[2024-01-24 11:59:22,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference
[2024-01-24 11:59:25,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,640] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,640] [INFO] Running command: gunzip -c /var/lib/cwl/stge8f92b0d-0795-4e84-aa7d-632e1ea4041a/GCF_008039575.1_ASM803957v1_genomic.fna.gz | prodigal -d GCF_008039575.1_ASM803957v1_genomic.fna/cds.fna -a GCF_008039575.1_ASM803957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:36,242] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:36,242] [INFO] Task started: HMMsearch
[2024-01-24 11:59:36,242] [INFO] Running command: hmmsearch --tblout GCF_008039575.1_ASM803957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/reference_markers.hmm GCF_008039575.1_ASM803957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:36,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:36,503] [INFO] Found 6/6 markers.
[2024-01-24 11:59:36,537] [INFO] Query marker FASTA was written to GCF_008039575.1_ASM803957v1_genomic.fna/markers.fasta
[2024-01-24 11:59:36,538] [INFO] Task started: Blastn
[2024-01-24 11:59:36,538] [INFO] Running command: blastn -query GCF_008039575.1_ASM803957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/reference_markers.fasta -out GCF_008039575.1_ASM803957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:37,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:37,558] [INFO] Selected 26 target genomes.
[2024-01-24 11:59:37,559] [INFO] Target genome list was writen to GCF_008039575.1_ASM803957v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:37,586] [INFO] Task started: fastANI
[2024-01-24 11:59:37,586] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f92b0d-0795-4e84-aa7d-632e1ea4041a/GCF_008039575.1_ASM803957v1_genomic.fna.gz --refList GCF_008039575.1_ASM803957v1_genomic.fna/target_genomes.txt --output GCF_008039575.1_ASM803957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:02,659] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:02,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:02,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:02,683] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:02,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:02,683] [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
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	78.1767	394	1267	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	78.1149	398	1267	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.0334	454	1267	95	below_threshold
Pigmentiphaga kullae	strain=K24	GCA_004216695.1	151784	151784	type	True	78.0256	373	1267	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.9166	475	1267	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.9051	375	1267	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.9039	384	1267	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	77.8479	422	1267	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.7213	356	1267	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.7165	260	1267	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.7075	351	1267	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	77.5659	519	1267	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	77.5602	380	1267	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	77.5446	544	1267	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	77.5289	404	1267	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	77.4986	394	1267	95	below_threshold
Burkholderia gladioli	strain=NCTC12378	GCA_900446225.1	28095	28095	type	True	77.473	531	1267	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	77.4035	465	1267	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	77.3981	465	1267	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.3394	503	1267	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3294	405	1267	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	77.2177	241	1267	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	77.2019	366	1267	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	77.1588	367	1267	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	77.1474	386	1267	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.6748	310	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:02,686] [INFO] DFAST Taxonomy check result was written to GCF_008039575.1_ASM803957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:02,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:02,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:02,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/checkm_data
[2024-01-24 12:00:02,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:02,725] [INFO] Task started: CheckM
[2024-01-24 12:00:02,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008039575.1_ASM803957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008039575.1_ASM803957v1_genomic.fna/checkm_input GCF_008039575.1_ASM803957v1_genomic.fna/checkm_result
[2024-01-24 12:00:44,298] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:44,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:44,317] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:44,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:44,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008039575.1_ASM803957v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:44,319] [INFO] Task started: Blastn
[2024-01-24 12:00:44,319] [INFO] Running command: blastn -query GCF_008039575.1_ASM803957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg030d8a46-d559-4590-b61f-fdd8ce8034cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_008039575.1_ASM803957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:46,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:46,174] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:46,175] [INFO] Target genome list was writen to GCF_008039575.1_ASM803957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:46,188] [INFO] Task started: fastANI
[2024-01-24 12:00:46,189] [INFO] Running command: fastANI --query /var/lib/cwl/stge8f92b0d-0795-4e84-aa7d-632e1ea4041a/GCF_008039575.1_ASM803957v1_genomic.fna.gz --refList GCF_008039575.1_ASM803957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008039575.1_ASM803957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:53,749] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:53,759] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:53,760] [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_008039575.1	s__SCN-69-89 sp008039575	100.0	1265	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001724315.1	s__SCN-69-89 sp001724315	94.7793	648	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513825.1	s__SCN-69-89 sp012513825	81.8242	640	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724855.1	s__SCN-69-89 sp001724855	81.6106	632	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	81.3047	657	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCA_003577305.1	s__SCN-69-89 sp003577305	81.144	565	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.77	99.54	0.93	0.87	4	-
GCF_014202215.1	s__Quisquiliibacterium transsilvanicum	80.4844	652	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Quisquiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576795.1	s__SCN-69-89 sp003576795	80.2893	438	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818495.1	s__UBA4615 sp003818495	79.438	574	1267	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:53,761] [INFO] GTDB search result was written to GCF_008039575.1_ASM803957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:53,761] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:53,766] [INFO] DFAST_QC result json was written to GCF_008039575.1_ASM803957v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:53,766] [INFO] DFAST_QC completed!
[2024-01-24 12:00:53,766] [INFO] Total running time: 0h1m31s