[2024-01-24 13:58:55,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference
[2024-01-24 13:58:57,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,292] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg779e638b-976f-4f05-b454-fc2fcf5f7606/GCF_004362525.1_ASM436252v1_genomic.fna.gz | prodigal -d GCF_004362525.1_ASM436252v1_genomic.fna/cds.fna -a GCF_004362525.1_ASM436252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:20,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:20,264] [INFO] Task started: HMMsearch
[2024-01-24 13:59:20,265] [INFO] Running command: hmmsearch --tblout GCF_004362525.1_ASM436252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/reference_markers.hmm GCF_004362525.1_ASM436252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:20,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:20,700] [INFO] Found 6/6 markers.
[2024-01-24 13:59:20,755] [INFO] Query marker FASTA was written to GCF_004362525.1_ASM436252v1_genomic.fna/markers.fasta
[2024-01-24 13:59:20,756] [INFO] Task started: Blastn
[2024-01-24 13:59:20,756] [INFO] Running command: blastn -query GCF_004362525.1_ASM436252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/reference_markers.fasta -out GCF_004362525.1_ASM436252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:21,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:21,744] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:21,744] [INFO] Target genome list was writen to GCF_004362525.1_ASM436252v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:21,763] [INFO] Task started: fastANI
[2024-01-24 13:59:21,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e638b-976f-4f05-b454-fc2fcf5f7606/GCF_004362525.1_ASM436252v1_genomic.fna.gz --refList GCF_004362525.1_ASM436252v1_genomic.fna/target_genomes.txt --output GCF_004362525.1_ASM436252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:47,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:47,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:47,486] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:47,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:47,486] [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
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	100.0	2105	2110	95	conclusive
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	80.2948	867	2110	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.0837	790	2110	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.9671	579	2110	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	79.881	653	2110	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.8499	654	2110	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.8385	653	2110	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.7552	679	2110	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.7075	651	2110	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.6761	801	2110	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	79.6364	697	2110	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.563	688	2110	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.4258	639	2110	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.1547	612	2110	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.1509	738	2110	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.1171	769	2110	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.021	676	2110	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.0167	676	2110	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.9383	685	2110	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.9287	784	2110	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.8129	545	2110	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	78.6791	593	2110	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.6691	269	2110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,489] [INFO] DFAST Taxonomy check result was written to GCF_004362525.1_ASM436252v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:47,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:47,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:47,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/checkm_data
[2024-01-24 13:59:47,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:47,548] [INFO] Task started: CheckM
[2024-01-24 13:59:47,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362525.1_ASM436252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362525.1_ASM436252v1_genomic.fna/checkm_input GCF_004362525.1_ASM436252v1_genomic.fna/checkm_result
[2024-01-24 14:01:08,232] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:08,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:08,258] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:08,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:08,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362525.1_ASM436252v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:08,260] [INFO] Task started: Blastn
[2024-01-24 14:01:08,260] [INFO] Running command: blastn -query GCF_004362525.1_ASM436252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bdfb468-446a-4ebd-be55-1c8445baee57/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362525.1_ASM436252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:10,030] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:10,035] [INFO] Selected 22 target genomes.
[2024-01-24 14:01:10,035] [INFO] Target genome list was writen to GCF_004362525.1_ASM436252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:10,074] [INFO] Task started: fastANI
[2024-01-24 14:01:10,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg779e638b-976f-4f05-b454-fc2fcf5f7606/GCF_004362525.1_ASM436252v1_genomic.fna.gz --refList GCF_004362525.1_ASM436252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362525.1_ASM436252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:37,136] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:37,159] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:37,160] [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_004362525.1	s__Paucibacter toxinivorans	100.0	2105	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018780645.1	s__Paucibacter sp018780645	92.8748	1646	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter	95.0	95.57	95.57	0.86	0.86	2	-
GCA_005503085.1	s__Paucibacter_A sp005503085	82.3071	1108	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624425.1	s__Kinneretia sp015624425	81.6967	1074	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657635.1	s__Kinneretia sp015657635	81.2034	838	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	80.8398	889	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	80.8079	854	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824165.1	s__Kinneretia sp013824165	80.8066	849	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255955.1	s__Paucibacter_A sp002255955	80.7111	888	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885975.1	s__Paucibacter_A aquatile	80.5979	890	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	80.0124	797	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	79.9856	840	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	79.9307	811	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	79.9172	818	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	79.887	858	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210455.1	s__Mitsuaria sp004210455	79.8438	724	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293525.1	s__Ideonella_A sakaiensis	79.4331	805	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852895.1	s__Albitalea terrae	79.3317	734	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Albitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322345.1	s__Aquabacterium sp004322345	78.9294	595	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.53	97.53	0.87	0.87	2	-
GCF_018304945.1	s__Collimonas sp018304945	76.6698	268	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_002564105.1	s__Collimonas sp002564105	76.6195	255	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883675.1	s__SCGC-AG-212-J23 sp005883675	75.873	175	2110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SCGC-AG-212-J23	95.0	98.58	98.58	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:37,161] [INFO] GTDB search result was written to GCF_004362525.1_ASM436252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:37,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:37,166] [INFO] DFAST_QC result json was written to GCF_004362525.1_ASM436252v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:37,167] [INFO] DFAST_QC completed!
[2024-01-24 14:01:37,167] [INFO] Total running time: 0h2m41s