[2024-01-25 20:16:35,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:35,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:35,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference
[2024-01-25 20:16:36,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:36,855] [INFO] Task started: Prodigal
[2024-01-25 20:16:36,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be46cf4-00a0-4f94-b3fa-87d6fb76be90/GCF_000807775.2_ASM80777v2_genomic.fna.gz | prodigal -d GCF_000807775.2_ASM80777v2_genomic.fna/cds.fna -a GCF_000807775.2_ASM80777v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:55,308] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:55,308] [INFO] Task started: HMMsearch
[2024-01-25 20:16:55,308] [INFO] Running command: hmmsearch --tblout GCF_000807775.2_ASM80777v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/reference_markers.hmm GCF_000807775.2_ASM80777v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:55,570] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:55,572] [INFO] Found 6/6 markers.
[2024-01-25 20:16:55,625] [INFO] Query marker FASTA was written to GCF_000807775.2_ASM80777v2_genomic.fna/markers.fasta
[2024-01-25 20:16:55,625] [INFO] Task started: Blastn
[2024-01-25 20:16:55,625] [INFO] Running command: blastn -query GCF_000807775.2_ASM80777v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/reference_markers.fasta -out GCF_000807775.2_ASM80777v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:56,510] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:56,513] [INFO] Selected 12 target genomes.
[2024-01-25 20:16:56,513] [INFO] Target genome list was writen to GCF_000807775.2_ASM80777v2_genomic.fna/target_genomes.txt
[2024-01-25 20:16:56,519] [INFO] Task started: fastANI
[2024-01-25 20:16:56,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be46cf4-00a0-4f94-b3fa-87d6fb76be90/GCF_000807775.2_ASM80777v2_genomic.fna.gz --refList GCF_000807775.2_ASM80777v2_genomic.fna/target_genomes.txt --output GCF_000807775.2_ASM80777v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:16,470] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:16,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:16,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:16,479] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:16,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:16,479] [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
Pandoraea fibrosis	strain=6399	GCA_000807775.2	1891094	1891094	type	True	100.0	1863	1864	95	conclusive
Pandoraea apista	strain=DSM 16535	GCA_001465595.2	93218	93218	type	True	89.8795	1540	1864	95	below_threshold
Pandoraea apista	strain=LMG16407	GCA_001049515.1	93218	93218	type	True	89.8298	1521	1864	95	below_threshold
Pandoraea bronchicola	strain=LMG 20603	GCA_902459805.1	2508287	2508287	type	True	88.9834	1449	1864	95	below_threshold
Pandoraea communis	strain=LMG 31110	GCA_902459745.1	2508297	2508297	type	True	88.9059	1458	1864	95	below_threshold
Pandoraea horticolens	strain=LMG 31112	GCA_902459555.1	2508298	2508298	type	True	88.7269	1436	1864	95	below_threshold
Pandoraea aquatica	strain=LMG 31011	GCA_902459565.1	2508290	2508290	type	True	85.6089	1436	1864	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.7342	551	1864	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	78.3249	479	1864	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	78.2831	520	1864	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	78.212	539	1864	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	78.1095	433	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:16,482] [INFO] DFAST Taxonomy check result was written to GCF_000807775.2_ASM80777v2_genomic.fna/tc_result.tsv
[2024-01-25 20:17:16,483] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:16,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:16,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/checkm_data
[2024-01-25 20:17:16,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:16,540] [INFO] Task started: CheckM
[2024-01-25 20:17:16,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000807775.2_ASM80777v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000807775.2_ASM80777v2_genomic.fna/checkm_input GCF_000807775.2_ASM80777v2_genomic.fna/checkm_result
[2024-01-25 20:18:17,885] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:17,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:17,909] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:17,909] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:17,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000807775.2_ASM80777v2_genomic.fna/markers.fasta)
[2024-01-25 20:18:17,911] [INFO] Task started: Blastn
[2024-01-25 20:18:17,911] [INFO] Running command: blastn -query GCF_000807775.2_ASM80777v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3665f886-2096-4c25-8761-cb96b396c86d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000807775.2_ASM80777v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:19,608] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:19,611] [INFO] Selected 6 target genomes.
[2024-01-25 20:18:19,611] [INFO] Target genome list was writen to GCF_000807775.2_ASM80777v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:19,616] [INFO] Task started: fastANI
[2024-01-25 20:18:19,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be46cf4-00a0-4f94-b3fa-87d6fb76be90/GCF_000807775.2_ASM80777v2_genomic.fna.gz --refList GCF_000807775.2_ASM80777v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000807775.2_ASM80777v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:28,405] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:28,410] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:28,411] [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_000807775.2	s__Pandoraea fibrosis	100.0	1862	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.41	98.83	0.97	0.94	3	conclusive
GCF_001465595.2	s__Pandoraea apista	89.8795	1540	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	99.24	99.05	0.93	0.91	21	-
GCF_902459805.1	s__Pandoraea bronchicola	88.9834	1449	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459745.1	s__Pandoraea communis	88.9056	1458	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	98.36	97.48	0.89	0.87	3	-
GCF_902459555.1	s__Pandoraea horticolens	88.717	1437	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0166	N/A	N/A	N/A	N/A	1	-
GCF_902459565.1	s__Pandoraea aquatica	85.6242	1434	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:28,412] [INFO] GTDB search result was written to GCF_000807775.2_ASM80777v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:28,413] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:28,415] [INFO] DFAST_QC result json was written to GCF_000807775.2_ASM80777v2_genomic.fna/dqc_result.json
[2024-01-25 20:18:28,415] [INFO] DFAST_QC completed!
[2024-01-25 20:18:28,415] [INFO] Total running time: 0h1m53s