[2024-01-25 19:54:05,878] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:05,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:05,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference
[2024-01-25 19:54:06,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:06,989] [INFO] Task started: Prodigal
[2024-01-25 19:54:06,989] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4b926d1-85d5-48bd-8bec-63761a4356be/GCF_000685055.1_ASM68505v1_genomic.fna.gz | prodigal -d GCF_000685055.1_ASM68505v1_genomic.fna/cds.fna -a GCF_000685055.1_ASM68505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:31,613] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:31,613] [INFO] Task started: HMMsearch
[2024-01-25 19:54:31,613] [INFO] Running command: hmmsearch --tblout GCF_000685055.1_ASM68505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/reference_markers.hmm GCF_000685055.1_ASM68505v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:31,961] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:31,962] [INFO] Found 6/6 markers.
[2024-01-25 19:54:32,024] [INFO] Query marker FASTA was written to GCF_000685055.1_ASM68505v1_genomic.fna/markers.fasta
[2024-01-25 19:54:32,024] [INFO] Task started: Blastn
[2024-01-25 19:54:32,025] [INFO] Running command: blastn -query GCF_000685055.1_ASM68505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/reference_markers.fasta -out GCF_000685055.1_ASM68505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:32,887] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:32,889] [INFO] Selected 12 target genomes.
[2024-01-25 19:54:32,890] [INFO] Target genome list was writen to GCF_000685055.1_ASM68505v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:32,896] [INFO] Task started: fastANI
[2024-01-25 19:54:32,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b926d1-85d5-48bd-8bec-63761a4356be/GCF_000685055.1_ASM68505v1_genomic.fna.gz --refList GCF_000685055.1_ASM68505v1_genomic.fna/target_genomes.txt --output GCF_000685055.1_ASM68505v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:57,837] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:57,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:57,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:57,846] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:54:57,846] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:54:57,847] [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 fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	100.0	2836	2842	95	inconclusive
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	99.9983	2841	2842	95	inconclusive
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	98.5495	2483	2842	95	inconclusive
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	95.5329	2073	2842	95	inconclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	89.8766	1738	2842	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	89.4072	1771	2842	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	89.3401	1842	2842	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	89.1487	1777	2842	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	89.0339	1821	2842	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	88.9473	1734	2842	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.0372	1174	2842	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.6435	1371	2842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:57,848] [INFO] DFAST Taxonomy check result was written to GCF_000685055.1_ASM68505v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:57,851] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:57,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:57,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/checkm_data
[2024-01-25 19:54:57,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:57,939] [INFO] Task started: CheckM
[2024-01-25 19:54:57,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685055.1_ASM68505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685055.1_ASM68505v1_genomic.fna/checkm_input GCF_000685055.1_ASM68505v1_genomic.fna/checkm_result
[2024-01-25 19:56:07,374] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:07,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:07,405] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:07,406] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:07,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685055.1_ASM68505v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:07,407] [INFO] Task started: Blastn
[2024-01-25 19:56:07,407] [INFO] Running command: blastn -query GCF_000685055.1_ASM68505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c648d5c-16a1-4eac-8068-6f6ba97cc84d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685055.1_ASM68505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:09,041] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:09,044] [INFO] Selected 15 target genomes.
[2024-01-25 19:56:09,044] [INFO] Target genome list was writen to GCF_000685055.1_ASM68505v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:09,058] [INFO] Task started: fastANI
[2024-01-25 19:56:09,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b926d1-85d5-48bd-8bec-63761a4356be/GCF_000685055.1_ASM68505v1_genomic.fna.gz --refList GCF_000685055.1_ASM68505v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000685055.1_ASM68505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:40,355] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:40,365] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:40,365] [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_902833645.1	s__Paraburkholderia fungorum	99.9983	2841	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	conclusive
GCF_003610895.1	s__Paraburkholderia fungorum_B	90.4189	2010	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	89.8661	1740	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	89.7664	1888	2842	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	89.6595	1516	2842	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	89.4023	1772	2842	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	89.3314	1940	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009690905.1	s__Paraburkholderia madseniana	89.3242	1835	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_900116445.1	s__Paraburkholderia aspalathi	89.2683	1908	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_900142905.1	s__Paraburkholderia sp900142905	89.2319	1901	2842	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	89.1711	1843	2842	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	89.1542	1775	2842	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	89.0052	1809	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	88.9492	1733	2842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003353175.1	s__Paraburkholderia lacunae	86.4556	1555	2842	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 19:56:40,367] [INFO] GTDB search result was written to GCF_000685055.1_ASM68505v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:40,368] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:40,370] [INFO] DFAST_QC result json was written to GCF_000685055.1_ASM68505v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:40,371] [INFO] DFAST_QC completed!
[2024-01-25 19:56:40,371] [INFO] Total running time: 0h2m34s