[2023-03-16 08:10:35,185] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,187] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,187] [INFO] DQC Reference Directory: /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference
[2023-03-16 08:10:36,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,286] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,287] [INFO] Running command: cat /var/lib/cwl/stgdfea7386-3fb1-4cac-bdb8-252f5fbc0bb1/OceanDNA-b23345.fa | prodigal -d OceanDNA-b23345/cds.fna -a OceanDNA-b23345/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:51,278] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:51,279] [INFO] Task started: HMMsearch
[2023-03-16 08:10:51,279] [INFO] Running command: hmmsearch --tblout OceanDNA-b23345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/reference_markers.hmm OceanDNA-b23345/protein.faa > /dev/null
[2023-03-16 08:10:51,469] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:51,469] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdfea7386-3fb1-4cac-bdb8-252f5fbc0bb1/OceanDNA-b23345.fa]
[2023-03-16 08:10:51,539] [INFO] Query marker FASTA was written to OceanDNA-b23345/markers.fasta
[2023-03-16 08:10:51,540] [INFO] Task started: Blastn
[2023-03-16 08:10:51,540] [INFO] Running command: blastn -query OceanDNA-b23345/markers.fasta -db /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/reference_markers.fasta -out OceanDNA-b23345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:52,323] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:52,340] [INFO] Selected 16 target genomes.
[2023-03-16 08:10:52,340] [INFO] Target genome list was writen to OceanDNA-b23345/target_genomes.txt
[2023-03-16 08:10:52,350] [INFO] Task started: fastANI
[2023-03-16 08:10:52,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfea7386-3fb1-4cac-bdb8-252f5fbc0bb1/OceanDNA-b23345.fa --refList OceanDNA-b23345/target_genomes.txt --output OceanDNA-b23345/fastani_result.tsv --threads 1
[2023-03-16 08:11:02,521] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:02,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:02,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:02,531] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:02,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:11:02,531] [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=MCS24	GCA_003730275.1	69670	69670	type	True	86.6077	658	826	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	86.5573	666	826	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.0858	495	826	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.982	489	826	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.869	509	826	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.81	528	826	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.789	496	826	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.7277	509	826	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.6224	452	826	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.4502	479	826	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.4005	478	826	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.3366	456	826	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.2957	469	826	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.1211	456	826	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0204	302	826	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.8685	264	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:11:02,535] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23345/tc_result.tsv
[2023-03-16 08:11:02,544] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:02,544] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:02,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/checkm_data
[2023-03-16 08:11:02,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:02,595] [INFO] Task started: CheckM
[2023-03-16 08:11:02,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23345/checkm_input OceanDNA-b23345/checkm_result
[2023-03-16 08:11:42,659] [INFO] Task succeeded: CheckM
[2023-03-16 08:11:42,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:11:42,826] [INFO] ===== Completeness check finished =====
[2023-03-16 08:11:42,826] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:11:42,826] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23345/markers.fasta)
[2023-03-16 08:11:42,827] [INFO] Task started: Blastn
[2023-03-16 08:11:42,828] [INFO] Running command: blastn -query OceanDNA-b23345/markers.fasta -db /var/lib/cwl/stge7f33e61-89dd-45a8-a5a2-e327e27ca363/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:11:44,272] [INFO] Task succeeded: Blastn
[2023-03-16 08:11:44,283] [INFO] Selected 13 target genomes.
[2023-03-16 08:11:44,283] [INFO] Target genome list was writen to OceanDNA-b23345/target_genomes_gtdb.txt
[2023-03-16 08:11:44,303] [INFO] Task started: fastANI
[2023-03-16 08:11:44,303] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfea7386-3fb1-4cac-bdb8-252f5fbc0bb1/OceanDNA-b23345.fa --refList OceanDNA-b23345/target_genomes_gtdb.txt --output OceanDNA-b23345/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:11:52,609] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:52,617] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:11:52,617] [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_017744255.1	s__Brevundimonas sp017744255	99.9639	808	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003730275.1	s__Brevundimonas halotolerans	86.6077	658	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCA_016742135.1	s__Brevundimonas sp016742135	86.3194	676	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826885.1	s__Brevundimonas sp018826885	86.0371	569	826	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	80.8658	523	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	80.8312	485	826	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	80.7804	505	826	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	80.5979	330	826	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	80.5858	382	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	80.4203	494	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701445.1	s__Brevundimonas bacteroides	80.3498	455	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270135.1	s__Brevundimonas sp012270135	80.3117	345	826	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	80.0139	437	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-16 08:11:52,622] [INFO] GTDB search result was written to OceanDNA-b23345/result_gtdb.tsv
[2023-03-16 08:11:52,631] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:11:52,637] [INFO] DFAST_QC result json was written to OceanDNA-b23345/dqc_result.json
[2023-03-16 08:11:52,637] [INFO] DFAST_QC completed!
[2023-03-16 08:11:52,637] [INFO] Total running time: 0h1m17s