[2023-06-27 10:50:07,813] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:50:07,833] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:50:07,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference
[2023-06-27 10:50:10,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:50:10,453] [INFO] Task started: Prodigal
[2023-06-27 10:50:10,453] [INFO] Running command: gunzip -c /var/lib/cwl/stg91fe54c6-951c-48b1-ac85-0a4cca27f702/GCA_026400775.1_ASM2640077v1_genomic.fna.gz | prodigal -d GCA_026400775.1_ASM2640077v1_genomic.fna/cds.fna -a GCA_026400775.1_ASM2640077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:50:22,176] [INFO] Task succeeded: Prodigal
[2023-06-27 10:50:22,177] [INFO] Task started: HMMsearch
[2023-06-27 10:50:22,177] [INFO] Running command: hmmsearch --tblout GCA_026400775.1_ASM2640077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/reference_markers.hmm GCA_026400775.1_ASM2640077v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:50:22,454] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:50:22,455] [INFO] Found 6/6 markers.
[2023-06-27 10:50:22,491] [INFO] Query marker FASTA was written to GCA_026400775.1_ASM2640077v1_genomic.fna/markers.fasta
[2023-06-27 10:50:22,492] [INFO] Task started: Blastn
[2023-06-27 10:50:22,492] [INFO] Running command: blastn -query GCA_026400775.1_ASM2640077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/reference_markers.fasta -out GCA_026400775.1_ASM2640077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:50:23,245] [INFO] Task succeeded: Blastn
[2023-06-27 10:50:23,249] [INFO] Selected 20 target genomes.
[2023-06-27 10:50:23,249] [INFO] Target genome list was writen to GCA_026400775.1_ASM2640077v1_genomic.fna/target_genomes.txt
[2023-06-27 10:50:23,254] [INFO] Task started: fastANI
[2023-06-27 10:50:23,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg91fe54c6-951c-48b1-ac85-0a4cca27f702/GCA_026400775.1_ASM2640077v1_genomic.fna.gz --refList GCA_026400775.1_ASM2640077v1_genomic.fna/target_genomes.txt --output GCA_026400775.1_ASM2640077v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:50:41,972] [INFO] Task succeeded: fastANI
[2023-06-27 10:50:41,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:50:41,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:50:41,989] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:50:41,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:50:41,990] [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
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	79.5626	626	1109	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	79.0124	620	1109	95	below_threshold
Roseococcus suduntuyensis	strain=SHET	GCA_017311525.1	455361	455361	type	True	78.82	566	1109	95	below_threshold
Roseococcus suduntuyensis	strain=DSM 19979	GCA_014196305.1	455361	455361	type	True	78.7821	572	1109	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	78.7412	565	1109	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	78.6877	553	1109	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.0999	435	1109	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.946	453	1109	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.8092	469	1109	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.8075	496	1109	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.7012	435	1109	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	77.5973	416	1109	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	77.5071	483	1109	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	77.5051	375	1109	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	77.4752	459	1109	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	77.4631	376	1109	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	77.4579	461	1109	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.3815	384	1109	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	77.2281	367	1109	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	77.1434	350	1109	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:50:42,003] [INFO] DFAST Taxonomy check result was written to GCA_026400775.1_ASM2640077v1_genomic.fna/tc_result.tsv
[2023-06-27 10:50:42,004] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:50:42,004] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:50:42,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/checkm_data
[2023-06-27 10:50:42,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:50:42,045] [INFO] Task started: CheckM
[2023-06-27 10:50:42,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400775.1_ASM2640077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400775.1_ASM2640077v1_genomic.fna/checkm_input GCA_026400775.1_ASM2640077v1_genomic.fna/checkm_result
[2023-06-27 10:51:21,680] [INFO] Task succeeded: CheckM
[2023-06-27 10:51:21,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:51:21,704] [INFO] ===== Completeness check finished =====
[2023-06-27 10:51:21,705] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:51:21,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400775.1_ASM2640077v1_genomic.fna/markers.fasta)
[2023-06-27 10:51:21,705] [INFO] Task started: Blastn
[2023-06-27 10:51:21,705] [INFO] Running command: blastn -query GCA_026400775.1_ASM2640077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d67768-8536-400c-88e5-688ec5759d3a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400775.1_ASM2640077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:51:22,954] [INFO] Task succeeded: Blastn
[2023-06-27 10:51:22,959] [INFO] Selected 22 target genomes.
[2023-06-27 10:51:22,959] [INFO] Target genome list was writen to GCA_026400775.1_ASM2640077v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:51:23,025] [INFO] Task started: fastANI
[2023-06-27 10:51:23,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg91fe54c6-951c-48b1-ac85-0a4cca27f702/GCA_026400775.1_ASM2640077v1_genomic.fna.gz --refList GCA_026400775.1_ASM2640077v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400775.1_ASM2640077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:51:41,868] [INFO] Task succeeded: fastANI
[2023-06-27 10:51:41,885] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 10:51:41,885] [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_013298245.1	s__Rhodovarius sp013298245	84.6927	686	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009900765.1	s__Rhodovarius lipocyclicus	79.5392	632	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005855.1	s__Rhodovarius sp004005855	79.0344	618	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083995.1	s__Roseococcus sp019083995	78.8241	593	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014764365.1	s__Roseococcus sp014764365	78.6828	574	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311575.1	s__Roseococcus thiosulfatophilus	78.6704	554	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	78.6529	551	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	78.4954	288	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376425.1	s__Rhodovarius sp014376425	78.2854	452	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	78.1992	519	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	78.106	446	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336745.1	s__Roseococcus sp004336745	77.9117	488	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	77.8513	505	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355885.1	s__Roseococcus sp017355885	77.8017	422	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222755.1	s__Roseomonas_B sp005222755	77.7585	495	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173615.1	s__Roseomonas_A sp003173615	77.7335	510	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	77.7133	456	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835235.1	s__CAIMOR01 sp903835235	77.702	530	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIMOR01	95.0	99.98	99.96	0.99	0.98	6	-
GCA_000245075.1	s__Roseomonas sp000245075	77.6255	290	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654485.1	s__Roseomonas sp017654485	77.5043	377	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.93	99.93	0.97	0.97	2	-
GCF_014283215.1	s__Siccirubricoccus deserti	77.4429	464	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016107285.1	s__Roseomonas sp016107285	77.3933	389	1109	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 10:51:41,887] [INFO] GTDB search result was written to GCA_026400775.1_ASM2640077v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:51:41,888] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:51:41,892] [INFO] DFAST_QC result json was written to GCA_026400775.1_ASM2640077v1_genomic.fna/dqc_result.json
[2023-06-27 10:51:41,892] [INFO] DFAST_QC completed!
[2023-06-27 10:51:41,892] [INFO] Total running time: 0h1m34s