[2023-06-27 22:41:03,804] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:41:03,806] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:41:03,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference
[2023-06-27 22:41:05,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:41:05,056] [INFO] Task started: Prodigal
[2023-06-27 22:41:05,056] [INFO] Running command: gunzip -c /var/lib/cwl/stg96696c4d-afb1-4df6-9be2-453d2c6ae40e/GCA_026225115.1_ASM2622511v1_genomic.fna.gz | prodigal -d GCA_026225115.1_ASM2622511v1_genomic.fna/cds.fna -a GCA_026225115.1_ASM2622511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:41:15,436] [INFO] Task succeeded: Prodigal
[2023-06-27 22:41:15,436] [INFO] Task started: HMMsearch
[2023-06-27 22:41:15,437] [INFO] Running command: hmmsearch --tblout GCA_026225115.1_ASM2622511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/reference_markers.hmm GCA_026225115.1_ASM2622511v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:41:15,681] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:41:15,683] [INFO] Found 6/6 markers.
[2023-06-27 22:41:15,725] [INFO] Query marker FASTA was written to GCA_026225115.1_ASM2622511v1_genomic.fna/markers.fasta
[2023-06-27 22:41:15,725] [INFO] Task started: Blastn
[2023-06-27 22:41:15,725] [INFO] Running command: blastn -query GCA_026225115.1_ASM2622511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/reference_markers.fasta -out GCA_026225115.1_ASM2622511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:41:16,473] [INFO] Task succeeded: Blastn
[2023-06-27 22:41:16,477] [INFO] Selected 22 target genomes.
[2023-06-27 22:41:16,477] [INFO] Target genome list was writen to GCA_026225115.1_ASM2622511v1_genomic.fna/target_genomes.txt
[2023-06-27 22:41:16,478] [INFO] Task started: fastANI
[2023-06-27 22:41:16,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg96696c4d-afb1-4df6-9be2-453d2c6ae40e/GCA_026225115.1_ASM2622511v1_genomic.fna.gz --refList GCA_026225115.1_ASM2622511v1_genomic.fna/target_genomes.txt --output GCA_026225115.1_ASM2622511v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:41:32,827] [INFO] Task succeeded: fastANI
[2023-06-27 22:41:32,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:41:32,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:41:32,849] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:41:32,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:41:32,850] [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
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	77.8296	290	1148	95	below_threshold
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	77.5684	251	1148	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.9082	186	1148	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.8381	191	1148	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.6784	211	1148	95	below_threshold
Acidocella aminolytica	strain=DSM 11237	GCA_900129125.1	33998	33998	type	True	76.5206	176	1148	95	below_threshold
Acidisoma cellulosilyticum	strain=HW T5.17	GCA_020621385.1	2802395	2802395	type	True	76.421	152	1148	95	below_threshold
Acidisoma silvae	strain=HW T2.11	GCA_020618775.1	2802396	2802396	type	True	76.4193	153	1148	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	76.2309	135	1148	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	76.1814	168	1148	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	76.1346	180	1148	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1303	194	1148	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	76.1133	181	1148	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.9484	180	1148	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	75.9028	160	1148	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.8151	140	1148	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	75.8142	137	1148	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.7522	78	1148	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	75.7422	107	1148	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.6596	152	1148	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	75.6488	155	1148	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.2836	73	1148	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:41:32,852] [INFO] DFAST Taxonomy check result was written to GCA_026225115.1_ASM2622511v1_genomic.fna/tc_result.tsv
[2023-06-27 22:41:32,853] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:41:32,853] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:41:32,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/checkm_data
[2023-06-27 22:41:32,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:41:32,896] [INFO] Task started: CheckM
[2023-06-27 22:41:32,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026225115.1_ASM2622511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026225115.1_ASM2622511v1_genomic.fna/checkm_input GCA_026225115.1_ASM2622511v1_genomic.fna/checkm_result
[2023-06-27 22:42:06,122] [INFO] Task succeeded: CheckM
[2023-06-27 22:42:06,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:42:06,147] [INFO] ===== Completeness check finished =====
[2023-06-27 22:42:06,147] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:42:06,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026225115.1_ASM2622511v1_genomic.fna/markers.fasta)
[2023-06-27 22:42:06,147] [INFO] Task started: Blastn
[2023-06-27 22:42:06,148] [INFO] Running command: blastn -query GCA_026225115.1_ASM2622511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4139c512-97a8-4af7-b88f-e7fede1fd748/dqc_reference/reference_markers_gtdb.fasta -out GCA_026225115.1_ASM2622511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:42:07,417] [INFO] Task succeeded: Blastn
[2023-06-27 22:42:07,423] [INFO] Selected 24 target genomes.
[2023-06-27 22:42:07,423] [INFO] Target genome list was writen to GCA_026225115.1_ASM2622511v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:42:07,433] [INFO] Task started: fastANI
[2023-06-27 22:42:07,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg96696c4d-afb1-4df6-9be2-453d2c6ae40e/GCA_026225115.1_ASM2622511v1_genomic.fna.gz --refList GCA_026225115.1_ASM2622511v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026225115.1_ASM2622511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:42:23,025] [INFO] Task succeeded: fastANI
[2023-06-27 22:42:23,054] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:42:23,054] [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_003164135.1	s__Acidocella sp003164135	78.0572	294	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCF_000687875.1	s__Acidocella facilis	77.8296	290	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_013044125.1	s__Acidocella sp013044125	77.776	220	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201825.1	s__Acidocella aromatica	77.5526	253	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003137135.1	s__Acidocella sp003137135	77.4757	281	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.49	99.49	0.84	0.84	2	-
GCA_002255575.1	s__Acidocella sp002255575	77.2637	225	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.72	99.72	0.92	0.92	2	-
GCA_002281005.1	s__Acidocella sp002281005	77.1099	114	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	97.68	97.68	0.73	0.73	2	-
GCA_018971725.1	s__Acidocella sp018971725	77.0787	161	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902712915.1	s__Acidiphilium sp002255515	76.7539	195	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCF_000202835.1	s__Acidiphilium multivorum	76.6784	211	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCA_903907955.1	s__BOG-930 sp903907955	76.4683	175	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_001899585.1	s__70-18 sp001899585	76.4268	228	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_003133065.1	s__BOG-908 sp003133065	76.3068	129	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-908	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	76.2004	176	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693795.1	s__SHWF01 sp009693795	76.133	61	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__SHWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918195.1	s__BOG-930 sp903918195	76.1198	158	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_001982615.1	s__Roseomonas deserti	75.9571	179	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896535.1	s__CAITYE01 sp903896535	75.9016	109	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAITYE01	95.0	99.30	99.07	0.87	0.85	4	-
GCF_902706185.1	s__Roseomonas sp902706185	75.8603	196	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	75.7704	93	1148	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	75.7422	107	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	75.6493	155	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164455.1	s__BOG-930 sp003164455	75.583	89	1148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:42:23,057] [INFO] GTDB search result was written to GCA_026225115.1_ASM2622511v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:42:23,058] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:42:23,065] [INFO] DFAST_QC result json was written to GCA_026225115.1_ASM2622511v1_genomic.fna/dqc_result.json
[2023-06-27 22:42:23,065] [INFO] DFAST_QC completed!
[2023-06-27 22:42:23,065] [INFO] Total running time: 0h1m19s