[2023-03-17 22:53:08,392] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:53:08,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:53:08,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference
[2023-03-17 22:53:10,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:53:10,526] [INFO] Task started: Prodigal
[2023-03-17 22:53:10,526] [INFO] Running command: cat /var/lib/cwl/stg8ff654a1-ced3-437f-9509-b652b43e2490/OceanDNA-b23400.fa | prodigal -d OceanDNA-b23400/cds.fna -a OceanDNA-b23400/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:53:22,239] [INFO] Task succeeded: Prodigal
[2023-03-17 22:53:22,239] [INFO] Task started: HMMsearch
[2023-03-17 22:53:22,239] [INFO] Running command: hmmsearch --tblout OceanDNA-b23400/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/reference_markers.hmm OceanDNA-b23400/protein.faa > /dev/null
[2023-03-17 22:53:22,407] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:53:22,407] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8ff654a1-ced3-437f-9509-b652b43e2490/OceanDNA-b23400.fa]
[2023-03-17 22:53:22,425] [INFO] Query marker FASTA was written to OceanDNA-b23400/markers.fasta
[2023-03-17 22:53:22,425] [INFO] Task started: Blastn
[2023-03-17 22:53:22,425] [INFO] Running command: blastn -query OceanDNA-b23400/markers.fasta -db /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/reference_markers.fasta -out OceanDNA-b23400/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:53:23,090] [INFO] Task succeeded: Blastn
[2023-03-17 22:53:23,091] [INFO] Selected 10 target genomes.
[2023-03-17 22:53:23,091] [INFO] Target genome list was writen to OceanDNA-b23400/target_genomes.txt
[2023-03-17 22:53:23,096] [INFO] Task started: fastANI
[2023-03-17 22:53:23,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff654a1-ced3-437f-9509-b652b43e2490/OceanDNA-b23400.fa --refList OceanDNA-b23400/target_genomes.txt --output OceanDNA-b23400/fastani_result.tsv --threads 1
[2023-03-17 22:53:29,511] [INFO] Task succeeded: fastANI
[2023-03-17 22:53:29,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:53:29,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:53:29,519] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:53:29,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:53:29,519] [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 vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	94.3623	520	625	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	93.5336	501	625	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	85.0416	451	625	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	84.1491	471	625	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	83.8072	437	625	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	83.4026	432	625	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.4638	325	625	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.2272	295	625	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.0016	181	625	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.7764	172	625	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:53:29,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23400/tc_result.tsv
[2023-03-17 22:53:29,520] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:53:29,520] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:53:29,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/checkm_data
[2023-03-17 22:53:29,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:53:29,524] [INFO] Task started: CheckM
[2023-03-17 22:53:29,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23400/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23400/checkm_input OceanDNA-b23400/checkm_result
[2023-03-17 22:54:01,370] [INFO] Task succeeded: CheckM
[2023-03-17 22:54:01,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:54:01,373] [INFO] ===== Completeness check finished =====
[2023-03-17 22:54:01,373] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:54:01,373] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23400/markers.fasta)
[2023-03-17 22:54:01,374] [INFO] Task started: Blastn
[2023-03-17 22:54:01,374] [INFO] Running command: blastn -query OceanDNA-b23400/markers.fasta -db /var/lib/cwl/stgd3812518-d034-4482-8a76-8258888fcfc0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23400/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:54:02,425] [INFO] Task succeeded: Blastn
[2023-03-17 22:54:02,426] [INFO] Selected 6 target genomes.
[2023-03-17 22:54:02,426] [INFO] Target genome list was writen to OceanDNA-b23400/target_genomes_gtdb.txt
[2023-03-17 22:54:02,429] [INFO] Task started: fastANI
[2023-03-17 22:54:02,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ff654a1-ced3-437f-9509-b652b43e2490/OceanDNA-b23400.fa --refList OceanDNA-b23400/target_genomes_gtdb.txt --output OceanDNA-b23400/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:54:06,112] [INFO] Task succeeded: fastANI
[2023-03-17 22:54:06,117] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:54:06,117] [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_001592205.1	s__Brevundimonas vesicularis	94.4008	519	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
GCF_005484585.1	s__Brevundimonas sp005484585	93.7582	511	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	-
GCF_017086445.1	s__Brevundimonas vesicularis_A	93.3754	506	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	-
GCF_000813765.1	s__Brevundimonas nasdae_A	93.327	519	625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	93.3192	509	625	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	93.0763	482	625	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 22:54:06,117] [INFO] GTDB search result was written to OceanDNA-b23400/result_gtdb.tsv
[2023-03-17 22:54:06,117] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:54:06,118] [INFO] DFAST_QC result json was written to OceanDNA-b23400/dqc_result.json
[2023-03-17 22:54:06,118] [INFO] DFAST_QC completed!
[2023-03-17 22:54:06,118] [INFO] Total running time: 0h0m58s