[2024-01-24 13:48:59,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,696] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference
[2024-01-24 13:49:01,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,058] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a2a5358-db4c-4158-8bf0-fee7ccbda66e/GCF_002879865.1_ASM287986v1_genomic.fna.gz | prodigal -d GCF_002879865.1_ASM287986v1_genomic.fna/cds.fna -a GCF_002879865.1_ASM287986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:26,686] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:26,687] [INFO] Task started: HMMsearch
[2024-01-24 13:49:26,687] [INFO] Running command: hmmsearch --tblout GCF_002879865.1_ASM287986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/reference_markers.hmm GCF_002879865.1_ASM287986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:27,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:27,102] [INFO] Found 6/6 markers.
[2024-01-24 13:49:27,166] [INFO] Query marker FASTA was written to GCF_002879865.1_ASM287986v1_genomic.fna/markers.fasta
[2024-01-24 13:49:27,166] [INFO] Task started: Blastn
[2024-01-24 13:49:27,166] [INFO] Running command: blastn -query GCF_002879865.1_ASM287986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/reference_markers.fasta -out GCF_002879865.1_ASM287986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:28,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,176] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:28,177] [INFO] Target genome list was writen to GCF_002879865.1_ASM287986v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:28,181] [INFO] Task started: fastANI
[2024-01-24 13:49:28,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2a5358-db4c-4158-8bf0-fee7ccbda66e/GCF_002879865.1_ASM287986v1_genomic.fna.gz --refList GCF_002879865.1_ASM287986v1_genomic.fna/target_genomes.txt --output GCF_002879865.1_ASM287986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,381] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,382] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,398] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:04,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,399] [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
Paraburkholderia rhynchosiae	strain=WSM 3937	GCA_002879865.1	487049	487049	type	True	100.0	2614	2619	95	conclusive
Paraburkholderia rhynchosiae	strain=LMG 27174	GCA_902859775.1	487049	487049	type	True	99.9926	2575	2619	95	conclusive
Paraburkholderia dilworthii	strain=WSM3556	GCA_000472525.1	948106	948106	type	True	89.1406	1821	2619	95	below_threshold
Paraburkholderia kirstenboschensis	strain=LMG 28727	GCA_904848585.1	1245436	1245436	type	True	88.4654	1762	2619	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	88.1819	1438	2619	95	below_threshold
Paraburkholderia caledonica	strain=LMG 19076	GCA_902833635.1	134536	134536	type	True	87.5896	1665	2619	95	below_threshold
Paraburkholderia caledonica	strain=NBRC 102488	GCA_000685095.1	134536	134536	type	True	87.5819	1641	2619	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	85.9007	1557	2619	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	85.8049	1423	2619	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000013645.1	36873	36873	type	True	85.6853	1510	2619	95	below_threshold
Paraburkholderia xenovorans	strain=LB400	GCA_000756045.1	36873	36873	type	True	85.6692	1493	2619	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	85.1124	1405	2619	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	85.0206	1506	2619	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	84.8729	1444	2619	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.7127	1558	2619	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.722	243	2619	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	76.7079	281	2619	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	76.5874	244	2619	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	76.4779	315	2619	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	76.3582	266	2619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,401] [INFO] DFAST Taxonomy check result was written to GCF_002879865.1_ASM287986v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/checkm_data
[2024-01-24 13:50:04,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,482] [INFO] Task started: CheckM
[2024-01-24 13:50:04,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002879865.1_ASM287986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002879865.1_ASM287986v1_genomic.fna/checkm_input GCF_002879865.1_ASM287986v1_genomic.fna/checkm_result
[2024-01-24 13:51:12,504] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:12,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:12,532] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:12,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:12,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002879865.1_ASM287986v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:12,533] [INFO] Task started: Blastn
[2024-01-24 13:51:12,534] [INFO] Running command: blastn -query GCF_002879865.1_ASM287986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ad0e9f-03db-400a-84ce-a778720f10ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_002879865.1_ASM287986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:14,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:14,085] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:14,085] [INFO] Target genome list was writen to GCF_002879865.1_ASM287986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:14,099] [INFO] Task started: fastANI
[2024-01-24 13:51:14,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a2a5358-db4c-4158-8bf0-fee7ccbda66e/GCF_002879865.1_ASM287986v1_genomic.fna.gz --refList GCF_002879865.1_ASM287986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002879865.1_ASM287986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:43,188] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:43,208] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:43,208] [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_002879865.1	s__Paraburkholderia rhynchosiae	100.0	2614	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000472525.1	s__Paraburkholderia dilworthii	89.1369	1822	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904848585.1	s__Paraburkholderia kirstenboschensis	88.4654	1762	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000172415.1	s__Paraburkholderia graminis	87.6448	1663	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.52	98.23	0.90	0.89	12	-
GCF_000685095.1	s__Paraburkholderia caledonica	87.5853	1641	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.03	95.65	0.88	0.80	10	-
GCF_000472445.1	s__Paraburkholderia sp000472445	87.2036	1613	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339745.1	s__Paraburkholderia sp004339745	86.1197	1630	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002025.1	s__Paraburkholderia sp003002025	85.9234	1604	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_902859915.1	s__Paraburkholderia ultramafica	85.8559	1439	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739735.1	s__Paraburkholderia ginsengisoli	85.8076	1423	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000013645.1	s__Paraburkholderia xenovorans	85.6874	1510	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.29	98.59	0.95	0.90	3	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	85.4879	1552	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369935.1	s__Paraburkholderia panacisoli	85.3566	1546	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	84.4413	1315	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCA_001544595.2	s__Caballeronia peredens	80.7482	979	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114705.1	s__Rugamonas rubra	76.4878	312	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_003011895.2	s__Massilia glaciei	76.3581	266	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344615.1	s__Janthinobacterium sp000344615	76.3243	332	2619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:43,213] [INFO] GTDB search result was written to GCF_002879865.1_ASM287986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:43,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:43,218] [INFO] DFAST_QC result json was written to GCF_002879865.1_ASM287986v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:43,218] [INFO] DFAST_QC completed!
[2024-01-24 13:51:43,219] [INFO] Total running time: 0h2m44s