602	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	80.6868	610	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725505.1	s__Rubrivivax sp001725505	80.6567	504	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799605.1	s__Rhizobacter sp000799605	80.5979	616	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	80.5918	564	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_001425825.1	s__Rhizobacter sp001425825	80.5806	620	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	80.5461	510	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCA_905339355.1	s__Albitalea sp905339355	80.1152	490	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Albitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217215.1	s__Rivibacter subsaxonicus	80.1058	557	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340905.1	s__Rubrivivax gelatinosus	80.0839	568	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_005884255.1	s__VBDL01 sp005884255	79.7366	381	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:44:05,584] [INFO] GTDB search result was written to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/result_gtdb.tsv
[2023-06-29 21:44:05,584] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:44:05,589] [INFO] DFAST_QC result json was written to GCA_903830565.1_freshwater_MAG_---_LinL3_bin-0015_genomic.fna/dqc_result.json
[2023-06-29 21:44:05,590] [INFO] DFAST_QC completed!
[2023-06-29 21:44:05,590] [INFO] Total running time: 0h1m31s