[2023-03-15 21:52:21,349] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:52:21,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:52:21,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference
[2023-03-15 21:52:22,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:52:22,451] [INFO] Task started: Prodigal
[2023-03-15 21:52:22,451] [INFO] Running command: cat /var/lib/cwl/stg196f067c-0bde-4b59-bd72-73848f9ab57e/OceanDNA-b23393.fa | prodigal -d OceanDNA-b23393/cds.fna -a OceanDNA-b23393/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:52:31,221] [INFO] Task succeeded: Prodigal
[2023-03-15 21:52:31,222] [INFO] Task started: HMMsearch
[2023-03-15 21:52:31,222] [INFO] Running command: hmmsearch --tblout OceanDNA-b23393/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/reference_markers.hmm OceanDNA-b23393/protein.faa > /dev/null
[2023-03-15 21:52:31,376] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:52:31,376] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg196f067c-0bde-4b59-bd72-73848f9ab57e/OceanDNA-b23393.fa]
[2023-03-15 21:52:31,393] [INFO] Query marker FASTA was written to OceanDNA-b23393/markers.fasta
[2023-03-15 21:52:31,394] [INFO] Task started: Blastn
[2023-03-15 21:52:31,394] [INFO] Running command: blastn -query OceanDNA-b23393/markers.fasta -db /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/reference_markers.fasta -out OceanDNA-b23393/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:52:31,982] [INFO] Task succeeded: Blastn
[2023-03-15 21:52:31,982] [INFO] Selected 16 target genomes.
[2023-03-15 21:52:31,983] [INFO] Target genome list was writen to OceanDNA-b23393/target_genomes.txt
[2023-03-15 21:52:32,003] [INFO] Task started: fastANI
[2023-03-15 21:52:32,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg196f067c-0bde-4b59-bd72-73848f9ab57e/OceanDNA-b23393.fa --refList OceanDNA-b23393/target_genomes.txt --output OceanDNA-b23393/fastani_result.tsv --threads 1
[2023-03-15 21:52:40,804] [INFO] Task succeeded: fastANI
[2023-03-15 21:52:40,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:52:40,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:52:40,814] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:52:40,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:52:40,815] [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 basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	85.3103	337	455	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	84.9963	347	455	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	83.3375	334	455	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	83.1125	330	455	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.1048	297	455	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.9699	306	455	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.8732	311	455	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.7345	272	455	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.7327	294	455	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	80.5055	256	455	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.4668	274	455	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	80.3805	261	455	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	79.8633	242	455	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.8594	272	455	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.771	145	455	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.6721	193	455	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:52:40,815] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23393/tc_result.tsv
[2023-03-15 21:52:40,815] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:52:40,815] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:52:40,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/checkm_data
[2023-03-15 21:52:40,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:52:40,819] [INFO] Task started: CheckM
[2023-03-15 21:52:40,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23393/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23393/checkm_input OceanDNA-b23393/checkm_result
[2023-03-15 21:53:06,945] [INFO] Task succeeded: CheckM
[2023-03-15 21:53:06,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:53:06,947] [INFO] ===== Completeness check finished =====
[2023-03-15 21:53:06,947] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:53:06,948] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23393/markers.fasta)
[2023-03-15 21:53:06,949] [INFO] Task started: Blastn
[2023-03-15 21:53:06,949] [INFO] Running command: blastn -query OceanDNA-b23393/markers.fasta -db /var/lib/cwl/stgb86c4f3f-d7e0-47f3-8e3b-be9da8a90eae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23393/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:53:07,829] [INFO] Task succeeded: Blastn
[2023-03-15 21:53:07,830] [INFO] Selected 13 target genomes.
[2023-03-15 21:53:07,830] [INFO] Target genome list was writen to OceanDNA-b23393/target_genomes_gtdb.txt
[2023-03-15 21:53:08,010] [INFO] Task started: fastANI
[2023-03-15 21:53:08,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg196f067c-0bde-4b59-bd72-73848f9ab57e/OceanDNA-b23393.fa --refList OceanDNA-b23393/target_genomes_gtdb.txt --output OceanDNA-b23393/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:53:14,625] [INFO] Task succeeded: fastANI
[2023-03-15 21:53:14,633] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:53:14,633] [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_018820665.1	s__Brevundimonas sp018820665	99.4377	415	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	conclusive
GCA_016183935.1	s__Brevundimonas sp016183935	86.1024	342	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202075.1	s__Brevundimonas basaltis	85.3103	337	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	85.0763	324	455	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	84.9963	347	455	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	84.7706	337	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_018826515.1	s__Brevundimonas sp018826515	84.6873	350	455	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	84.486	333	455	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	84.3424	244	455	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	83.4818	333	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	83.1855	323	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006515835.1	s__Brevundimonas sp006515835	82.8643	283	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547065.1	s__Brevundimonas sp006547065	81.8652	325	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:53:14,633] [INFO] GTDB search result was written to OceanDNA-b23393/result_gtdb.tsv
[2023-03-15 21:53:14,634] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:53:14,635] [INFO] DFAST_QC result json was written to OceanDNA-b23393/dqc_result.json
[2023-03-15 21:53:14,636] [INFO] DFAST_QC completed!
[2023-03-15 21:53:14,636] [INFO] Total running time: 0h0m53s