[2024-01-24 14:05:15,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:15,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:15,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference
[2024-01-24 14:05:17,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,194] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg37d8d218-5437-4569-afc8-11f96fb6f652/GCF_030160755.1_ASM3016075v1_genomic.fna.gz | prodigal -d GCF_030160755.1_ASM3016075v1_genomic.fna/cds.fna -a GCF_030160755.1_ASM3016075v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:24,491] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:24,491] [INFO] Task started: HMMsearch
[2024-01-24 14:05:24,491] [INFO] Running command: hmmsearch --tblout GCF_030160755.1_ASM3016075v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/reference_markers.hmm GCF_030160755.1_ASM3016075v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:24,772] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:24,774] [INFO] Found 6/6 markers.
[2024-01-24 14:05:24,809] [INFO] Query marker FASTA was written to GCF_030160755.1_ASM3016075v1_genomic.fna/markers.fasta
[2024-01-24 14:05:24,810] [INFO] Task started: Blastn
[2024-01-24 14:05:24,810] [INFO] Running command: blastn -query GCF_030160755.1_ASM3016075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/reference_markers.fasta -out GCF_030160755.1_ASM3016075v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:25,797] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:25,800] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:25,801] [INFO] Target genome list was writen to GCF_030160755.1_ASM3016075v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:25,806] [INFO] Task started: fastANI
[2024-01-24 14:05:25,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d8d218-5437-4569-afc8-11f96fb6f652/GCF_030160755.1_ASM3016075v1_genomic.fna.gz --refList GCF_030160755.1_ASM3016075v1_genomic.fna/target_genomes.txt --output GCF_030160755.1_ASM3016075v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:37,058] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:37,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:37,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:37,079] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:37,079] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:37,079] [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
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	84.6683	685	907	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	84.5567	650	907	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	84.3217	709	907	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	83.6856	663	907	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	82.2511	637	907	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	82.0399	561	907	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	81.8152	586	907	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.5316	529	907	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.7884	545	907	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.2802	493	907	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.3214	381	907	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.1944	335	907	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.83	67	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:37,081] [INFO] DFAST Taxonomy check result was written to GCF_030160755.1_ASM3016075v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:37,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:37,082] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:37,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/checkm_data
[2024-01-24 14:05:37,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:37,120] [INFO] Task started: CheckM
[2024-01-24 14:05:37,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160755.1_ASM3016075v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160755.1_ASM3016075v1_genomic.fna/checkm_input GCF_030160755.1_ASM3016075v1_genomic.fna/checkm_result
[2024-01-24 14:06:04,084] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:04,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:04,109] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:04,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:04,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160755.1_ASM3016075v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:04,110] [INFO] Task started: Blastn
[2024-01-24 14:06:04,110] [INFO] Running command: blastn -query GCF_030160755.1_ASM3016075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f61b185-5e8c-4f37-980c-914ce8a87b5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160755.1_ASM3016075v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:06,069] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:06,074] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:06,074] [INFO] Target genome list was writen to GCF_030160755.1_ASM3016075v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:06,090] [INFO] Task started: fastANI
[2024-01-24 14:06:06,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d8d218-5437-4569-afc8-11f96fb6f652/GCF_030160755.1_ASM3016075v1_genomic.fna.gz --refList GCF_030160755.1_ASM3016075v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160755.1_ASM3016075v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:17,172] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:17,191] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:06:17,191] [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
GCA_002343425.1	s__Brevundimonas sp002343425	89.1733	669	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.78	0.93	0.93	2	-
GCA_002483305.1	s__Brevundimonas sp002483305	88.9397	709	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	88.9083	742	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_006515835.1	s__Brevundimonas sp006515835	88.6751	614	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826515.1	s__Brevundimonas sp018826515	88.4819	723	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCF_001427825.1	s__Brevundimonas sp001427825	87.2582	708	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820665.1	s__Brevundimonas sp018820665	84.9976	579	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_011927945.1	s__Brevundimonas alba	84.6833	684	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	84.3261	708	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	84.2639	409	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	84.1742	683	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	83.7534	653	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003400305.1	s__4M-Z18 sp003400305	76.2167	85	907	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__4M-Z18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,193] [INFO] GTDB search result was written to GCF_030160755.1_ASM3016075v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:17,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:17,197] [INFO] DFAST_QC result json was written to GCF_030160755.1_ASM3016075v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:17,197] [INFO] DFAST_QC completed!
[2024-01-24 14:06:17,197] [INFO] Total running time: 0h1m1s