[2024-01-24 12:06:49,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:49,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:49,700] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference
[2024-01-24 12:06:50,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:50,957] [INFO] Task started: Prodigal
[2024-01-24 12:06:50,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg28804da5-3c20-4d26-91ae-c27f02071bb8/GCF_013177735.1_ASM1317773v1_genomic.fna.gz | prodigal -d GCF_013177735.1_ASM1317773v1_genomic.fna/cds.fna -a GCF_013177735.1_ASM1317773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:23,690] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:23,691] [INFO] Task started: HMMsearch
[2024-01-24 12:07:23,691] [INFO] Running command: hmmsearch --tblout GCF_013177735.1_ASM1317773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/reference_markers.hmm GCF_013177735.1_ASM1317773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:24,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:24,099] [INFO] Found 6/6 markers.
[2024-01-24 12:07:24,185] [INFO] Query marker FASTA was written to GCF_013177735.1_ASM1317773v1_genomic.fna/markers.fasta
[2024-01-24 12:07:24,185] [INFO] Task started: Blastn
[2024-01-24 12:07:24,185] [INFO] Running command: blastn -query GCF_013177735.1_ASM1317773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/reference_markers.fasta -out GCF_013177735.1_ASM1317773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:25,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:25,030] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:25,030] [INFO] Target genome list was writen to GCF_013177735.1_ASM1317773v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:25,040] [INFO] Task started: fastANI
[2024-01-24 12:07:25,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg28804da5-3c20-4d26-91ae-c27f02071bb8/GCF_013177735.1_ASM1317773v1_genomic.fna.gz --refList GCF_013177735.1_ASM1317773v1_genomic.fna/target_genomes.txt --output GCF_013177735.1_ASM1317773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:54,474] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:54,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:54,491] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:54,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:54,492] [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 elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	100.0	3457	3509	95	conclusive
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	92.0816	1946	3509	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	91.6619	1911	3509	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	91.5683	2224	3509	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	91.3809	2106	3509	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	91.075	1902	3509	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	90.884	1948	3509	95	below_threshold
Paraburkholderia caffeinilytica	strain=CGMCC 1.15103	GCA_014640695.1	1761016	1761016	type	True	90.7941	1822	3509	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	90.7248	1840	3509	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	90.6875	1917	3509	95	below_threshold
Paraburkholderia lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	87.4234	1747	3509	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.0707	1240	3509	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	83.81	1506	3509	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	75.2427	51	3509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,495] [INFO] DFAST Taxonomy check result was written to GCF_013177735.1_ASM1317773v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:54,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:54,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:54,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/checkm_data
[2024-01-24 12:07:54,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:54,602] [INFO] Task started: CheckM
[2024-01-24 12:07:54,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177735.1_ASM1317773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177735.1_ASM1317773v1_genomic.fna/checkm_input GCF_013177735.1_ASM1317773v1_genomic.fna/checkm_result
[2024-01-24 12:09:22,590] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:22,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:22,619] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:22,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:22,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177735.1_ASM1317773v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:22,620] [INFO] Task started: Blastn
[2024-01-24 12:09:22,620] [INFO] Running command: blastn -query GCF_013177735.1_ASM1317773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2dd0d0f-1290-4768-a3c7-cc52376a8108/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177735.1_ASM1317773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:23,979] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:23,984] [INFO] Selected 15 target genomes.
[2024-01-24 12:09:23,984] [INFO] Target genome list was writen to GCF_013177735.1_ASM1317773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:23,994] [INFO] Task started: fastANI
[2024-01-24 12:09:23,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg28804da5-3c20-4d26-91ae-c27f02071bb8/GCF_013177735.1_ASM1317773v1_genomic.fna.gz --refList GCF_013177735.1_ASM1317773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177735.1_ASM1317773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:53,867] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:53,886] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:53,887] [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_013177735.1	s__Paraburkholderia sp013177735	100.0	3455	3509	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_012927345.1	s__Paraburkholderia sp012927345	92.0848	1946	3509	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	91.8646	1781	3509	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	91.6617	1911	3509	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	91.5597	2225	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_013177695.1	s__Paraburkholderia sp013177695	91.3881	2106	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610295.1	s__Paraburkholderia sp003610295	91.1793	1928	3509	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	91.1248	1885	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_900230185.1	s__Paraburkholderia sp900230185	91.1182	2174	3509	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	91.0555	2018	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_003353175.1	s__Paraburkholderia lacunae	87.4305	1745	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315705.1	s__Trinickia sp017315705	81.8171	1247	3509	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	75.0599	116	3509	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826865.1	s__Ga0077550 sp902826865	74.5612	89	3509	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:53,889] [INFO] GTDB search result was written to GCF_013177735.1_ASM1317773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:53,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:53,893] [INFO] DFAST_QC result json was written to GCF_013177735.1_ASM1317773v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:53,894] [INFO] DFAST_QC completed!
[2024-01-24 12:09:53,894] [INFO] Total running time: 0h3m4s