[2024-01-24 12:37:37,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,925] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference
[2024-01-24 12:37:41,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,016] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,016] [INFO] Running command: gunzip -c /var/lib/cwl/stga5f5252f-48ce-4b61-b524-7ce64a6571b6/GCF_902859935.1_LMG_27177_genomic.fna.gz | prodigal -d GCF_902859935.1_LMG_27177_genomic.fna/cds.fna -a GCF_902859935.1_LMG_27177_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:38:07,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:38:07,054] [INFO] Task started: HMMsearch
[2024-01-24 12:38:07,054] [INFO] Running command: hmmsearch --tblout GCF_902859935.1_LMG_27177_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/reference_markers.hmm GCF_902859935.1_LMG_27177_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:07,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:07,431] [INFO] Found 6/6 markers.
[2024-01-24 12:38:07,497] [INFO] Query marker FASTA was written to GCF_902859935.1_LMG_27177_genomic.fna/markers.fasta
[2024-01-24 12:38:07,497] [INFO] Task started: Blastn
[2024-01-24 12:38:07,497] [INFO] Running command: blastn -query GCF_902859935.1_LMG_27177_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/reference_markers.fasta -out GCF_902859935.1_LMG_27177_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:08,501] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:08,505] [INFO] Selected 14 target genomes.
[2024-01-24 12:38:08,505] [INFO] Target genome list was writen to GCF_902859935.1_LMG_27177_genomic.fna/target_genomes.txt
[2024-01-24 12:38:08,524] [INFO] Task started: fastANI
[2024-01-24 12:38:08,524] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f5252f-48ce-4b61-b524-7ce64a6571b6/GCF_902859935.1_LMG_27177_genomic.fna.gz --refList GCF_902859935.1_LMG_27177_genomic.fna/target_genomes.txt --output GCF_902859935.1_LMG_27177_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:37,679] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:37,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:37,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:37,692] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:37,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:37,693] [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 fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	100.0	2780	2784	95	conclusive
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	90.3602	1719	2784	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	89.5087	1641	2784	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	88.378	1850	2784	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	87.7942	1508	2784	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	86.8348	1672	2784	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	86.595	1669	2784	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.2289	1561	2784	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	86.2085	1525	2784	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.0352	1593	2784	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	85.9167	1552	2784	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	85.8424	1533	2784	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	85.6661	1650	2784	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.8113	1307	2784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:37,696] [INFO] DFAST Taxonomy check result was written to GCF_902859935.1_LMG_27177_genomic.fna/tc_result.tsv
[2024-01-24 12:38:37,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:37,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:37,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/checkm_data
[2024-01-24 12:38:37,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:37,790] [INFO] Task started: CheckM
[2024-01-24 12:38:37,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859935.1_LMG_27177_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859935.1_LMG_27177_genomic.fna/checkm_input GCF_902859935.1_LMG_27177_genomic.fna/checkm_result
[2024-01-24 12:39:50,644] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:50,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:50,676] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:50,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:50,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859935.1_LMG_27177_genomic.fna/markers.fasta)
[2024-01-24 12:39:50,678] [INFO] Task started: Blastn
[2024-01-24 12:39:50,678] [INFO] Running command: blastn -query GCF_902859935.1_LMG_27177_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8318672-1f13-4feb-a450-fe241651663e/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859935.1_LMG_27177_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:52,557] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:52,561] [INFO] Selected 6 target genomes.
[2024-01-24 12:39:52,562] [INFO] Target genome list was writen to GCF_902859935.1_LMG_27177_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:52,566] [INFO] Task started: fastANI
[2024-01-24 12:39:52,567] [INFO] Running command: fastANI --query /var/lib/cwl/stga5f5252f-48ce-4b61-b524-7ce64a6571b6/GCF_902859935.1_LMG_27177_genomic.fna.gz --refList GCF_902859935.1_LMG_27177_genomic.fna/target_genomes_gtdb.txt --output GCF_902859935.1_LMG_27177_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:04,784] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:04,798] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:04,798] [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_902859935.1	s__Paraburkholderia fynbosensis	100.0	2780	2784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.83	96.83	0.79	0.79	2	conclusive
GCF_012275575.1	s__Paraburkholderia sp012275575	94.7869	1812	2784	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	90.3565	1720	2784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902859915.1	s__Paraburkholderia ultramafica	89.4981	1643	2784	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	88.3705	1852	2784	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	86.6022	1667	2784	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 12:40:04,800] [INFO] GTDB search result was written to GCF_902859935.1_LMG_27177_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:04,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:04,804] [INFO] DFAST_QC result json was written to GCF_902859935.1_LMG_27177_genomic.fna/dqc_result.json
[2024-01-24 12:40:04,804] [INFO] DFAST_QC completed!
[2024-01-24 12:40:04,804] [INFO] Total running time: 0h2m27s