[2024-01-24 12:53:49,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference
[2024-01-24 12:53:51,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,742] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg89d1a30a-743f-4953-8888-d0e8165d3791/GCF_007954405.1_ASM795440v1_genomic.fna.gz | prodigal -d GCF_007954405.1_ASM795440v1_genomic.fna/cds.fna -a GCF_007954405.1_ASM795440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:02,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:02,942] [INFO] Task started: HMMsearch
[2024-01-24 12:54:02,942] [INFO] Running command: hmmsearch --tblout GCF_007954405.1_ASM795440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/reference_markers.hmm GCF_007954405.1_ASM795440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:03,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:03,213] [INFO] Found 6/6 markers.
[2024-01-24 12:54:03,251] [INFO] Query marker FASTA was written to GCF_007954405.1_ASM795440v1_genomic.fna/markers.fasta
[2024-01-24 12:54:03,251] [INFO] Task started: Blastn
[2024-01-24 12:54:03,252] [INFO] Running command: blastn -query GCF_007954405.1_ASM795440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/reference_markers.fasta -out GCF_007954405.1_ASM795440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:04,332] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:04,337] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:04,338] [INFO] Target genome list was writen to GCF_007954405.1_ASM795440v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:04,489] [INFO] Task started: fastANI
[2024-01-24 12:54:04,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d1a30a-743f-4953-8888-d0e8165d3791/GCF_007954405.1_ASM795440v1_genomic.fna.gz --refList GCF_007954405.1_ASM795440v1_genomic.fna/target_genomes.txt --output GCF_007954405.1_ASM795440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:24,024] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:24,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:24,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:24,045] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:24,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:24,046] [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
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	82.1443	416	1111	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	81.9087	606	1111	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	81.8373	666	1111	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.2818	571	1111	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.1619	532	1111	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.1522	526	1111	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.1506	539	1111	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.137	556	1111	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0352	571	1111	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	79.9617	568	1111	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.9283	601	1111	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.9051	579	1111	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.7135	535	1111	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.6228	524	1111	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.457	553	1111	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	79.3771	472	1111	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.3732	513	1111	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.3626	563	1111	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.2514	604	1111	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.9422	547	1111	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	78.8895	471	1111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:24,048] [INFO] DFAST Taxonomy check result was written to GCF_007954405.1_ASM795440v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:24,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:24,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:24,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/checkm_data
[2024-01-24 12:54:24,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:24,090] [INFO] Task started: CheckM
[2024-01-24 12:54:24,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007954405.1_ASM795440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007954405.1_ASM795440v1_genomic.fna/checkm_input GCF_007954405.1_ASM795440v1_genomic.fna/checkm_result
[2024-01-24 12:55:10,361] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:10,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:10,383] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:10,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:10,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007954405.1_ASM795440v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:10,384] [INFO] Task started: Blastn
[2024-01-24 12:55:10,385] [INFO] Running command: blastn -query GCF_007954405.1_ASM795440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg820869c9-bd19-4ec5-9c29-9ba6dcd819a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_007954405.1_ASM795440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:12,701] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:12,705] [INFO] Selected 12 target genomes.
[2024-01-24 12:55:12,706] [INFO] Target genome list was writen to GCF_007954405.1_ASM795440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:12,715] [INFO] Task started: fastANI
[2024-01-24 12:55:12,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d1a30a-743f-4953-8888-d0e8165d3791/GCF_007954405.1_ASM795440v1_genomic.fna.gz --refList GCF_007954405.1_ASM795440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007954405.1_ASM795440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:24,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:24,303] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:24,304] [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_007954405.1	s__Comamonas_C sp007954405	100.0	1111	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019195435.1	s__Comamonas_C sp019195435	92.2333	890	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725255.1	s__Comamonas_C sp001725255	84.8898	772	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.57	95.76	0.95	0.89	4	-
GCF_000484635.1	s__Comamonas_C badia	84.7822	785	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.01	98.01	0.89	0.89	2	-
GCA_001724135.1	s__Comamonas_C sp001724135	84.1555	738	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204645.1	s__Alicycliphilus denitrificans	82.5331	699	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_017811175.1	s__Melaminivora_A jejuensis	81.8223	668	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307865.1	s__Ottowia sp017307865	81.5994	644	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCA_016702555.1	s__Ottowia sp016702555	80.4469	559	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCA_018241325.1	s__Ottowia sp018241325	80.4048	603	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	80.1412	527	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	79.4307	597	1111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:24,306] [INFO] GTDB search result was written to GCF_007954405.1_ASM795440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:24,307] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:24,312] [INFO] DFAST_QC result json was written to GCF_007954405.1_ASM795440v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:24,313] [INFO] DFAST_QC completed!
[2024-01-24 12:55:24,313] [INFO] Total running time: 0h1m35s