[2024-01-24 14:14:45,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,732] [INFO] DQC Reference Directory: /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference
[2024-01-24 14:14:47,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:47,120] [INFO] Task started: Prodigal
[2024-01-24 14:14:47,120] [INFO] Running command: gunzip -c /var/lib/cwl/stga5900eda-1cf9-404f-90bf-ff2f602565dd/GCF_002885975.1_ASM288597v1_genomic.fna.gz | prodigal -d GCF_002885975.1_ASM288597v1_genomic.fna/cds.fna -a GCF_002885975.1_ASM288597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:05,623] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:05,623] [INFO] Task started: HMMsearch
[2024-01-24 14:15:05,624] [INFO] Running command: hmmsearch --tblout GCF_002885975.1_ASM288597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/reference_markers.hmm GCF_002885975.1_ASM288597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:05,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:05,948] [INFO] Found 6/6 markers.
[2024-01-24 14:15:05,995] [INFO] Query marker FASTA was written to GCF_002885975.1_ASM288597v1_genomic.fna/markers.fasta
[2024-01-24 14:15:05,996] [INFO] Task started: Blastn
[2024-01-24 14:15:05,996] [INFO] Running command: blastn -query GCF_002885975.1_ASM288597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/reference_markers.fasta -out GCF_002885975.1_ASM288597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:07,042] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:07,045] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:07,046] [INFO] Target genome list was writen to GCF_002885975.1_ASM288597v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:07,059] [INFO] Task started: fastANI
[2024-01-24 14:15:07,060] [INFO] Running command: fastANI --query /var/lib/cwl/stga5900eda-1cf9-404f-90bf-ff2f602565dd/GCF_002885975.1_ASM288597v1_genomic.fna.gz --refList GCF_002885975.1_ASM288597v1_genomic.fna/target_genomes.txt --output GCF_002885975.1_ASM288597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:25,697] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:25,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:25,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:25,718] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:25,718] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:25,718] [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
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	80.6166	835	1839	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	80.4385	915	1839	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	80.242	824	1839	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.064	752	1839	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.0626	713	1839	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.7343	509	1839	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.6546	678	1839	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.6521	682	1839	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.4214	612	1839	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	79.32	746	1839	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.2788	557	1839	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.1774	583	1839	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	78.7211	584	1839	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	78.6943	590	1839	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.6894	523	1839	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	78.6364	575	1839	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	78.5858	599	1839	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.063	500	1839	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:25,722] [INFO] DFAST Taxonomy check result was written to GCF_002885975.1_ASM288597v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:25,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:25,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:25,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/checkm_data
[2024-01-24 14:15:25,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:25,779] [INFO] Task started: CheckM
[2024-01-24 14:15:25,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002885975.1_ASM288597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002885975.1_ASM288597v1_genomic.fna/checkm_input GCF_002885975.1_ASM288597v1_genomic.fna/checkm_result
[2024-01-24 14:17:14,134] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:14,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:14,159] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:14,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:14,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002885975.1_ASM288597v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:14,160] [INFO] Task started: Blastn
[2024-01-24 14:17:14,160] [INFO] Running command: blastn -query GCF_002885975.1_ASM288597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc748fc7a-9c39-49ab-8fc1-52f533d2ea17/dqc_reference/reference_markers_gtdb.fasta -out GCF_002885975.1_ASM288597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:16,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:16,263] [INFO] Selected 12 target genomes.
[2024-01-24 14:17:16,263] [INFO] Target genome list was writen to GCF_002885975.1_ASM288597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:16,279] [INFO] Task started: fastANI
[2024-01-24 14:17:16,279] [INFO] Running command: fastANI --query /var/lib/cwl/stga5900eda-1cf9-404f-90bf-ff2f602565dd/GCF_002885975.1_ASM288597v1_genomic.fna.gz --refList GCF_002885975.1_ASM288597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002885975.1_ASM288597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:32,170] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:32,184] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:32,185] [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_002885975.1	s__Paucibacter_A aquatile	100.0	1834	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002255955.1	s__Paucibacter_A sp002255955	94.4929	1519	1839	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_014204525.1	s__Paucibacter_A oligotrophus	82.7696	1006	1839	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_004362405.1	s__Kinneretia asaccharophila	82.2459	884	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	82.0537	1007	1839	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_005503085.1	s__Paucibacter_A sp005503085	81.9797	983	1839	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_001477625.1	s__Paucibacter_A sp001477625	81.9688	952	1839	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	81.6775	1007	1839	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	81.4449	805	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	80.5617	879	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467315.1	s__OAE585 sp016467315	80.5172	878	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425705.1	s__Pelomonas sp001425705	80.2311	820	1839	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:32,186] [INFO] GTDB search result was written to GCF_002885975.1_ASM288597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:32,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:32,190] [INFO] DFAST_QC result json was written to GCF_002885975.1_ASM288597v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:32,191] [INFO] DFAST_QC completed!
[2024-01-24 14:17:32,191] [INFO] Total running time: 0h2m46s