[2024-01-24 13:31:32,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:32,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:32,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference
[2024-01-24 13:31:33,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:33,873] [INFO] Task started: Prodigal
[2024-01-24 13:31:33,873] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7b31543-cd6f-49f6-b6d4-08c75757644c/GCF_902833645.1_ASM90283364v1_genomic.fna.gz | prodigal -d GCF_902833645.1_ASM90283364v1_genomic.fna/cds.fna -a GCF_902833645.1_ASM90283364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:02,915] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:02,916] [INFO] Task started: HMMsearch
[2024-01-24 13:32:02,916] [INFO] Running command: hmmsearch --tblout GCF_902833645.1_ASM90283364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/reference_markers.hmm GCF_902833645.1_ASM90283364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:03,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:03,351] [INFO] Found 6/6 markers.
[2024-01-24 13:32:03,427] [INFO] Query marker FASTA was written to GCF_902833645.1_ASM90283364v1_genomic.fna/markers.fasta
[2024-01-24 13:32:03,428] [INFO] Task started: Blastn
[2024-01-24 13:32:03,428] [INFO] Running command: blastn -query GCF_902833645.1_ASM90283364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/reference_markers.fasta -out GCF_902833645.1_ASM90283364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:04,405] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:04,410] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:04,410] [INFO] Target genome list was writen to GCF_902833645.1_ASM90283364v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:04,416] [INFO] Task started: fastANI
[2024-01-24 13:32:04,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b31543-cd6f-49f6-b6d4-08c75757644c/GCF_902833645.1_ASM90283364v1_genomic.fna.gz --refList GCF_902833645.1_ASM90283364v1_genomic.fna/target_genomes.txt --output GCF_902833645.1_ASM90283364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:30,751] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:30,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:30,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:30,768] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:32:30,768] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:32:30,768] [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=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	100.0	2961	2962	95	inconclusive
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	99.9768	2829	2962	95	inconclusive
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	98.5399	2597	2962	95	inconclusive
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	95.5818	2174	2962	95	inconclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	89.7832	1795	2962	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	89.3265	1858	2962	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	89.194	1938	2962	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	89.105	1857	2962	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	89.0695	1896	2962	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	88.9957	1792	2962	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.012	1222	2962	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.6448	1409	2962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:30,770] [INFO] DFAST Taxonomy check result was written to GCF_902833645.1_ASM90283364v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:30,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:30,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:30,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/checkm_data
[2024-01-24 13:32:30,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:30,854] [INFO] Task started: CheckM
[2024-01-24 13:32:30,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902833645.1_ASM90283364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902833645.1_ASM90283364v1_genomic.fna/checkm_input GCF_902833645.1_ASM90283364v1_genomic.fna/checkm_result
[2024-01-24 13:33:54,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:54,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,951] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:54,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:54,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902833645.1_ASM90283364v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:54,953] [INFO] Task started: Blastn
[2024-01-24 13:33:54,953] [INFO] Running command: blastn -query GCF_902833645.1_ASM90283364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6d7f89-86b7-48fc-b354-b42d65facac5/dqc_reference/reference_markers_gtdb.fasta -out GCF_902833645.1_ASM90283364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:56,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:56,651] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:56,651] [INFO] Target genome list was writen to GCF_902833645.1_ASM90283364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:56,662] [INFO] Task started: fastANI
[2024-01-24 13:33:56,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7b31543-cd6f-49f6-b6d4-08c75757644c/GCF_902833645.1_ASM90283364v1_genomic.fna.gz --refList GCF_902833645.1_ASM90283364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_902833645.1_ASM90283364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:29,193] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:29,210] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:29,210] [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	100.0	2961	2962	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	90.4957	2095	2962	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	89.7697	1799	2962	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	89.664	1967	2962	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	89.5479	1577	2962	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	89.3217	1858	2962	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	89.2932	1909	2962	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	89.2791	1977	2962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_003610295.1	s__Paraburkholderia sp003610295	89.2717	1910	2962	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	89.2446	2025	2962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142905.1	s__Paraburkholderia sp900142905	89.1632	2004	2962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_013177695.1	s__Paraburkholderia sp013177695	89.0924	1861	2962	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	89.035	1889	2962	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	88.9997	1791	2962	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	86.4593	1604	2962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:29,212] [INFO] GTDB search result was written to GCF_902833645.1_ASM90283364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:29,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:29,216] [INFO] DFAST_QC result json was written to GCF_902833645.1_ASM90283364v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:29,216] [INFO] DFAST_QC completed!
[2024-01-24 13:34:29,216] [INFO] Total running time: 0h2m57s