[2023-06-14 01:06:50,260] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:06:50,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:06:50,263] [INFO] DQC Reference Directory: /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference
[2023-06-14 01:06:52,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:06:52,690] [INFO] Task started: Prodigal
[2023-06-14 01:06:52,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b6b0547-f586-49d5-804e-888ca04697f6/GCA_947464995.1_RE-4nov15-292_genomic.fna.gz | prodigal -d GCA_947464995.1_RE-4nov15-292_genomic.fna/cds.fna -a GCA_947464995.1_RE-4nov15-292_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:01,312] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:01,313] [INFO] Task started: HMMsearch
[2023-06-14 01:07:01,313] [INFO] Running command: hmmsearch --tblout GCA_947464995.1_RE-4nov15-292_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/reference_markers.hmm GCA_947464995.1_RE-4nov15-292_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:01,574] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:01,575] [INFO] Found 6/6 markers.
[2023-06-14 01:07:01,607] [INFO] Query marker FASTA was written to GCA_947464995.1_RE-4nov15-292_genomic.fna/markers.fasta
[2023-06-14 01:07:01,607] [INFO] Task started: Blastn
[2023-06-14 01:07:01,607] [INFO] Running command: blastn -query GCA_947464995.1_RE-4nov15-292_genomic.fna/markers.fasta -db /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/reference_markers.fasta -out GCA_947464995.1_RE-4nov15-292_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:02,395] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:02,399] [INFO] Selected 19 target genomes.
[2023-06-14 01:07:02,400] [INFO] Target genome list was writen to GCA_947464995.1_RE-4nov15-292_genomic.fna/target_genomes.txt
[2023-06-14 01:07:02,410] [INFO] Task started: fastANI
[2023-06-14 01:07:02,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b6b0547-f586-49d5-804e-888ca04697f6/GCA_947464995.1_RE-4nov15-292_genomic.fna.gz --refList GCA_947464995.1_RE-4nov15-292_genomic.fna/target_genomes.txt --output GCA_947464995.1_RE-4nov15-292_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:16,422] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:16,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:16,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:16,440] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:16,441] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:07:16,441] [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
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.2416	356	771	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	78.5198	302	771	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	78.5122	307	771	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	78.3071	294	771	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	78.2587	256	771	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	78.2017	257	771	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.1154	263	771	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	77.9249	241	771	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	77.8708	236	771	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	77.8615	265	771	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	77.7906	245	771	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.7439	228	771	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.7374	227	771	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	77.726	212	771	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	77.7194	244	771	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.7121	258	771	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	77.5727	165	771	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	77.5506	200	771	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	77.4705	212	771	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:07:16,443] [INFO] DFAST Taxonomy check result was written to GCA_947464995.1_RE-4nov15-292_genomic.fna/tc_result.tsv
[2023-06-14 01:07:16,444] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:16,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:16,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/checkm_data
[2023-06-14 01:07:16,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:16,481] [INFO] Task started: CheckM
[2023-06-14 01:07:16,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947464995.1_RE-4nov15-292_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947464995.1_RE-4nov15-292_genomic.fna/checkm_input GCA_947464995.1_RE-4nov15-292_genomic.fna/checkm_result
[2023-06-14 01:07:45,711] [INFO] Task succeeded: CheckM
[2023-06-14 01:07:45,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:07:45,733] [INFO] ===== Completeness check finished =====
[2023-06-14 01:07:45,734] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:07:45,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947464995.1_RE-4nov15-292_genomic.fna/markers.fasta)
[2023-06-14 01:07:45,735] [INFO] Task started: Blastn
[2023-06-14 01:07:45,735] [INFO] Running command: blastn -query GCA_947464995.1_RE-4nov15-292_genomic.fna/markers.fasta -db /var/lib/cwl/stga69e5aea-11ad-4ad2-9ff1-2557e5a8ccf6/dqc_reference/reference_markers_gtdb.fasta -out GCA_947464995.1_RE-4nov15-292_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:47,125] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:47,129] [INFO] Selected 19 target genomes.
[2023-06-14 01:07:47,130] [INFO] Target genome list was writen to GCA_947464995.1_RE-4nov15-292_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:07:47,147] [INFO] Task started: fastANI
[2023-06-14 01:07:47,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b6b0547-f586-49d5-804e-888ca04697f6/GCA_947464995.1_RE-4nov15-292_genomic.fna.gz --refList GCA_947464995.1_RE-4nov15-292_genomic.fna/target_genomes_gtdb.txt --output GCA_947464995.1_RE-4nov15-292_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:07:59,672] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:59,694] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:07:59,694] [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_903928325.1	s__Rhodoferax sp903928325	86.3642	382	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928635.1	s__Rhodoferax sp903928635	80.6721	376	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.42	99.41	0.86	0.86	3	-
GCA_903914985.1	s__Rhodoferax sp903914985	79.6459	254	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869595.1	s__Rhodoferax sp903869595	79.2921	394	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415675.1	s__Rhodoferax sp003415675	79.2218	357	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951445.1	s__Rhodoferax sp903951445	79.0587	369	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886275.1	s__Rhodoferax sp903886275	78.9405	341	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCA_903845935.1	s__Rhodoferax sp903845935	78.8128	291	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCF_002251855.1	s__Rhodoferax sp002251855	78.6695	286	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943465.1	s__Rhodoferax sp002943465	78.5864	328	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955715.1	s__Rhodoferax saidenbachensis	78.5095	306	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016463455.1	s__Rhodoferax sp016463455	78.5006	220	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097105.1	s__Rhodoferax_B sp003097105	78.0411	275	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780565.1	s__Rhodoferax sp018780565	77.9866	218	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454975.1	s__Hylemonella sp002454975	77.9724	229	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708345.1	s__Rhodoferax sp016708345	77.9053	224	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.29	99.29	0.95	0.95	2	-
GCA_011391595.1	s__JAABQG01 sp011391595	77.8134	202	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907163135.1	s__Brachymonas denitrificans_A	77.4301	156	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987795.1	s__Curvibacter sp003987795	77.4102	203	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:07:59,696] [INFO] GTDB search result was written to GCA_947464995.1_RE-4nov15-292_genomic.fna/result_gtdb.tsv
[2023-06-14 01:07:59,697] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:07:59,701] [INFO] DFAST_QC result json was written to GCA_947464995.1_RE-4nov15-292_genomic.fna/dqc_result.json
[2023-06-14 01:07:59,701] [INFO] DFAST_QC completed!
[2023-06-14 01:07:59,701] [INFO] Total running time: 0h1m9s