[2024-01-24 13:41:18,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference
[2024-01-24 13:41:19,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:19,467] [INFO] Task started: Prodigal
[2024-01-24 13:41:19,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e10140e-faec-4e2f-9e64-21b2c193dee4/GCF_002762215.1_ASM276221v1_genomic.fna.gz | prodigal -d GCF_002762215.1_ASM276221v1_genomic.fna/cds.fna -a GCF_002762215.1_ASM276221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:41,318] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:41,319] [INFO] Task started: HMMsearch
[2024-01-24 13:41:41,319] [INFO] Running command: hmmsearch --tblout GCF_002762215.1_ASM276221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/reference_markers.hmm GCF_002762215.1_ASM276221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:41,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:41,677] [INFO] Found 6/6 markers.
[2024-01-24 13:41:41,730] [INFO] Query marker FASTA was written to GCF_002762215.1_ASM276221v1_genomic.fna/markers.fasta
[2024-01-24 13:41:41,730] [INFO] Task started: Blastn
[2024-01-24 13:41:41,731] [INFO] Running command: blastn -query GCF_002762215.1_ASM276221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/reference_markers.fasta -out GCF_002762215.1_ASM276221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:42,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:42,785] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:42,786] [INFO] Target genome list was writen to GCF_002762215.1_ASM276221v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:42,793] [INFO] Task started: fastANI
[2024-01-24 13:41:42,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e10140e-faec-4e2f-9e64-21b2c193dee4/GCF_002762215.1_ASM276221v1_genomic.fna.gz --refList GCF_002762215.1_ASM276221v1_genomic.fna/target_genomes.txt --output GCF_002762215.1_ASM276221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:07,295] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:07,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:07,311] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:42:07,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:07,312] [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
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	100.0	2131	2132	95	conclusive
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	99.9999	2131	2132	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.5229	710	2132	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4902	730	2132	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.4778	720	2132	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	79.9073	674	2132	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.855	698	2132	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	79.7818	713	2132	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.6702	684	2132	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.6632	733	2132	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.6604	639	2132	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	79.5189	656	2132	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	79.4709	679	2132	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.4432	649	2132	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.4077	739	2132	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.2581	723	2132	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.2212	624	2132	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	79.216	816	2132	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.1377	705	2132	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.0665	783	2132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,313] [INFO] DFAST Taxonomy check result was written to GCF_002762215.1_ASM276221v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:07,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:07,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:07,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/checkm_data
[2024-01-24 13:42:07,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:07,374] [INFO] Task started: CheckM
[2024-01-24 13:42:07,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002762215.1_ASM276221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002762215.1_ASM276221v1_genomic.fna/checkm_input GCF_002762215.1_ASM276221v1_genomic.fna/checkm_result
[2024-01-24 13:45:38,719] [INFO] Task succeeded: CheckM
[2024-01-24 13:45:38,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:45:38,744] [INFO] ===== Completeness check finished =====
[2024-01-24 13:45:38,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:45:38,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002762215.1_ASM276221v1_genomic.fna/markers.fasta)
[2024-01-24 13:45:38,746] [INFO] Task started: Blastn
[2024-01-24 13:45:38,746] [INFO] Running command: blastn -query GCF_002762215.1_ASM276221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd305ea7c-4b19-42cb-9dea-84fce0c9351b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002762215.1_ASM276221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:40,914] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:40,919] [INFO] Selected 17 target genomes.
[2024-01-24 13:45:40,919] [INFO] Target genome list was writen to GCF_002762215.1_ASM276221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:45:40,976] [INFO] Task started: fastANI
[2024-01-24 13:45:40,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e10140e-faec-4e2f-9e64-21b2c193dee4/GCF_002762215.1_ASM276221v1_genomic.fna.gz --refList GCF_002762215.1_ASM276221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002762215.1_ASM276221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:01,832] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:01,848] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:01,848] [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_002116905.1	s__Rhizobacter gummiphilus	99.9999	2131	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001425785.1	s__Rhizobacter sp001425785	85.1786	1283	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	81.736	1055	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	81.7289	1027	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932665.1	s__Rhizobacter sp012932665	81.6855	1082	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425825.1	s__Rhizobacter sp001425825	81.5837	1036	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	99.93	99.87	0.98	0.98	3	-
GCF_016735515.1	s__Rhizobacter sp016735515	81.4811	963	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275445.1	s__Rhizobacter sp012275445	81.4517	1061	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706565.1	s__Piscinibacter sp016706565	80.9232	798	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.8653	784	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_017795745.1	s__Piscinibacter sp017795745	80.8359	810	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425865.1	s__LMDS01 sp001425865	80.5475	786	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799305.1	s__Rhizobacter sp000799305	80.5343	937	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905475.1	s__PBB1 sp903905475	79.8871	420	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	99.20	99.17	0.87	0.87	3	-
GCA_002255905.1	s__PBB1 sp002255905	79.7836	511	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017986065.1	s__PBB1 sp017986065	79.5139	451	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	99.66	99.66	0.90	0.90	2	-
GCA_016702655.1	s__CAIKUF01 sp016702655	79.4887	659	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:01,856] [INFO] GTDB search result was written to GCF_002762215.1_ASM276221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:01,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:01,862] [INFO] DFAST_QC result json was written to GCF_002762215.1_ASM276221v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:01,863] [INFO] DFAST_QC completed!
[2024-01-24 13:46:01,863] [INFO] Total running time: 0h4m44s