[2023-03-18 00:58:44,625] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,625] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stg342f0e97-29ff-4390-8b06-206404866970/OceanDNA-b23355.fa | prodigal -d OceanDNA-b23355/cds.fna -a OceanDNA-b23355/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:59:05,479] [INFO] Task succeeded: Prodigal
[2023-03-18 00:59:05,479] [INFO] Task started: HMMsearch
[2023-03-18 00:59:05,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b23355/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/reference_markers.hmm OceanDNA-b23355/protein.faa > /dev/null
[2023-03-18 00:59:05,677] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:59:05,678] [INFO] Found 6/6 markers.
[2023-03-18 00:59:05,700] [INFO] Query marker FASTA was written to OceanDNA-b23355/markers.fasta
[2023-03-18 00:59:05,701] [INFO] Task started: Blastn
[2023-03-18 00:59:05,701] [INFO] Running command: blastn -query OceanDNA-b23355/markers.fasta -db /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/reference_markers.fasta -out OceanDNA-b23355/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:06,501] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:06,504] [INFO] Selected 18 target genomes.
[2023-03-18 00:59:06,504] [INFO] Target genome list was writen to OceanDNA-b23355/target_genomes.txt
[2023-03-18 00:59:06,509] [INFO] Task started: fastANI
[2023-03-18 00:59:06,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg342f0e97-29ff-4390-8b06-206404866970/OceanDNA-b23355.fa --refList OceanDNA-b23355/target_genomes.txt --output OceanDNA-b23355/fastani_result.tsv --threads 1
[2023-03-18 00:59:20,292] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:20,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:20,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:20,304] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:20,304] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:59:20,304] [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	82.0428	605	1054	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.644	612	1054	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.547	630	1054	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.5368	586	1054	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.2746	602	1054	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.259	577	1054	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.0697	632	1054	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	81.0693	614	1054	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.8809	583	1054	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.6403	606	1054	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	80.5981	571	1054	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.5894	530	1054	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5389	540	1054	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	80.2818	485	1054	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.2553	527	1054	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.476	333	1054	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.3313	377	1054	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.8948	170	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:59:20,305] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23355/tc_result.tsv
[2023-03-18 00:59:20,307] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:20,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:20,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/checkm_data
[2023-03-18 00:59:20,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:20,384] [INFO] Task started: CheckM
[2023-03-18 00:59:20,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23355/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23355/checkm_input OceanDNA-b23355/checkm_result
[2023-03-18 01:00:09,162] [INFO] Task succeeded: CheckM
[2023-03-18 01:00:09,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:00:09,167] [INFO] ===== Completeness check finished =====
[2023-03-18 01:00:09,167] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:00:09,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23355/markers.fasta)
[2023-03-18 01:00:09,167] [INFO] Task started: Blastn
[2023-03-18 01:00:09,167] [INFO] Running command: blastn -query OceanDNA-b23355/markers.fasta -db /var/lib/cwl/stg11f82e73-cbf8-4609-a993-4851fc40846b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23355/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:00:10,745] [INFO] Task succeeded: Blastn
[2023-03-18 01:00:10,748] [INFO] Selected 20 target genomes.
[2023-03-18 01:00:10,748] [INFO] Target genome list was writen to OceanDNA-b23355/target_genomes_gtdb.txt
[2023-03-18 01:00:10,811] [INFO] Task started: fastANI
[2023-03-18 01:00:10,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg342f0e97-29ff-4390-8b06-206404866970/OceanDNA-b23355.fa --refList OceanDNA-b23355/target_genomes_gtdb.txt --output OceanDNA-b23355/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:00:24,101] [INFO] Task succeeded: fastANI
[2023-03-18 01:00:24,113] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:00:24,113] [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_002483305.1	s__Brevundimonas sp002483305	82.7174	629	1054	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	82.6665	650	1054	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	82.5799	651	1054	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	82.5149	640	1054	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	82.2004	550	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCF_014202075.1	s__Brevundimonas basaltis	82.0545	605	1054	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	81.9557	593	1054	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	81.6883	374	1054	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	81.6068	616	1054	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	81.526	632	1054	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	81.4918	592	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	81.3959	634	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_000144605.1	s__Brevundimonas subvibrioides	81.2993	603	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795885.1	s__Brevundimonas sp017795885	81.0372	559	1054	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	81.0069	462	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	81.0051	609	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	80.9017	576	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207965.1	s__Brevundimonas bullata_A	80.7962	607	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836405.1	s__Brevundimonas sp014836405	80.5781	531	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280475.1	s__Brevundimonas subvibrioides_C	80.5047	551	1054	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:00:24,115] [INFO] GTDB search result was written to OceanDNA-b23355/result_gtdb.tsv
[2023-03-18 01:00:24,117] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:00:24,120] [INFO] DFAST_QC result json was written to OceanDNA-b23355/dqc_result.json
[2023-03-18 01:00:24,120] [INFO] DFAST_QC completed!
[2023-03-18 01:00:24,120] [INFO] Total running time: 0h1m39s