[2024-01-24 13:57:30,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:30,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:30,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference
[2024-01-24 13:57:31,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:31,414] [INFO] Task started: Prodigal
[2024-01-24 13:57:31,414] [INFO] Running command: gunzip -c /var/lib/cwl/stge127443b-d0fd-4a10-abe5-c45772582957/GCF_003353175.1_ASM335317v1_genomic.fna.gz | prodigal -d GCF_003353175.1_ASM335317v1_genomic.fna/cds.fna -a GCF_003353175.1_ASM335317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:58,907] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:58,907] [INFO] Task started: HMMsearch
[2024-01-24 13:57:58,908] [INFO] Running command: hmmsearch --tblout GCF_003353175.1_ASM335317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/reference_markers.hmm GCF_003353175.1_ASM335317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,238] [INFO] Found 6/6 markers.
[2024-01-24 13:57:59,307] [INFO] Query marker FASTA was written to GCF_003353175.1_ASM335317v1_genomic.fna/markers.fasta
[2024-01-24 13:57:59,307] [INFO] Task started: Blastn
[2024-01-24 13:57:59,308] [INFO] Running command: blastn -query GCF_003353175.1_ASM335317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/reference_markers.fasta -out GCF_003353175.1_ASM335317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,344] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:00,344] [INFO] Target genome list was writen to GCF_003353175.1_ASM335317v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,351] [INFO] Task started: fastANI
[2024-01-24 13:58:00,351] [INFO] Running command: fastANI --query /var/lib/cwl/stge127443b-d0fd-4a10-abe5-c45772582957/GCF_003353175.1_ASM335317v1_genomic.fna.gz --refList GCF_003353175.1_ASM335317v1_genomic.fna/target_genomes.txt --output GCF_003353175.1_ASM335317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:35,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:35,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:35,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:35,096] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:35,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:35,096] [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 lacunae	strain=S27	GCA_003353175.1	2211104	2211104	type	True	100.0	2749	2753	95	conclusive
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	87.49	1746	2753	95	below_threshold
Paraburkholderia caffeinilytica	strain=CGMCC 1.15103	GCA_014640695.1	1761016	1761016	type	True	87.4116	1790	2753	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	87.3964	1764	2753	95	below_threshold
Paraburkholderia caffeinilytica	strain=LMG 28690	GCA_902859905.1	1761016	1761016	type	True	87.3583	1772	2753	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	87.2013	1757	2753	95	below_threshold
Paraburkholderia madseniana	strain=RP11	GCA_009690905.1	2599607	2599607	type	True	87.1701	1821	2753	95	below_threshold
Paraburkholderia polaris	strain=RP-4-7	GCA_012927345.1	2728848	2728848	type	True	87.0502	1623	2753	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	87.0408	1644	2753	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	86.9909	1670	2753	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	86.8559	1662	2753	95	below_threshold
Paraburkholderia ultramafica	strain=LMG 28614	GCA_902859915.1	1544867	1544867	type	True	86.7268	1494	2753	95	below_threshold
Paraburkholderia ginsengisoli	strain=NBRC 100965	GCA_000739735.1	311231	311231	type	True	86.4283	1423	2753	95	below_threshold
Paraburkholderia aromaticivorans	strain=BN5	GCA_002278075.1	2026199	2026199	type	True	86.4252	1569	2753	95	below_threshold
Paraburkholderia panacisoli	strain=DCY113	GCA_008369935.1	2603818	2603818	type	True	86.0193	1662	2753	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	84.3761	1479	2753	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	84.2108	1178	2753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,098] [INFO] DFAST Taxonomy check result was written to GCF_003353175.1_ASM335317v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:35,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:35,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:35,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/checkm_data
[2024-01-24 13:58:35,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:35,183] [INFO] Task started: CheckM
[2024-01-24 13:58:35,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003353175.1_ASM335317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003353175.1_ASM335317v1_genomic.fna/checkm_input GCF_003353175.1_ASM335317v1_genomic.fna/checkm_result
[2024-01-24 13:59:49,405] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:49,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:49,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:49,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003353175.1_ASM335317v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:49,422] [INFO] Task started: Blastn
[2024-01-24 13:59:49,422] [INFO] Running command: blastn -query GCF_003353175.1_ASM335317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg455baeab-62b9-44b4-a539-b0f53c2d5ebb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003353175.1_ASM335317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,253] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,256] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:51,257] [INFO] Target genome list was writen to GCF_003353175.1_ASM335317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,320] [INFO] Task started: fastANI
[2024-01-24 13:59:51,320] [INFO] Running command: fastANI --query /var/lib/cwl/stge127443b-d0fd-4a10-abe5-c45772582957/GCF_003353175.1_ASM335317v1_genomic.fna.gz --refList GCF_003353175.1_ASM335317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003353175.1_ASM335317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:22,387] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:22,402] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:22,402] [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_003353175.1	s__Paraburkholderia lacunae	100.0	2749	2753	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_013177735.1	s__Paraburkholderia sp013177735	87.51	1744	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	87.398	1764	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001634365.1	s__Paraburkholderia sp001634365	87.3287	1512	2753	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	87.1527	1824	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_012927345.1	s__Paraburkholderia sp012927345	87.0473	1624	2753	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	87.0441	1643	2753	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	87.0204	1633	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_013177695.1	s__Paraburkholderia sp013177695	86.9968	1669	2753	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	86.7446	1699	2753	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	86.7185	1495	2753	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	86.647	1652	2753	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	86.4397	1421	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	86.4163	1570	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001645125.1	s__Paraburkholderia ginsengiterrae	86.0103	1646	2753	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.96	99.96	1.00	1.00	2	-
GCF_008369935.1	s__Paraburkholderia panacisoli	86.0053	1664	2753	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 14:00:22,404] [INFO] GTDB search result was written to GCF_003353175.1_ASM335317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:22,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:22,409] [INFO] DFAST_QC result json was written to GCF_003353175.1_ASM335317v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:22,410] [INFO] DFAST_QC completed!
[2024-01-24 14:00:22,410] [INFO] Total running time: 0h2m52s