[2024-01-24 13:56:27,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,237] [INFO] DQC Reference Directory: /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference
[2024-01-24 13:56:28,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,520] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgd04fafa0-9514-44e3-b7b5-bae8c4ecd1ed/GCF_000484635.1_ASM48463v1_genomic.fna.gz | prodigal -d GCF_000484635.1_ASM48463v1_genomic.fna/cds.fna -a GCF_000484635.1_ASM48463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:41,026] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:41,027] [INFO] Task started: HMMsearch
[2024-01-24 13:56:41,027] [INFO] Running command: hmmsearch --tblout GCF_000484635.1_ASM48463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/reference_markers.hmm GCF_000484635.1_ASM48463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:41,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:41,297] [INFO] Found 6/6 markers.
[2024-01-24 13:56:41,329] [INFO] Query marker FASTA was written to GCF_000484635.1_ASM48463v1_genomic.fna/markers.fasta
[2024-01-24 13:56:41,330] [INFO] Task started: Blastn
[2024-01-24 13:56:41,330] [INFO] Running command: blastn -query GCF_000484635.1_ASM48463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/reference_markers.fasta -out GCF_000484635.1_ASM48463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:42,371] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:42,375] [INFO] Selected 24 target genomes.
[2024-01-24 13:56:42,376] [INFO] Target genome list was writen to GCF_000484635.1_ASM48463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:42,404] [INFO] Task started: fastANI
[2024-01-24 13:56:42,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04fafa0-9514-44e3-b7b5-bae8c4ecd1ed/GCF_000484635.1_ASM48463v1_genomic.fna.gz --refList GCF_000484635.1_ASM48463v1_genomic.fna/target_genomes.txt --output GCF_000484635.1_ASM48463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:02,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:02,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:02,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:02,912] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:02,913] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:02,913] [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	81.2804	405	1216	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	81.1807	574	1216	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	80.8672	650	1216	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.6111	617	1216	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.2067	557	1216	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.1997	547	1216	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.1331	519	1216	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	79.9781	543	1216	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	79.9676	535	1216	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	79.9515	567	1216	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.9295	559	1216	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	79.7989	550	1216	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.7847	474	1216	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.7374	544	1216	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.6759	512	1216	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.5888	510	1216	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	79.5479	605	1216	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.4299	535	1216	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.3646	477	1216	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	79.2416	505	1216	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0872	497	1216	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	79.0527	570	1216	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	78.5108	298	1216	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	77.45	295	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:02,915] [INFO] DFAST Taxonomy check result was written to GCF_000484635.1_ASM48463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:02,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:02,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:02,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/checkm_data
[2024-01-24 13:57:02,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:02,954] [INFO] Task started: CheckM
[2024-01-24 13:57:02,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000484635.1_ASM48463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000484635.1_ASM48463v1_genomic.fna/checkm_input GCF_000484635.1_ASM48463v1_genomic.fna/checkm_result
[2024-01-24 13:57:52,352] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:52,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:52,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:52,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:52,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000484635.1_ASM48463v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:52,386] [INFO] Task started: Blastn
[2024-01-24 13:57:52,386] [INFO] Running command: blastn -query GCF_000484635.1_ASM48463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8379d85-2302-473e-8642-dc857f874d48/dqc_reference/reference_markers_gtdb.fasta -out GCF_000484635.1_ASM48463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:54,636] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:54,641] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:54,641] [INFO] Target genome list was writen to GCF_000484635.1_ASM48463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:54,655] [INFO] Task started: fastANI
[2024-01-24 13:57:54,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04fafa0-9514-44e3-b7b5-bae8c4ecd1ed/GCF_000484635.1_ASM48463v1_genomic.fna.gz --refList GCF_000484635.1_ASM48463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000484635.1_ASM48463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:09,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,278] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:09,279] [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_000484635.1	s__Comamonas_C badia	100.0	1213	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.01	98.01	0.89	0.89	2	conclusive
GCA_001724135.1	s__Comamonas_C sp001724135	88.8812	916	1216	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_007954405.1	s__Comamonas_C sp007954405	84.7372	794	1216	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	84.0331	779	1216	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_019195435.1	s__Comamonas_C sp019195435	83.8736	729	1216	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	82.1726	686	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_017307865.1	s__Ottowia sp017307865	81.6168	635	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCA_018240985.1	s__Alicycliphilus sp018240985	81.4872	575	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_018241405.1	s__Alicycliphilus sp018241405	81.4123	582	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCA_001725235.1	s__Acidovorax_C sp001725235	80.9672	642	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_017811175.1	s__Melaminivora_A jejuensis	80.9039	647	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303755.1	s__Acidovorax_C sp011303755	80.7408	530	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241325.1	s__Ottowia sp018241325	80.5252	574	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,280] [INFO] GTDB search result was written to GCF_000484635.1_ASM48463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:09,281] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:09,285] [INFO] DFAST_QC result json was written to GCF_000484635.1_ASM48463v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:09,285] [INFO] DFAST_QC completed!
[2024-01-24 13:58:09,285] [INFO] Total running time: 0h1m42s