[2024-01-24 13:46:18,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference
[2024-01-24 13:46:19,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,435] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg301c622a-039d-40b4-985d-08cf2869c3cd/GCF_007004665.1_ASM700466v1_genomic.fna.gz | prodigal -d GCF_007004665.1_ASM700466v1_genomic.fna/cds.fna -a GCF_007004665.1_ASM700466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:37,956] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:37,956] [INFO] Task started: HMMsearch
[2024-01-24 13:46:37,956] [INFO] Running command: hmmsearch --tblout GCF_007004665.1_ASM700466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/reference_markers.hmm GCF_007004665.1_ASM700466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:38,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:38,382] [INFO] Found 6/6 markers.
[2024-01-24 13:46:38,434] [INFO] Query marker FASTA was written to GCF_007004665.1_ASM700466v1_genomic.fna/markers.fasta
[2024-01-24 13:46:38,434] [INFO] Task started: Blastn
[2024-01-24 13:46:38,434] [INFO] Running command: blastn -query GCF_007004665.1_ASM700466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/reference_markers.fasta -out GCF_007004665.1_ASM700466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:39,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:39,130] [INFO] Selected 23 target genomes.
[2024-01-24 13:46:39,130] [INFO] Target genome list was writen to GCF_007004665.1_ASM700466v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:39,146] [INFO] Task started: fastANI
[2024-01-24 13:46:39,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg301c622a-039d-40b4-985d-08cf2869c3cd/GCF_007004665.1_ASM700466v1_genomic.fna.gz --refList GCF_007004665.1_ASM700466v1_genomic.fna/target_genomes.txt --output GCF_007004665.1_ASM700466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:58,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:58,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:58,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:58,982] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:58,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:58,983] [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
Denitrobaculum tricleocarpae	strain=R148	GCA_007004665.1	2591009	2591009	type	True	100.0	2130	2133	95	conclusive
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.319	298	2133	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	77.013	280	2133	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.5124	269	2133	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4507	275	2133	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	76.2039	105	2133	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1936	150	2133	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.0159	138	2133	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.8819	141	2133	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.8565	144	2133	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.8414	90	2133	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8406	161	2133	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.7094	91	2133	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	75.653	85	2133	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.6043	90	2133	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.5716	102	2133	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	75.5279	53	2133	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.4388	114	2133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,985] [INFO] DFAST Taxonomy check result was written to GCF_007004665.1_ASM700466v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:58,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:58,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:58,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/checkm_data
[2024-01-24 13:46:58,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:59,052] [INFO] Task started: CheckM
[2024-01-24 13:46:59,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004665.1_ASM700466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004665.1_ASM700466v1_genomic.fna/checkm_input GCF_007004665.1_ASM700466v1_genomic.fna/checkm_result
[2024-01-24 13:47:52,972] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:52,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:52,995] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:52,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:52,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004665.1_ASM700466v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:52,996] [INFO] Task started: Blastn
[2024-01-24 13:47:52,996] [INFO] Running command: blastn -query GCF_007004665.1_ASM700466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18d7fc15-4812-443e-873a-fd2d012d81fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004665.1_ASM700466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:53,983] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:53,988] [INFO] Selected 21 target genomes.
[2024-01-24 13:47:53,988] [INFO] Target genome list was writen to GCF_007004665.1_ASM700466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:54,026] [INFO] Task started: fastANI
[2024-01-24 13:47:54,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg301c622a-039d-40b4-985d-08cf2869c3cd/GCF_007004665.1_ASM700466v1_genomic.fna.gz --refList GCF_007004665.1_ASM700466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004665.1_ASM700466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:10,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:10,967] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:10,967] [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_007004665.1	s__Denitrobaculum tricleocarpae	100.0	2130	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Denitrobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014925385.1	s__WHTV01 sp014925385	77.3285	297	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683915.1	s__Pelagibius litoralis	77.0314	278	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657395.1	s__Pelagibius sp001657395	76.8764	285	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	76.8325	240	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.4655	273	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_006969625.1	s__Algihabitans sp006969625	76.4042	201	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003572205.1	s__Algihabitans albus	76.2663	161	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	76.1936	150	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_006739055.1	s__Stella vacuolata	76.1691	141	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	76.0283	73	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.0155	138	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	75.9165	160	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.808	165	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031265.1	s__Rhodopseudomonas palustris_H	75.7888	87	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	96.56	96.03	0.93	0.93	4	-
GCF_000164635.1	s__Roseomonas cervicalis	75.5926	91	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	75.5279	53	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	75.4744	84	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:10,969] [INFO] GTDB search result was written to GCF_007004665.1_ASM700466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:10,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:10,974] [INFO] DFAST_QC result json was written to GCF_007004665.1_ASM700466v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:10,974] [INFO] DFAST_QC completed!
[2024-01-24 13:48:10,974] [INFO] Total running time: 0h1m53s