[2023-03-17 01:23:45,110] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,111] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,111] [INFO] DQC Reference Directory: /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference
[2023-03-17 01:23:46,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,317] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,317] [INFO] Running command: cat /var/lib/cwl/stg6df47728-0264-44fd-9786-ae3fb502f045/OceanDNA-b23348.fa | prodigal -d OceanDNA-b23348/cds.fna -a OceanDNA-b23348/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:24:01,930] [INFO] Task succeeded: Prodigal
[2023-03-17 01:24:01,930] [INFO] Task started: HMMsearch
[2023-03-17 01:24:01,930] [INFO] Running command: hmmsearch --tblout OceanDNA-b23348/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/reference_markers.hmm OceanDNA-b23348/protein.faa > /dev/null
[2023-03-17 01:24:02,102] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:24:02,102] [INFO] Found 6/6 markers.
[2023-03-17 01:24:02,117] [INFO] Query marker FASTA was written to OceanDNA-b23348/markers.fasta
[2023-03-17 01:24:02,118] [INFO] Task started: Blastn
[2023-03-17 01:24:02,118] [INFO] Running command: blastn -query OceanDNA-b23348/markers.fasta -db /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/reference_markers.fasta -out OceanDNA-b23348/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:02,954] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:02,955] [INFO] Selected 17 target genomes.
[2023-03-17 01:24:02,955] [INFO] Target genome list was writen to OceanDNA-b23348/target_genomes.txt
[2023-03-17 01:24:02,965] [INFO] Task started: fastANI
[2023-03-17 01:24:02,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df47728-0264-44fd-9786-ae3fb502f045/OceanDNA-b23348.fa --refList OceanDNA-b23348/target_genomes.txt --output OceanDNA-b23348/fastani_result.tsv --threads 1
[2023-03-17 01:24:14,682] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:14,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:24:14,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:24:14,692] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:24:14,692] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:24:14,693] [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	82.5292	564	867	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.974	553	867	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.9266	584	867	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.7745	535	867	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.5453	526	867	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.4822	568	867	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.3586	520	867	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	81.2367	549	867	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	81.185	530	867	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.1536	532	867	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.9302	510	867	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.8409	479	867	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.6746	502	867	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.6414	487	867	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.3221	462	867	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.2103	294	867	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.1365	346	867	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:24:14,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23348/tc_result.tsv
[2023-03-17 01:24:14,694] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:24:14,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:24:14,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/checkm_data
[2023-03-17 01:24:14,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:24:14,699] [INFO] Task started: CheckM
[2023-03-17 01:24:14,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23348/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23348/checkm_input OceanDNA-b23348/checkm_result
[2023-03-17 01:24:56,258] [INFO] Task succeeded: CheckM
[2023-03-17 01:24:56,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:24:56,260] [INFO] ===== Completeness check finished =====
[2023-03-17 01:24:56,261] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:24:56,261] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23348/markers.fasta)
[2023-03-17 01:24:56,261] [INFO] Task started: Blastn
[2023-03-17 01:24:56,261] [INFO] Running command: blastn -query OceanDNA-b23348/markers.fasta -db /var/lib/cwl/stgd02cddac-05d5-4aae-a884-4e9c1bcf8fa3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23348/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:57,931] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:57,932] [INFO] Selected 26 target genomes.
[2023-03-17 01:24:57,932] [INFO] Target genome list was writen to OceanDNA-b23348/target_genomes_gtdb.txt
[2023-03-17 01:24:58,386] [INFO] Task started: fastANI
[2023-03-17 01:24:58,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg6df47728-0264-44fd-9786-ae3fb502f045/OceanDNA-b23348.fa --refList OceanDNA-b23348/target_genomes_gtdb.txt --output OceanDNA-b23348/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:25:14,999] [INFO] Task succeeded: fastANI
[2023-03-17 01:25:15,013] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:25:15,013] [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_004296955.1	s__Brevundimonas sp004296955	83.1994	581	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_002483305.1	s__Brevundimonas sp002483305	83.1419	563	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427825.1	s__Brevundimonas sp001427825	83.0134	566	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826515.1	s__Brevundimonas sp018826515	82.8906	590	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_016183935.1	s__Brevundimonas sp016183935	82.5464	539	867	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	82.5364	563	867	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	81.9922	552	867	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	81.9186	535	867	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	81.9103	585	867	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	81.8833	349	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	81.7879	534	867	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	81.7046	555	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280785.1	s__Brevundimonas subvibrioides_B	81.6786	538	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144605.1	s__Brevundimonas subvibrioides	81.5589	525	867	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	81.4452	531	867	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	81.3156	530	867	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	81.2592	537	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017795885.1	s__Brevundimonas sp017795885	81.259	509	867	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	81.2227	517	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820275.1	s__Brevundimonas sp018820275	81.2094	493	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_002292165.1	s__Brevundimonas sp002292165	81.0894	471	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	80.9996	492	867	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	80.9684	432	867	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	80.9315	417	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002484265.1	s__Brevundimonas sp002484265	80.545	515	867	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.51	99.05	0.94	0.88	3	-
GCF_014199945.1	s__Brevundimonas variabilis	80.3282	463	867	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 01:25:15,013] [INFO] GTDB search result was written to OceanDNA-b23348/result_gtdb.tsv
[2023-03-17 01:25:15,014] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:25:15,016] [INFO] DFAST_QC result json was written to OceanDNA-b23348/dqc_result.json
[2023-03-17 01:25:15,016] [INFO] DFAST_QC completed!
[2023-03-17 01:25:15,016] [INFO] Total running time: 0h1m30s