[2024-01-24 12:47:26,065] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:26,067] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:26,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference
[2024-01-24 12:47:27,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:27,430] [INFO] Task started: Prodigal
[2024-01-24 12:47:27,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg86812ed2-7480-433c-970c-ca7c871c519c/GCF_002205845.1_ASM220584v1_genomic.fna.gz | prodigal -d GCF_002205845.1_ASM220584v1_genomic.fna/cds.fna -a GCF_002205845.1_ASM220584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:48,206] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:48,207] [INFO] Task started: HMMsearch
[2024-01-24 12:47:48,207] [INFO] Running command: hmmsearch --tblout GCF_002205845.1_ASM220584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/reference_markers.hmm GCF_002205845.1_ASM220584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:48,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:48,570] [INFO] Found 6/6 markers.
[2024-01-24 12:47:48,621] [INFO] Query marker FASTA was written to GCF_002205845.1_ASM220584v1_genomic.fna/markers.fasta
[2024-01-24 12:47:48,621] [INFO] Task started: Blastn
[2024-01-24 12:47:48,622] [INFO] Running command: blastn -query GCF_002205845.1_ASM220584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/reference_markers.fasta -out GCF_002205845.1_ASM220584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:49,664] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:49,669] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:49,669] [INFO] Target genome list was writen to GCF_002205845.1_ASM220584v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:49,678] [INFO] Task started: fastANI
[2024-01-24 12:47:49,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg86812ed2-7480-433c-970c-ca7c871c519c/GCF_002205845.1_ASM220584v1_genomic.fna.gz --refList GCF_002205845.1_ASM220584v1_genomic.fna/target_genomes.txt --output GCF_002205845.1_ASM220584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:10,929] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:10,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:10,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:10,943] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:10,943] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:10,943] [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 puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	100.0	1998	2000	95	conclusive
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	85.0588	1239	2000	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	80.4136	824	2000	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	80.144	784	2000	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.0731	682	2000	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.8991	631	2000	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.7561	641	2000	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	79.6923	525	2000	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.6555	640	2000	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	79.5937	743	2000	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.5325	829	2000	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.3798	557	2000	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	79.3694	475	2000	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	79.2056	694	2000	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	79.2024	694	2000	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	78.9967	650	2000	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	78.9967	577	2000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:10,945] [INFO] DFAST Taxonomy check result was written to GCF_002205845.1_ASM220584v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:10,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:10,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:10,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/checkm_data
[2024-01-24 12:48:10,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:11,009] [INFO] Task started: CheckM
[2024-01-24 12:48:11,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002205845.1_ASM220584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002205845.1_ASM220584v1_genomic.fna/checkm_input GCF_002205845.1_ASM220584v1_genomic.fna/checkm_result
[2024-01-24 12:50:02,767] [INFO] Task succeeded: CheckM
[2024-01-24 12:50:02,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:50:02,791] [INFO] ===== Completeness check finished =====
[2024-01-24 12:50:02,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:50:02,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002205845.1_ASM220584v1_genomic.fna/markers.fasta)
[2024-01-24 12:50:02,792] [INFO] Task started: Blastn
[2024-01-24 12:50:02,792] [INFO] Running command: blastn -query GCF_002205845.1_ASM220584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc9bdd9-db85-4c4b-b27e-463b1c2d970c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002205845.1_ASM220584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:50:04,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:50:04,814] [INFO] Selected 11 target genomes.
[2024-01-24 12:50:04,814] [INFO] Target genome list was writen to GCF_002205845.1_ASM220584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:50:04,839] [INFO] Task started: fastANI
[2024-01-24 12:50:04,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg86812ed2-7480-433c-970c-ca7c871c519c/GCF_002205845.1_ASM220584v1_genomic.fna.gz --refList GCF_002205845.1_ASM220584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002205845.1_ASM220584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:20,228] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:20,240] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:20,240] [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_002205845.1	s__Pelomonas puraquae	100.0	1998	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016790285.1	s__Pelomonas sp016790285	87.1131	1340	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963005.1	s__Pelomonas sp003963005	86.9887	1343	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996515.1	s__Pelomonas sp009996515	85.6167	1137	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342485.1	s__Pelomonas saccharophila	85.0406	1240	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237615.1	s__Pelomonas sp019237615	84.956	1125	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963075.1	s__Pelomonas sp003963075	84.8331	1046	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	96.90	96.90	0.86	0.86	2	-
GCF_003550215.1	s__Pelomonas sp003550215	84.7713	1333	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425705.1	s__Pelomonas sp001425705	84.31	1299	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195825.1	s__Pelomonas sp016195825	84.2314	1235	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241055.1	s__Pelomonas depolymerans_A	83.6682	1077	2000	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 12:50:20,242] [INFO] GTDB search result was written to GCF_002205845.1_ASM220584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:20,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:20,246] [INFO] DFAST_QC result json was written to GCF_002205845.1_ASM220584v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:20,246] [INFO] DFAST_QC completed!
[2024-01-24 12:50:20,246] [INFO] Total running time: 0h2m54s