[2023-06-29 05:14:09,647] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:14:09,654] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:14:09,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference
[2023-06-29 05:14:11,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:14:11,015] [INFO] Task started: Prodigal
[2023-06-29 05:14:11,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg3369c95f-1ebc-4df7-8c38-e9bfca50de84/GCA_027490925.1_ASM2749092v1_genomic.fna.gz | prodigal -d GCA_027490925.1_ASM2749092v1_genomic.fna/cds.fna -a GCA_027490925.1_ASM2749092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:14:21,467] [INFO] Task succeeded: Prodigal
[2023-06-29 05:14:21,468] [INFO] Task started: HMMsearch
[2023-06-29 05:14:21,468] [INFO] Running command: hmmsearch --tblout GCA_027490925.1_ASM2749092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/reference_markers.hmm GCA_027490925.1_ASM2749092v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:14:21,725] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:14:21,726] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3369c95f-1ebc-4df7-8c38-e9bfca50de84/GCA_027490925.1_ASM2749092v1_genomic.fna.gz]
[2023-06-29 05:14:21,763] [INFO] Query marker FASTA was written to GCA_027490925.1_ASM2749092v1_genomic.fna/markers.fasta
[2023-06-29 05:14:21,763] [INFO] Task started: Blastn
[2023-06-29 05:14:21,763] [INFO] Running command: blastn -query GCA_027490925.1_ASM2749092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/reference_markers.fasta -out GCA_027490925.1_ASM2749092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:14:22,623] [INFO] Task succeeded: Blastn
[2023-06-29 05:14:22,628] [INFO] Selected 21 target genomes.
[2023-06-29 05:14:22,628] [INFO] Target genome list was writen to GCA_027490925.1_ASM2749092v1_genomic.fna/target_genomes.txt
[2023-06-29 05:14:22,630] [INFO] Task started: fastANI
[2023-06-29 05:14:22,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg3369c95f-1ebc-4df7-8c38-e9bfca50de84/GCA_027490925.1_ASM2749092v1_genomic.fna.gz --refList GCA_027490925.1_ASM2749092v1_genomic.fna/target_genomes.txt --output GCA_027490925.1_ASM2749092v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:14:41,912] [INFO] Task succeeded: fastANI
[2023-06-29 05:14:41,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:14:41,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:14:41,936] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:14:41,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 05:14:41,937] [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
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0849	364	901	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.8592	368	901	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	78.8318	402	901	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	78.5946	317	901	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.5939	373	901	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	78.5847	365	901	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	78.5115	359	901	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	78.4201	331	901	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.3667	379	901	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.3639	366	901	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	78.3553	367	901	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.351	304	901	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.2936	374	901	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	78.2788	315	901	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.2608	356	901	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	78.2533	315	901	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.2525	351	901	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	78.0796	321	901	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	77.949	271	901	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	77.9239	300	901	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.17	159	901	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 05:14:41,939] [INFO] DFAST Taxonomy check result was written to GCA_027490925.1_ASM2749092v1_genomic.fna/tc_result.tsv
[2023-06-29 05:14:41,940] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:14:41,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:14:41,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/checkm_data
[2023-06-29 05:14:41,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:14:41,975] [INFO] Task started: CheckM
[2023-06-29 05:14:41,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027490925.1_ASM2749092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027490925.1_ASM2749092v1_genomic.fna/checkm_input GCA_027490925.1_ASM2749092v1_genomic.fna/checkm_result
[2023-06-29 05:15:22,333] [INFO] Task succeeded: CheckM
[2023-06-29 05:15:22,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 05:15:22,356] [INFO] ===== Completeness check finished =====
[2023-06-29 05:15:22,356] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:15:22,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027490925.1_ASM2749092v1_genomic.fna/markers.fasta)
[2023-06-29 05:15:22,357] [INFO] Task started: Blastn
[2023-06-29 05:15:22,357] [INFO] Running command: blastn -query GCA_027490925.1_ASM2749092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9792450b-609c-4b2d-88d7-1eb039e9d723/dqc_reference/reference_markers_gtdb.fasta -out GCA_027490925.1_ASM2749092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:15:23,928] [INFO] Task succeeded: Blastn
[2023-06-29 05:15:23,933] [INFO] Selected 24 target genomes.
[2023-06-29 05:15:23,934] [INFO] Target genome list was writen to GCA_027490925.1_ASM2749092v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:15:23,987] [INFO] Task started: fastANI
[2023-06-29 05:15:23,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg3369c95f-1ebc-4df7-8c38-e9bfca50de84/GCA_027490925.1_ASM2749092v1_genomic.fna.gz --refList GCA_027490925.1_ASM2749092v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027490925.1_ASM2749092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:15:42,283] [INFO] Task succeeded: fastANI
[2023-06-29 05:15:42,304] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 05:15:42,305] [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_017848435.1	s__PCRC01 sp017848435	82.0622	612	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PCRC01	95.0	99.98	99.98	0.99	0.98	3	-
GCA_016185015.1	s__Hylemonella sp016185015	79.2367	326	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	79.0406	363	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	78.8729	363	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001797315.1	s__Hylemonella sp001797315	78.7226	325	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002002705.1	s__Rhodoferax_A sp002002705	78.6639	346	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697775.1	s__Ramlibacter sp013697775	78.6098	323	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381265.1	s__Curvibacter lanceolatus	78.5828	374	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
GCF_001422445.1	s__Pseudorhodoferax sp001422445	78.5791	360	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104385.1	s__Rhodoferax_B sp900104385	78.5536	320	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006970865.1	s__Rhodoferax_A sediminis	78.5356	334	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	78.4739	320	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_016703145.1	s__Ottowia sp016703145	78.4718	336	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCF_003097105.1	s__Rhodoferax_B sp003097105	78.4492	339	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	78.3577	366	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004682015.1	s__Ramlibacter henchirensis	78.2671	316	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765735.1	s__Variovorax sp009765735	78.2401	318	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879655.1	s__JAABQG01 sp014879655	78.2208	279	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454975.1	s__Hylemonella sp002454975	78.1347	249	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984055.1	s__Variovorax sp001984055	78.1244	325	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844215.1	s__CAIKVZ01 sp903844215	77.9471	256	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	77.9397	298	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897925.1	s__Rhodoferax sp903897925	77.4469	196	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCF_002778325.1	s__Limnohabitans sp002778325	76.9739	201	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 05:15:42,307] [INFO] GTDB search result was written to GCA_027490925.1_ASM2749092v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:15:42,307] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:15:42,312] [INFO] DFAST_QC result json was written to GCA_027490925.1_ASM2749092v1_genomic.fna/dqc_result.json
[2023-06-29 05:15:42,313] [INFO] DFAST_QC completed!
[2023-06-29 05:15:42,313] [INFO] Total running time: 0h1m33s