[2024-01-25 19:57:20,874] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:20,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:20,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference
[2024-01-25 19:57:22,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:22,042] [INFO] Task started: Prodigal
[2024-01-25 19:57:22,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg15cf14bf-f081-41d4-85d5-6a4c67d3ac27/GCF_904848645.1_LMG_24235_genomic.fna.gz | prodigal -d GCF_904848645.1_LMG_24235_genomic.fna/cds.fna -a GCF_904848645.1_LMG_24235_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:49,015] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:49,016] [INFO] Task started: HMMsearch
[2024-01-25 19:57:49,016] [INFO] Running command: hmmsearch --tblout GCF_904848645.1_LMG_24235_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/reference_markers.hmm GCF_904848645.1_LMG_24235_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:49,419] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:49,420] [INFO] Found 6/6 markers.
[2024-01-25 19:57:49,488] [INFO] Query marker FASTA was written to GCF_904848645.1_LMG_24235_genomic.fna/markers.fasta
[2024-01-25 19:57:49,489] [INFO] Task started: Blastn
[2024-01-25 19:57:49,489] [INFO] Running command: blastn -query GCF_904848645.1_LMG_24235_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/reference_markers.fasta -out GCF_904848645.1_LMG_24235_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:50,430] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:50,434] [INFO] Selected 14 target genomes.
[2024-01-25 19:57:50,435] [INFO] Target genome list was writen to GCF_904848645.1_LMG_24235_genomic.fna/target_genomes.txt
[2024-01-25 19:57:50,441] [INFO] Task started: fastANI
[2024-01-25 19:57:50,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cf14bf-f081-41d4-85d5-6a4c67d3ac27/GCF_904848645.1_LMG_24235_genomic.fna.gz --refList GCF_904848645.1_LMG_24235_genomic.fna/target_genomes.txt --output GCF_904848645.1_LMG_24235_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:23,084] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:23,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:23,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:23,095] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:23,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:23,095] [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 sabiae	strain=LMG 24235	GCA_904848645.1	273251	273251	type	True	100.0	3165	3170	95	conclusive
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	91.7636	2401	3170	95	below_threshold
Paraburkholderia phymatum	strain=LMG 21445	GCA_902833665.1	148447	148447	type	True	89.1523	2105	3170	95	below_threshold
Paraburkholderia phymatum	strain=STM815	GCA_000020045.1	148447	148447	type	True	89.1075	2117	3170	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	88.2734	2135	3170	95	below_threshold
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	88.2076	2211	3170	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	88.1094	2226	3170	95	below_threshold
Paraburkholderia caribensis	strain=LMG 18531	GCA_902833515.1	75105	75105	type	True	88.0285	2088	3170	95	below_threshold
Paraburkholderia caribensis	strain=DSM 13236	GCA_002902945.1	75105	75105	type	True	88.0184	2122	3170	95	below_threshold
Paraburkholderia piptadeniae	strain=STM 7183	GCA_900007165.2	1701573	1701573	type	True	87.0916	1870	3170	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	82.9334	1333	3170	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.6012	1238	3170	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.5305	1424	3170	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	81.7042	1344	3170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:23,097] [INFO] DFAST Taxonomy check result was written to GCF_904848645.1_LMG_24235_genomic.fna/tc_result.tsv
[2024-01-25 19:58:23,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:23,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:23,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/checkm_data
[2024-01-25 19:58:23,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:23,187] [INFO] Task started: CheckM
[2024-01-25 19:58:23,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904848645.1_LMG_24235_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904848645.1_LMG_24235_genomic.fna/checkm_input GCF_904848645.1_LMG_24235_genomic.fna/checkm_result
[2024-01-25 19:59:40,737] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:40,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:40,757] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:40,757] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:40,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904848645.1_LMG_24235_genomic.fna/markers.fasta)
[2024-01-25 19:59:40,758] [INFO] Task started: Blastn
[2024-01-25 19:59:40,758] [INFO] Running command: blastn -query GCF_904848645.1_LMG_24235_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a1bbe8f-75b0-40ef-aa77-d5ef90c0ad5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_904848645.1_LMG_24235_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:42,615] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:42,618] [INFO] Selected 10 target genomes.
[2024-01-25 19:59:42,618] [INFO] Target genome list was writen to GCF_904848645.1_LMG_24235_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:42,623] [INFO] Task started: fastANI
[2024-01-25 19:59:42,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg15cf14bf-f081-41d4-85d5-6a4c67d3ac27/GCF_904848645.1_LMG_24235_genomic.fna.gz --refList GCF_904848645.1_LMG_24235_genomic.fna/target_genomes_gtdb.txt --output GCF_904848645.1_LMG_24235_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:10,380] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:10,387] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:10,388] [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_904848645.1	s__Paraburkholderia sabiae	100.0	3165	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007995085.1	s__Paraburkholderia azotifigens	91.7723	2400	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.91	98.91	0.86	0.86	2	-
GCF_017104565.1	s__Paraburkholderia sp017104565	90.67	2260	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020045.1	s__Paraburkholderia phymatum	89.1214	2115	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002902925.1	s__Paraburkholderia terrae	88.1901	2213	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_013426895.1	s__Paraburkholderia sp013426895	88.1326	2213	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104715.1	s__Paraburkholderia sp017104715	87.9413	2157	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121405.1	s__Paraburkholderia sp003121405	87.3793	1947	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900007165.1	s__Paraburkholderia piptadeniae	87.0916	1869	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001319865.1	s__Paraburkholderia sp001319865	86.7917	1705	3170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:10,390] [INFO] GTDB search result was written to GCF_904848645.1_LMG_24235_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:10,390] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:10,393] [INFO] DFAST_QC result json was written to GCF_904848645.1_LMG_24235_genomic.fna/dqc_result.json
[2024-01-25 20:00:10,393] [INFO] DFAST_QC completed!
[2024-01-25 20:00:10,393] [INFO] Total running time: 0h2m50s