[2024-01-25 18:50:35,282] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:35,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:35,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference
[2024-01-25 18:50:36,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:36,467] [INFO] Task started: Prodigal
[2024-01-25 18:50:36,468] [INFO] Running command: gunzip -c /var/lib/cwl/stgf668bf02-e18e-4265-883f-68af5df47119/GCF_000701585.1_ASM70158v1_genomic.fna.gz | prodigal -d GCF_000701585.1_ASM70158v1_genomic.fna/cds.fna -a GCF_000701585.1_ASM70158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:47,288] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:47,289] [INFO] Task started: HMMsearch
[2024-01-25 18:50:47,289] [INFO] Running command: hmmsearch --tblout GCF_000701585.1_ASM70158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/reference_markers.hmm GCF_000701585.1_ASM70158v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:47,497] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:47,498] [INFO] Found 6/6 markers.
[2024-01-25 18:50:47,533] [INFO] Query marker FASTA was written to GCF_000701585.1_ASM70158v1_genomic.fna/markers.fasta
[2024-01-25 18:50:47,533] [INFO] Task started: Blastn
[2024-01-25 18:50:47,533] [INFO] Running command: blastn -query GCF_000701585.1_ASM70158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/reference_markers.fasta -out GCF_000701585.1_ASM70158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:48,301] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:48,303] [INFO] Selected 18 target genomes.
[2024-01-25 18:50:48,304] [INFO] Target genome list was writen to GCF_000701585.1_ASM70158v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:48,349] [INFO] Task started: fastANI
[2024-01-25 18:50:48,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgf668bf02-e18e-4265-883f-68af5df47119/GCF_000701585.1_ASM70158v1_genomic.fna.gz --refList GCF_000701585.1_ASM70158v1_genomic.fna/target_genomes.txt --output GCF_000701585.1_ASM70158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:02,793] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:02,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:02,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:02,805] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:51:02,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:51:02,806] [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
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	79.5667	576	1291	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	79.3436	559	1291	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	79.2845	505	1291	95	below_threshold
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	77.116	269	1291	95	below_threshold
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	76.8777	189	1291	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	76.6605	242	1291	95	below_threshold
Acidisoma silvae	strain=HW T2.11	GCA_020618775.1	2802396	2802396	type	True	76.6288	175	1291	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	76.5982	185	1291	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5358	280	1291	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.4616	226	1291	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.2168	225	1291	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	76.1519	177	1291	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.0443	173	1291	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.9843	178	1291	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.9714	184	1291	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.8869	179	1291	95	below_threshold
Pleomorphomonas oryzae	strain=DSM 16300	GCA_000422965.1	261934	261934	type	True	75.7067	79	1291	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	75.4924	103	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:02,807] [INFO] DFAST Taxonomy check result was written to GCF_000701585.1_ASM70158v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:02,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:02,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:02,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/checkm_data
[2024-01-25 18:51:02,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:02,850] [INFO] Task started: CheckM
[2024-01-25 18:51:02,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000701585.1_ASM70158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000701585.1_ASM70158v1_genomic.fna/checkm_input GCF_000701585.1_ASM70158v1_genomic.fna/checkm_result
[2024-01-25 18:51:41,810] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:41,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:41,828] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:41,828] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:41,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000701585.1_ASM70158v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:41,829] [INFO] Task started: Blastn
[2024-01-25 18:51:41,829] [INFO] Running command: blastn -query GCF_000701585.1_ASM70158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg687d79dd-2596-4af0-86f4-68a8c214ef1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000701585.1_ASM70158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:43,325] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:43,329] [INFO] Selected 17 target genomes.
[2024-01-25 18:51:43,329] [INFO] Target genome list was writen to GCF_000701585.1_ASM70158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:43,358] [INFO] Task started: fastANI
[2024-01-25 18:51:43,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgf668bf02-e18e-4265-883f-68af5df47119/GCF_000701585.1_ASM70158v1_genomic.fna.gz --refList GCF_000701585.1_ASM70158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000701585.1_ASM70158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:57,533] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:57,545] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:57,545] [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_900156265.1	s__Acidiphilium rubrum	99.9714	1238	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	conclusive
GCF_000202835.1	s__Acidiphilium multivorum	79.3349	560	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_902712915.1	s__Acidiphilium sp002255515	79.296	533	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCA_002279355.1	s__Acidiphilium sp002279355	77.6141	272	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.80	99.77	0.93	0.92	3	-
GCF_000687875.1	s__Acidocella facilis	77.1166	269	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_002255495.1	s__20-60-12 sp002255495	76.9635	215	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__20-60-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	76.7698	291	1291	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_003164135.1	s__Acidocella sp003164135	76.6247	203	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCA_003133265.1	s__PALSA-911 sp003133265	76.6047	205	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944925.1	s__Rhodopila sp903944925	76.5646	190	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCA_017307285.1	s__JAFKFI01 sp017307285	76.4053	214	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900905.1	s__CAIXEA01 sp903900905	76.2959	156	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01	95.0	98.81	98.71	0.81	0.80	4	-
GCA_903928045.1	s__CAIYPH01 sp903928045	76.2488	168	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	98.55	98.55	0.76	0.76	2	-
GCF_003604215.1	s__Roseomonas vastitatis	76.1616	176	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427645.1	s__Sphingomonas phyllosphaerae	75.5149	101	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506455.1	s__Sphingomonas sp902506455	75.489	110	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:57,551] [INFO] GTDB search result was written to GCF_000701585.1_ASM70158v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:57,554] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:57,559] [INFO] DFAST_QC result json was written to GCF_000701585.1_ASM70158v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:57,559] [INFO] DFAST_QC completed!
[2024-01-25 18:51:57,559] [INFO] Total running time: 0h1m22s