[2023-03-15 07:25:31,264] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,265] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference
[2023-03-15 07:25:32,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,917] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,917] [INFO] Running command: cat /var/lib/cwl/stg527b5b8a-7414-4f13-940c-687f8a14353f/OceanDNA-b23452.fa | prodigal -d OceanDNA-b23452/cds.fna -a OceanDNA-b23452/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:37,558] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:37,558] [INFO] Task started: HMMsearch
[2023-03-15 07:25:37,558] [INFO] Running command: hmmsearch --tblout OceanDNA-b23452/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/reference_markers.hmm OceanDNA-b23452/protein.faa > /dev/null
[2023-03-15 07:25:37,700] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:37,700] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg527b5b8a-7414-4f13-940c-687f8a14353f/OceanDNA-b23452.fa]
[2023-03-15 07:25:37,722] [INFO] Query marker FASTA was written to OceanDNA-b23452/markers.fasta
[2023-03-15 07:25:37,723] [INFO] Task started: Blastn
[2023-03-15 07:25:37,723] [INFO] Running command: blastn -query OceanDNA-b23452/markers.fasta -db /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/reference_markers.fasta -out OceanDNA-b23452/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:38,398] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:38,404] [INFO] Selected 11 target genomes.
[2023-03-15 07:25:38,404] [INFO] Target genome list was writen to OceanDNA-b23452/target_genomes.txt
[2023-03-15 07:25:38,410] [INFO] Task started: fastANI
[2023-03-15 07:25:38,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg527b5b8a-7414-4f13-940c-687f8a14353f/OceanDNA-b23452.fa --refList OceanDNA-b23452/target_genomes.txt --output OceanDNA-b23452/fastani_result.tsv --threads 1
[2023-03-15 07:25:45,115] [INFO] Task succeeded: fastANI
[2023-03-15 07:25:45,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:25:45,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:25:45,123] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:25:45,123] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:25:45,123] [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 albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	92.1387	230	236	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	86.0836	224	236	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	85.973	222	236	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	85.5921	222	236	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	85.4705	217	236	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	85.2878	215	236	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	83.2787	197	236	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	82.5109	195	236	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.5292	184	236	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.153	150	236	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.6751	130	236	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:25:45,126] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23452/tc_result.tsv
[2023-03-15 07:25:45,127] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:25:45,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:25:45,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/checkm_data
[2023-03-15 07:25:45,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:25:45,132] [INFO] Task started: CheckM
[2023-03-15 07:25:45,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23452/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23452/checkm_input OceanDNA-b23452/checkm_result
[2023-03-15 07:26:02,831] [INFO] Task succeeded: CheckM
[2023-03-15 07:26:02,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.42%
Contamintation: 3.12%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:26:02,896] [INFO] ===== Completeness check finished =====
[2023-03-15 07:26:02,896] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:26:02,897] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23452/markers.fasta)
[2023-03-15 07:26:02,898] [INFO] Task started: Blastn
[2023-03-15 07:26:02,898] [INFO] Running command: blastn -query OceanDNA-b23452/markers.fasta -db /var/lib/cwl/stg19bd0de5-0552-4ca5-a986-0dc575ac0e67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23452/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:04,096] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:04,110] [INFO] Selected 12 target genomes.
[2023-03-15 07:26:04,111] [INFO] Target genome list was writen to OceanDNA-b23452/target_genomes_gtdb.txt
[2023-03-15 07:26:04,124] [INFO] Task started: fastANI
[2023-03-15 07:26:04,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg527b5b8a-7414-4f13-940c-687f8a14353f/OceanDNA-b23452.fa --refList OceanDNA-b23452/target_genomes_gtdb.txt --output OceanDNA-b23452/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:26:10,605] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:10,613] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:26:10,614] [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_002479325.1	s__Brevundimonas sp002479325	97.2189	217	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003248925.1	s__Brevundimonas sp003248925	91.4913	210	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434505.1	s__Brevundimonas sp002434505	86.4587	220	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_002157625.1	s__Brevundimonas sp002157625	86.3829	223	236	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	86.1498	223	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCA_003248455.1	s__Brevundimonas sp003248455	86.0292	217	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248965.1	s__Brevundimonas sp003248965	85.9252	218	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.48	95.48	0.80	0.80	2	-
GCF_902506205.1	s__Brevundimonas sp902506205	85.8218	216	236	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	85.7076	222	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.51	99.05	0.94	0.88	3	-
GCA_013912065.1	s__Brevundimonas sp013912065	85.681	216	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335735.1	s__Brevundimonas sp000335735	85.5479	218	236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016654005.1	s__Brevundimonas nasdae	85.2878	215	236	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 07:26:10,617] [INFO] GTDB search result was written to OceanDNA-b23452/result_gtdb.tsv
[2023-03-15 07:26:10,622] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:26:10,628] [INFO] DFAST_QC result json was written to OceanDNA-b23452/dqc_result.json
[2023-03-15 07:26:10,628] [INFO] DFAST_QC completed!
[2023-03-15 07:26:10,628] [INFO] Total running time: 0h0m39s