[2023-03-15 08:11:06,080] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:06,080] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:06,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference
[2023-03-15 08:11:07,237] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,238] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,238] [INFO] Running command: cat /var/lib/cwl/stge6a51374-aacf-4681-acbe-a6961968bf8e/OceanDNA-b23344.fa | prodigal -d OceanDNA-b23344/cds.fna -a OceanDNA-b23344/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:20,543] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:20,543] [INFO] Task started: HMMsearch
[2023-03-15 08:11:20,543] [INFO] Running command: hmmsearch --tblout OceanDNA-b23344/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/reference_markers.hmm OceanDNA-b23344/protein.faa > /dev/null
[2023-03-15 08:11:20,722] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:20,723] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6a51374-aacf-4681-acbe-a6961968bf8e/OceanDNA-b23344.fa]
[2023-03-15 08:11:20,779] [INFO] Query marker FASTA was written to OceanDNA-b23344/markers.fasta
[2023-03-15 08:11:20,781] [INFO] Task started: Blastn
[2023-03-15 08:11:20,781] [INFO] Running command: blastn -query OceanDNA-b23344/markers.fasta -db /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/reference_markers.fasta -out OceanDNA-b23344/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:21,526] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:21,537] [INFO] Selected 15 target genomes.
[2023-03-15 08:11:21,538] [INFO] Target genome list was writen to OceanDNA-b23344/target_genomes.txt
[2023-03-15 08:11:21,548] [INFO] Task started: fastANI
[2023-03-15 08:11:21,548] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a51374-aacf-4681-acbe-a6961968bf8e/OceanDNA-b23344.fa --refList OceanDNA-b23344/target_genomes.txt --output OceanDNA-b23344/fastani_result.tsv --threads 1
[2023-03-15 08:11:30,916] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:30,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:30,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:30,925] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:30,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:11:30,926] [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	90.9965	608	727	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	90.9568	605	727	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.4531	424	727	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.4034	439	727	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.3925	432	727	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.1152	425	727	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.9559	438	727	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	79.9099	409	727	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.8748	426	727	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	79.8741	417	727	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	79.8687	414	727	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.8281	393	727	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.5769	440	727	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.3526	246	727	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.0453	215	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:11:30,931] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23344/tc_result.tsv
[2023-03-15 08:11:30,935] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:30,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:30,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/checkm_data
[2023-03-15 08:11:30,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:30,949] [INFO] Task started: CheckM
[2023-03-15 08:11:30,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23344/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23344/checkm_input OceanDNA-b23344/checkm_result
[2023-03-15 08:12:06,597] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:06,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:06,621] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:06,621] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:06,622] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23344/markers.fasta)
[2023-03-15 08:12:06,623] [INFO] Task started: Blastn
[2023-03-15 08:12:06,623] [INFO] Running command: blastn -query OceanDNA-b23344/markers.fasta -db /var/lib/cwl/stg7bb33c25-5532-40cd-b38f-cfef9802c0df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23344/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:08,001] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:08,002] [INFO] Selected 12 target genomes.
[2023-03-15 08:12:08,002] [INFO] Target genome list was writen to OceanDNA-b23344/target_genomes_gtdb.txt
[2023-03-15 08:12:08,010] [INFO] Task started: fastANI
[2023-03-15 08:12:08,010] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a51374-aacf-4681-acbe-a6961968bf8e/OceanDNA-b23344.fa --refList OceanDNA-b23344/target_genomes_gtdb.txt --output OceanDNA-b23344/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:12:15,093] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:15,100] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:12:15,100] [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_018826885.1	s__Brevundimonas sp018826885	92.1278	513	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730275.1	s__Brevundimonas halotolerans	90.9819	609	727	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	88.5215	579	727	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	86.3579	614	727	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	80.4715	405	727	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	80.43	437	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308115.1	s__Brevundimonas sp017308115	80.3454	391	727	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	80.3407	417	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934285.1	s__Brevundimonas fluminis	79.9495	438	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836405.1	s__Brevundimonas sp014836405	79.8446	391	727	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	79.749	425	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.98	5	-
GCA_002292165.1	s__Brevundimonas sp002292165	79.7388	387	727	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 08:12:15,100] [INFO] GTDB search result was written to OceanDNA-b23344/result_gtdb.tsv
[2023-03-15 08:12:15,101] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:12:15,102] [INFO] DFAST_QC result json was written to OceanDNA-b23344/dqc_result.json
[2023-03-15 08:12:15,102] [INFO] DFAST_QC completed!
[2023-03-15 08:12:15,102] [INFO] Total running time: 0h1m9s