[2024-01-24 12:14:34,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference
[2024-01-24 12:14:36,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,181] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e534993-bcf7-4bad-b305-5be21923af66/GCF_012927345.1_ASM1292734v1_genomic.fna.gz | prodigal -d GCF_012927345.1_ASM1292734v1_genomic.fna/cds.fna -a GCF_012927345.1_ASM1292734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:06,125] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:06,126] [INFO] Task started: HMMsearch
[2024-01-24 12:15:06,126] [INFO] Running command: hmmsearch --tblout GCF_012927345.1_ASM1292734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/reference_markers.hmm GCF_012927345.1_ASM1292734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:06,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:06,566] [INFO] Found 6/6 markers.
[2024-01-24 12:15:06,645] [INFO] Query marker FASTA was written to GCF_012927345.1_ASM1292734v1_genomic.fna/markers.fasta
[2024-01-24 12:15:06,646] [INFO] Task started: Blastn
[2024-01-24 12:15:06,646] [INFO] Running command: blastn -query GCF_012927345.1_ASM1292734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/reference_markers.fasta -out GCF_012927345.1_ASM1292734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:07,620] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:07,624] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:07,624] [INFO] Target genome list was writen to GCF_012927345.1_ASM1292734v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:07,628] [INFO] Task started: fastANI
[2024-01-24 12:15:07,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e534993-bcf7-4bad-b305-5be21923af66/GCF_012927345.1_ASM1292734v1_genomic.fna.gz --refList GCF_012927345.1_ASM1292734v1_genomic.fna/target_genomes.txt --output GCF_012927345.1_ASM1292734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:31,422] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:31,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:31,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:31,432] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:31,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:31,432] [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 polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	100.0	3131	3140	95	conclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	92.0075	1970	3140	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	91.1248	2008	3140	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	91.0452	1903	3140	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	90.9872	2019	3140	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	90.9273	2045	3140	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	90.8223	2011	3140	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	90.6081	2029	3140	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	90.5009	1874	3140	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.2392	1204	3140	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.8766	1422	3140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:31,434] [INFO] DFAST Taxonomy check result was written to GCF_012927345.1_ASM1292734v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:31,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:31,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:31,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/checkm_data
[2024-01-24 12:15:31,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:31,521] [INFO] Task started: CheckM
[2024-01-24 12:15:31,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927345.1_ASM1292734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927345.1_ASM1292734v1_genomic.fna/checkm_input GCF_012927345.1_ASM1292734v1_genomic.fna/checkm_result
[2024-01-24 12:16:52,721] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:52,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:52,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:52,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:52,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927345.1_ASM1292734v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:52,742] [INFO] Task started: Blastn
[2024-01-24 12:16:52,742] [INFO] Running command: blastn -query GCF_012927345.1_ASM1292734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d98c5f7-1a6b-4e7b-bda9-cf0a0ac2bdbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927345.1_ASM1292734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:54,436] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:54,441] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:54,442] [INFO] Target genome list was writen to GCF_012927345.1_ASM1292734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:54,450] [INFO] Task started: fastANI
[2024-01-24 12:16:54,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e534993-bcf7-4bad-b305-5be21923af66/GCF_012927345.1_ASM1292734v1_genomic.fna.gz --refList GCF_012927345.1_ASM1292734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927345.1_ASM1292734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:20,614] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:20,628] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:20,629] [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_012927345.1	s__Paraburkholderia sp012927345	100.0	3131	3140	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_013177735.1	s__Paraburkholderia sp013177735	92.0175	1969	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	91.3704	1713	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	91.1207	2009	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230185.1	s__Paraburkholderia sp900230185	91.1199	2113	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220975.1	s__Paraburkholderia sp905220975	91.0446	1904	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220835.1	s__Paraburkholderia sp905220835	90.981	1995	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_009690905.1	s__Paraburkholderia madseniana	90.979	2020	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_900142905.1	s__Paraburkholderia sp900142905	90.9676	2195	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_003610295.1	s__Paraburkholderia sp003610295	90.916	1874	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859805.1	s__Paraburkholderia sediminicola	90.6012	2030	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409845.1	s__Paraburkholderia metrosideri_A	89.7229	1879	3140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:20,630] [INFO] GTDB search result was written to GCF_012927345.1_ASM1292734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:20,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:20,634] [INFO] DFAST_QC result json was written to GCF_012927345.1_ASM1292734v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:20,634] [INFO] DFAST_QC completed!
[2024-01-24 12:17:20,634] [INFO] Total running time: 0h2m46s