[2024-01-24 12:53:41,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,241] [INFO] DQC Reference Directory: /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference
[2024-01-24 12:53:42,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:42,771] [INFO] Task started: Prodigal
[2024-01-24 12:53:42,771] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1675066-d555-4ad3-9d0d-6434ac2f621b/GCF_000739735.1_ASM73973v1_genomic.fna.gz | prodigal -d GCF_000739735.1_ASM73973v1_genomic.fna/cds.fna -a GCF_000739735.1_ASM73973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:03,939] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:03,939] [INFO] Task started: HMMsearch
[2024-01-24 12:54:03,939] [INFO] Running command: hmmsearch --tblout GCF_000739735.1_ASM73973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/reference_markers.hmm GCF_000739735.1_ASM73973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:04,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:04,307] [INFO] Found 6/6 markers.
[2024-01-24 12:54:04,365] [INFO] Query marker FASTA was written to GCF_000739735.1_ASM73973v1_genomic.fna/markers.fasta
[2024-01-24 12:54:04,366] [INFO] Task started: Blastn
[2024-01-24 12:54:04,366] [INFO] Running command: blastn -query GCF_000739735.1_ASM73973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/reference_markers.fasta -out GCF_000739735.1_ASM73973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:05,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:05,258] [INFO] Selected 19 target genomes.
[2024-01-24 12:54:05,258] [INFO] Target genome list was writen to GCF_000739735.1_ASM73973v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:05,265] [INFO] Task started: fastANI
[2024-01-24 12:54:05,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1675066-d555-4ad3-9d0d-6434ac2f621b/GCF_000739735.1_ASM73973v1_genomic.fna.gz --refList GCF_000739735.1_ASM73973v1_genomic.fna/target_genomes.txt --output GCF_000739735.1_ASM73973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:40,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:40,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:40,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:40,920] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:40,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:40,920] [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 ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	100.0	2155	2156	95	conclusive
Paraburkholderia fynbosensis	strain=LMG 27177	GCA_902859935.1	1200993	1200993	type	True	90.2955	1725	2156	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	90.1107	1562	2156	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	89.4067	1694	2156	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	88.2219	1486	2156	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	87.4474	1583	2156	95	below_threshold
Paraburkholderia dipogonis	strain=ICMP 19430	GCA_004402975.1	1211383	1211383	type	True	87.4021	1628	2156	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	87.0739	1624	2156	95	below_threshold
Paraburkholderia bryophila	strain=LMG 23644	GCA_003269035.1	420952	420952	type	True	86.9241	1546	2156	95	below_threshold
Paraburkholderia metrosideri	strain=LMG 28140	GCA_904848625.1	580937	580937	type	True	86.6093	1576	2156	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	86.5097	1526	2156	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	86.4638	1496	2156	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	86.4534	1560	2156	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	86.4033	1468	2156	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	86.3613	1563	2156	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.2627	1548	2156	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	86.107	1453	2156	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	85.0905	1157	2156	95	below_threshold
Caballeronia concitans		GCA_001544615.2	1777133	1777133	type	True	81.3229	998	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:40,922] [INFO] DFAST Taxonomy check result was written to GCF_000739735.1_ASM73973v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:40,923] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:40,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:40,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/checkm_data
[2024-01-24 12:54:40,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:41,005] [INFO] Task started: CheckM
[2024-01-24 12:54:41,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739735.1_ASM73973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739735.1_ASM73973v1_genomic.fna/checkm_input GCF_000739735.1_ASM73973v1_genomic.fna/checkm_result
[2024-01-24 12:55:41,660] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:41,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:41,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:41,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:41,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739735.1_ASM73973v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:41,687] [INFO] Task started: Blastn
[2024-01-24 12:55:41,687] [INFO] Running command: blastn -query GCF_000739735.1_ASM73973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fba716-9b11-404d-8515-2ed05728e91c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739735.1_ASM73973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:44,934] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:44,948] [INFO] Selected 15 target genomes.
[2024-01-24 12:55:44,948] [INFO] Target genome list was writen to GCF_000739735.1_ASM73973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:44,968] [INFO] Task started: fastANI
[2024-01-24 12:55:44,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1675066-d555-4ad3-9d0d-6434ac2f621b/GCF_000739735.1_ASM73973v1_genomic.fna.gz --refList GCF_000739735.1_ASM73973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739735.1_ASM73973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:16,813] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:16,839] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:16,840] [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_000739735.1	s__Paraburkholderia ginsengisoli	100.0	2155	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_902859935.1	s__Paraburkholderia fynbosensis	90.2864	1726	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.83	96.83	0.79	0.79	2	-
GCF_012275575.1	s__Paraburkholderia sp012275575	90.1661	1608	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859915.1	s__Paraburkholderia ultramafica	90.1106	1562	2156	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	89.419	1692	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339745.1	s__Paraburkholderia sp004339745	87.68	1640	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002025.1	s__Paraburkholderia sp003002025	87.334	1575	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	97.08	96.80	0.83	0.80	5	-
GCF_900177725.1	s__Paraburkholderia susongensis	87.1816	1465	2156	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	87.0948	1620	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	86.7874	1403	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_904848625.1	s__Paraburkholderia metrosideri	86.6239	1573	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116445.1	s__Paraburkholderia aspalathi	86.3692	1561	2156	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	86.2571	1575	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_005144415.1	s__Trinickia sp005144415	81.9573	1063	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449515.1	s__Caballeronia sp018449515	79.6679	893	2156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:16,842] [INFO] GTDB search result was written to GCF_000739735.1_ASM73973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:16,843] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:16,850] [INFO] DFAST_QC result json was written to GCF_000739735.1_ASM73973v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:16,850] [INFO] DFAST_QC completed!
[2024-01-24 12:56:16,850] [INFO] Total running time: 0h2m36s