[2023-06-28 01:42:56,193] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:42:56,195] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:42:56,196] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference
[2023-06-28 01:42:57,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:42:57,493] [INFO] Task started: Prodigal
[2023-06-28 01:42:57,493] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9350c9f-742e-45c6-93e4-81d0a30d7881/GCA_026461575.1_ASM2646157v1_genomic.fna.gz | prodigal -d GCA_026461575.1_ASM2646157v1_genomic.fna/cds.fna -a GCA_026461575.1_ASM2646157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:04,498] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:04,498] [INFO] Task started: HMMsearch
[2023-06-28 01:43:04,499] [INFO] Running command: hmmsearch --tblout GCA_026461575.1_ASM2646157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/reference_markers.hmm GCA_026461575.1_ASM2646157v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:04,715] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:04,717] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf9350c9f-742e-45c6-93e4-81d0a30d7881/GCA_026461575.1_ASM2646157v1_genomic.fna.gz]
[2023-06-28 01:43:04,751] [INFO] Query marker FASTA was written to GCA_026461575.1_ASM2646157v1_genomic.fna/markers.fasta
[2023-06-28 01:43:04,751] [INFO] Task started: Blastn
[2023-06-28 01:43:04,751] [INFO] Running command: blastn -query GCA_026461575.1_ASM2646157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/reference_markers.fasta -out GCA_026461575.1_ASM2646157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:05,327] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:05,331] [INFO] Selected 20 target genomes.
[2023-06-28 01:43:05,332] [INFO] Target genome list was writen to GCA_026461575.1_ASM2646157v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:05,334] [INFO] Task started: fastANI
[2023-06-28 01:43:05,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9350c9f-742e-45c6-93e4-81d0a30d7881/GCA_026461575.1_ASM2646157v1_genomic.fna.gz --refList GCA_026461575.1_ASM2646157v1_genomic.fna/target_genomes.txt --output GCA_026461575.1_ASM2646157v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:43:22,108] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:22,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:43:22,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:43:22,128] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:43:22,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:43:22,128] [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	79.2121	130	328	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	78.2448	92	328	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	78.2175	92	328	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.9785	85	328	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.1547	79	328	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.1319	71	328	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	77.0787	74	328	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.0173	60	328	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.0134	79	328	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	77.009	72	328	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	77.0054	74	328	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	76.9961	79	328	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	76.9809	60	328	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.4243	55	328	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:43:22,130] [INFO] DFAST Taxonomy check result was written to GCA_026461575.1_ASM2646157v1_genomic.fna/tc_result.tsv
[2023-06-28 01:43:22,131] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:43:22,131] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:43:22,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/checkm_data
[2023-06-28 01:43:22,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:43:22,159] [INFO] Task started: CheckM
[2023-06-28 01:43:22,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026461575.1_ASM2646157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026461575.1_ASM2646157v1_genomic.fna/checkm_input GCA_026461575.1_ASM2646157v1_genomic.fna/checkm_result
[2023-06-28 01:43:47,974] [INFO] Task succeeded: CheckM
[2023-06-28 01:43:47,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 01:43:48,000] [INFO] ===== Completeness check finished =====
[2023-06-28 01:43:48,000] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:43:48,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026461575.1_ASM2646157v1_genomic.fna/markers.fasta)
[2023-06-28 01:43:48,001] [INFO] Task started: Blastn
[2023-06-28 01:43:48,001] [INFO] Running command: blastn -query GCA_026461575.1_ASM2646157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc481b91-9a85-4175-a5d4-a06074bb8a49/dqc_reference/reference_markers_gtdb.fasta -out GCA_026461575.1_ASM2646157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:48,523] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:48,529] [INFO] Selected 18 target genomes.
[2023-06-28 01:43:48,529] [INFO] Target genome list was writen to GCA_026461575.1_ASM2646157v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:43:48,545] [INFO] Task started: fastANI
[2023-06-28 01:43:48,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9350c9f-742e-45c6-93e4-81d0a30d7881/GCA_026461575.1_ASM2646157v1_genomic.fna.gz --refList GCA_026461575.1_ASM2646157v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026461575.1_ASM2646157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:43:59,021] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:59,039] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 01:43:59,040] [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_003415675.1	s__Rhodoferax sp003415675	79.2121	130	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845935.1	s__Rhodoferax sp903845935	79.1453	127	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_903886275.1	s__Rhodoferax sp903886275	78.6338	131	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCA_001795455.1	s__Rhodoferax sp001795455	78.2934	97	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_001955715.1	s__Rhodoferax saidenbachensis	78.2448	92	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903863395.1	s__Rhodoferax sp903863395	77.8733	78	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.94	98.87	0.83	0.81	5	-
GCA_903870955.1	s__Rhodoferax sp903870955	77.8534	67	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.51	98.51	0.73	0.73	2	-
GCF_002943465.1	s__Rhodoferax sp002943465	77.8399	100	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897925.1	s__Rhodoferax sp903897925	77.726	95	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCA_016719405.1	s__Rhodoferax sp016719405	77.5896	68	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	-
GCF_006716905.1	s__Acidovorax temperans	77.0054	74	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.32	95.61	0.84	0.79	8	-
GCA_011391545.1	s__Rhodoferax sp011391545	77.005	57	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110225.1	s__Brachymonas denitrificans	76.4243	55	328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:43:59,042] [INFO] GTDB search result was written to GCA_026461575.1_ASM2646157v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:43:59,042] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:43:59,046] [INFO] DFAST_QC result json was written to GCA_026461575.1_ASM2646157v1_genomic.fna/dqc_result.json
[2023-06-28 01:43:59,046] [INFO] DFAST_QC completed!
[2023-06-28 01:43:59,046] [INFO] Total running time: 0h1m3s