[2024-01-24 14:46:55,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stga470f7b2-b28c-4cbd-946c-6b458d1a2ef6/GCF_030160635.1_ASM3016063v1_genomic.fna.gz | prodigal -d GCF_030160635.1_ASM3016063v1_genomic.fna/cds.fna -a GCF_030160635.1_ASM3016063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:10,905] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:10,906] [INFO] Task started: HMMsearch
[2024-01-24 14:47:10,906] [INFO] Running command: hmmsearch --tblout GCF_030160635.1_ASM3016063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/reference_markers.hmm GCF_030160635.1_ASM3016063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:11,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:11,230] [INFO] Found 6/6 markers.
[2024-01-24 14:47:11,270] [INFO] Query marker FASTA was written to GCF_030160635.1_ASM3016063v1_genomic.fna/markers.fasta
[2024-01-24 14:47:11,271] [INFO] Task started: Blastn
[2024-01-24 14:47:11,271] [INFO] Running command: blastn -query GCF_030160635.1_ASM3016063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/reference_markers.fasta -out GCF_030160635.1_ASM3016063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:12,102] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:12,107] [INFO] Selected 22 target genomes.
[2024-01-24 14:47:12,107] [INFO] Target genome list was writen to GCF_030160635.1_ASM3016063v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:12,127] [INFO] Task started: fastANI
[2024-01-24 14:47:12,127] [INFO] Running command: fastANI --query /var/lib/cwl/stga470f7b2-b28c-4cbd-946c-6b458d1a2ef6/GCF_030160635.1_ASM3016063v1_genomic.fna.gz --refList GCF_030160635.1_ASM3016063v1_genomic.fna/target_genomes.txt --output GCF_030160635.1_ASM3016063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:28,098] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:28,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:28,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:28,115] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:28,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:28,115] [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 aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	79.213	443	1280	95	below_threshold
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	78.5002	442	1280	95	below_threshold
Acidocella aminolytica	strain=DSM 11237	GCA_900129125.1	33998	33998	type	True	78.1493	258	1280	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	77.3593	230	1280	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.2764	243	1280	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.236	272	1280	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.885	247	1280	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	76.869	129	1280	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.7045	218	1280	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.5225	207	1280	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.4363	181	1280	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	76.3054	183	1280	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.2423	209	1280	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	76.0528	76	1280	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.9726	113	1280	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.9394	131	1280	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	75.8459	52	1280	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.7937	158	1280	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.7762	155	1280	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.692	191	1280	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	75.6919	52	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:28,118] [INFO] DFAST Taxonomy check result was written to GCF_030160635.1_ASM3016063v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:28,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:28,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:28,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/checkm_data
[2024-01-24 14:47:28,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:28,160] [INFO] Task started: CheckM
[2024-01-24 14:47:28,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160635.1_ASM3016063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160635.1_ASM3016063v1_genomic.fna/checkm_input GCF_030160635.1_ASM3016063v1_genomic.fna/checkm_result
[2024-01-24 14:48:07,482] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:07,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:07,507] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:07,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:07,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160635.1_ASM3016063v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:07,508] [INFO] Task started: Blastn
[2024-01-24 14:48:07,508] [INFO] Running command: blastn -query GCF_030160635.1_ASM3016063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24342c17-425e-4152-8f5d-a27a9612331b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160635.1_ASM3016063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:08,965] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:08,970] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:08,970] [INFO] Target genome list was writen to GCF_030160635.1_ASM3016063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:08,977] [INFO] Task started: fastANI
[2024-01-24 14:48:08,978] [INFO] Running command: fastANI --query /var/lib/cwl/stga470f7b2-b28c-4cbd-946c-6b458d1a2ef6/GCF_030160635.1_ASM3016063v1_genomic.fna.gz --refList GCF_030160635.1_ASM3016063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160635.1_ASM3016063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:17,925] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:17,935] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:48:17,936] [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_013044125.1	s__Acidocella sp013044125	89.8877	634	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164135.1	s__Acidocella sp003164135	85.3754	792	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCF_014201825.1	s__Acidocella aromatica	79.2237	442	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687875.1	s__Acidocella facilis	78.4989	442	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_018971725.1	s__Acidocella sp018971725	78.3629	249	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129125.1	s__Acidocella aminolytica	78.1349	259	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018971905.1	s__Acidocella sp018971905	77.9599	202	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255575.1	s__Acidocella sp002255575	77.6277	232	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.72	99.72	0.92	0.92	2	-
GCA_003137135.1	s__Acidocella sp003137135	77.5284	273	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.49	99.49	0.84	0.84	2	-
GCA_903643085.1	s__BOG-908 sp903643085	76.4448	122	1280	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_013340935.1	s__Azospirillum melinis	75.7847	159	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_017876095.1	s__Azospirillum agricola	75.6863	194	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.584	79	1280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,937] [INFO] GTDB search result was written to GCF_030160635.1_ASM3016063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:17,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:17,942] [INFO] DFAST_QC result json was written to GCF_030160635.1_ASM3016063v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:17,942] [INFO] DFAST_QC completed!
[2024-01-24 14:48:17,942] [INFO] Total running time: 0h1m22s