[2023-03-17 00:45:47,098] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,098] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,285] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,285] [INFO] Running command: cat /var/lib/cwl/stgafa4f2d7-83c7-4d40-8e3c-80067d7b2c01/OceanDNA-b23333.fa | prodigal -d OceanDNA-b23333/cds.fna -a OceanDNA-b23333/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:55,854] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:55,855] [INFO] Task started: HMMsearch
[2023-03-17 00:45:55,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b23333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/reference_markers.hmm OceanDNA-b23333/protein.faa > /dev/null
[2023-03-17 00:45:56,033] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:56,034] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgafa4f2d7-83c7-4d40-8e3c-80067d7b2c01/OceanDNA-b23333.fa]
[2023-03-17 00:45:56,048] [INFO] Query marker FASTA was written to OceanDNA-b23333/markers.fasta
[2023-03-17 00:45:56,049] [INFO] Task started: Blastn
[2023-03-17 00:45:56,049] [INFO] Running command: blastn -query OceanDNA-b23333/markers.fasta -db /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/reference_markers.fasta -out OceanDNA-b23333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:56,901] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:56,901] [INFO] Selected 17 target genomes.
[2023-03-17 00:45:56,902] [INFO] Target genome list was writen to OceanDNA-b23333/target_genomes.txt
[2023-03-17 00:45:56,973] [INFO] Task started: fastANI
[2023-03-17 00:45:56,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgafa4f2d7-83c7-4d40-8e3c-80067d7b2c01/OceanDNA-b23333.fa --refList OceanDNA-b23333/target_genomes.txt --output OceanDNA-b23333/fastani_result.tsv --threads 1
[2023-03-17 00:46:05,933] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:05,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:05,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:06,038] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:06,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:06,038] [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 halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	88.9662	302	359	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	88.9109	302	359	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	79.655	199	359	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.5893	201	359	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.5314	202	359	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	79.5122	198	359	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.4953	174	359	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	79.4192	202	359	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.4095	200	359	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	79.3871	195	359	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	79.277	198	359	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	79.2409	204	359	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	79.2069	188	359	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	79.1252	201	359	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	78.9981	171	359	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.87	93	359	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.8511	84	359	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:06,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23333/tc_result.tsv
[2023-03-17 00:46:06,039] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:06,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:06,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/checkm_data
[2023-03-17 00:46:06,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:06,121] [INFO] Task started: CheckM
[2023-03-17 00:46:06,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23333/checkm_input OceanDNA-b23333/checkm_result
[2023-03-17 00:46:32,142] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:32,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:32,145] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:32,145] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:32,145] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23333/markers.fasta)
[2023-03-17 00:46:32,146] [INFO] Task started: Blastn
[2023-03-17 00:46:32,146] [INFO] Running command: blastn -query OceanDNA-b23333/markers.fasta -db /var/lib/cwl/stg23b1ca42-3aa8-41a0-b85a-75ea285e50ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:33,660] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:33,661] [INFO] Selected 13 target genomes.
[2023-03-17 00:46:33,661] [INFO] Target genome list was writen to OceanDNA-b23333/target_genomes_gtdb.txt
[2023-03-17 00:46:33,995] [INFO] Task started: fastANI
[2023-03-17 00:46:33,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgafa4f2d7-83c7-4d40-8e3c-80067d7b2c01/OceanDNA-b23333.fa --refList OceanDNA-b23333/target_genomes_gtdb.txt --output OceanDNA-b23333/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:40,489] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:40,497] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:40,497] [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_003730275.1	s__Brevundimonas halotolerans	88.9109	302	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCA_018826885.1	s__Brevundimonas sp018826885	88.1718	282	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	86.9398	306	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742135.1	s__Brevundimonas sp016742135	86.9182	305	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979535.1	s__Brevundimonas sp002979535	79.3734	188	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCA_000318405.1	s__Brevundimonas diminuta_B	79.3316	182	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.76	96.50	0.85	0.82	10	-
GCF_002002865.1	s__Brevundimonas sp002002865	79.328	183	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479495.1	s__Brevundimonas sp002479495	79.2727	197	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	79.2409	204	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248925.1	s__Brevundimonas sp003248925	79.0848	177	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302335.1	s__Brevundimonas sp017302335	78.9999	177	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466985.1	s__Brevundimonas abyssalis	78.8929	169	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_013823285.1	s__Brevundimonas sp013823285	78.3181	175	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:40,497] [INFO] GTDB search result was written to OceanDNA-b23333/result_gtdb.tsv
[2023-03-17 00:46:40,497] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:40,499] [INFO] DFAST_QC result json was written to OceanDNA-b23333/dqc_result.json
[2023-03-17 00:46:40,499] [INFO] DFAST_QC completed!
[2023-03-17 00:46:40,499] [INFO] Total running time: 0h0m53s