[2023-03-15 05:43:38,871] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:43:38,873] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:43:38,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference
[2023-03-15 05:43:39,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:43:39,964] [INFO] Task started: Prodigal
[2023-03-15 05:43:39,964] [INFO] Running command: cat /var/lib/cwl/stgc054fe22-a79f-45cf-ae7b-a8128a6e0c39/OceanDNA-b23392.fa | prodigal -d OceanDNA-b23392/cds.fna -a OceanDNA-b23392/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:43:51,091] [INFO] Task succeeded: Prodigal
[2023-03-15 05:43:51,092] [INFO] Task started: HMMsearch
[2023-03-15 05:43:51,092] [INFO] Running command: hmmsearch --tblout OceanDNA-b23392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/reference_markers.hmm OceanDNA-b23392/protein.faa > /dev/null
[2023-03-15 05:43:51,250] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:43:51,251] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc054fe22-a79f-45cf-ae7b-a8128a6e0c39/OceanDNA-b23392.fa]
[2023-03-15 05:43:51,275] [INFO] Query marker FASTA was written to OceanDNA-b23392/markers.fasta
[2023-03-15 05:43:51,276] [INFO] Task started: Blastn
[2023-03-15 05:43:51,276] [INFO] Running command: blastn -query OceanDNA-b23392/markers.fasta -db /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/reference_markers.fasta -out OceanDNA-b23392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:43:51,772] [INFO] Task succeeded: Blastn
[2023-03-15 05:43:51,778] [INFO] Selected 9 target genomes.
[2023-03-15 05:43:51,778] [INFO] Target genome list was writen to OceanDNA-b23392/target_genomes.txt
[2023-03-15 05:43:51,783] [INFO] Task started: fastANI
[2023-03-15 05:43:51,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgc054fe22-a79f-45cf-ae7b-a8128a6e0c39/OceanDNA-b23392.fa --refList OceanDNA-b23392/target_genomes.txt --output OceanDNA-b23392/fastani_result.tsv --threads 1
[2023-03-15 05:43:57,312] [INFO] Task succeeded: fastANI
[2023-03-15 05:43:57,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:43:57,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:43:57,319] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:43:57,319] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:43:57,319] [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	88.6302	511	637	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	85.8181	526	637	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	83.5446	494	637	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	83.4904	504	637	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.775	404	637	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.4694	405	637	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.337	414	637	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.2633	391	637	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	79.6755	391	637	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:43:57,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23392/tc_result.tsv
[2023-03-15 05:43:57,345] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:43:57,345] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:43:57,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/checkm_data
[2023-03-15 05:43:57,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:43:57,350] [INFO] Task started: CheckM
[2023-03-15 05:43:57,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23392/checkm_input OceanDNA-b23392/checkm_result
[2023-03-15 05:44:28,170] [INFO] Task succeeded: CheckM
[2023-03-15 05:44:28,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:44:28,188] [INFO] ===== Completeness check finished =====
[2023-03-15 05:44:28,188] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:44:28,189] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23392/markers.fasta)
[2023-03-15 05:44:28,190] [INFO] Task started: Blastn
[2023-03-15 05:44:28,190] [INFO] Running command: blastn -query OceanDNA-b23392/markers.fasta -db /var/lib/cwl/stg39c9592a-5984-41a5-bcac-bd8eb23de7bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:44:28,769] [INFO] Task succeeded: Blastn
[2023-03-15 05:44:28,778] [INFO] Selected 9 target genomes.
[2023-03-15 05:44:28,778] [INFO] Target genome list was writen to OceanDNA-b23392/target_genomes_gtdb.txt
[2023-03-15 05:44:28,787] [INFO] Task started: fastANI
[2023-03-15 05:44:28,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgc054fe22-a79f-45cf-ae7b-a8128a6e0c39/OceanDNA-b23392.fa --refList OceanDNA-b23392/target_genomes_gtdb.txt --output OceanDNA-b23392/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:44:34,674] [INFO] Task succeeded: fastANI
[2023-03-15 05:44:34,680] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:44:34,680] [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_014202075.1	s__Brevundimonas basaltis	88.6302	511	637	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	86.5761	493	637	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	86.0132	347	637	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	85.8181	526	637	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	84.4458	504	637	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	84.2607	499	637	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	84.2349	507	637	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_013912005.1	s__Brevundimonas sp013912005	83.5716	482	637	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	83.5522	493	637	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 05:44:34,684] [INFO] GTDB search result was written to OceanDNA-b23392/result_gtdb.tsv
[2023-03-15 05:44:34,685] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:44:34,686] [INFO] DFAST_QC result json was written to OceanDNA-b23392/dqc_result.json
[2023-03-15 05:44:34,686] [INFO] DFAST_QC completed!
[2023-03-15 05:44:34,686] [INFO] Total running time: 0h0m56s