[2023-03-17 23:13:17,474] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:13:17,474] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:13:17,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference
[2023-03-17 23:13:18,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:13:18,561] [INFO] Task started: Prodigal
[2023-03-17 23:13:18,561] [INFO] Running command: cat /var/lib/cwl/stg42489047-60d2-4725-9780-2b414e2b9e26/OceanDNA-b23945.fa | prodigal -d OceanDNA-b23945/cds.fna -a OceanDNA-b23945/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:13:36,141] [INFO] Task succeeded: Prodigal
[2023-03-17 23:13:36,141] [INFO] Task started: HMMsearch
[2023-03-17 23:13:36,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b23945/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/reference_markers.hmm OceanDNA-b23945/protein.faa > /dev/null
[2023-03-17 23:13:36,335] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:13:36,335] [INFO] Found 6/6 markers.
[2023-03-17 23:13:36,353] [INFO] Query marker FASTA was written to OceanDNA-b23945/markers.fasta
[2023-03-17 23:13:36,355] [INFO] Task started: Blastn
[2023-03-17 23:13:36,355] [INFO] Running command: blastn -query OceanDNA-b23945/markers.fasta -db /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/reference_markers.fasta -out OceanDNA-b23945/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:13:37,251] [INFO] Task succeeded: Blastn
[2023-03-17 23:13:37,252] [INFO] Selected 17 target genomes.
[2023-03-17 23:13:37,252] [INFO] Target genome list was writen to OceanDNA-b23945/target_genomes.txt
[2023-03-17 23:13:37,260] [INFO] Task started: fastANI
[2023-03-17 23:13:37,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg42489047-60d2-4725-9780-2b414e2b9e26/OceanDNA-b23945.fa --refList OceanDNA-b23945/target_genomes.txt --output OceanDNA-b23945/fastani_result.tsv --threads 1
[2023-03-17 23:13:47,434] [INFO] Task succeeded: fastANI
[2023-03-17 23:13:47,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:13:47,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:13:47,451] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:13:47,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:13:47,451] [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
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	82.2983	631	935	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	79.052	438	935	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.614	428	935	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.0237	195	935	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.7092	173	935	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.7092	173	935	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.6853	185	935	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.6388	187	935	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	76.2651	60	935	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	76.0229	54	935	95	below_threshold
Afipia felis	strain=NCTC12499	GCA_900445155.1	1035	1035	type	True	76.0229	54	935	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	75.8043	83	935	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.7032	71	935	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	75.6976	73	935	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.1007	60	935	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:13:47,452] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23945/tc_result.tsv
[2023-03-17 23:13:47,452] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:13:47,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:13:47,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/checkm_data
[2023-03-17 23:13:47,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:13:47,457] [INFO] Task started: CheckM
[2023-03-17 23:13:47,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23945/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23945/checkm_input OceanDNA-b23945/checkm_result
[2023-03-17 23:14:33,929] [INFO] Task succeeded: CheckM
[2023-03-17 23:14:33,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:14:33,943] [INFO] ===== Completeness check finished =====
[2023-03-17 23:14:33,943] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:14:33,943] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23945/markers.fasta)
[2023-03-17 23:14:33,944] [INFO] Task started: Blastn
[2023-03-17 23:14:33,944] [INFO] Running command: blastn -query OceanDNA-b23945/markers.fasta -db /var/lib/cwl/stg2626130b-aca3-4833-baed-5500392d3212/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23945/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:14:35,731] [INFO] Task succeeded: Blastn
[2023-03-17 23:14:35,733] [INFO] Selected 11 target genomes.
[2023-03-17 23:14:35,733] [INFO] Target genome list was writen to OceanDNA-b23945/target_genomes_gtdb.txt
[2023-03-17 23:14:35,742] [INFO] Task started: fastANI
[2023-03-17 23:14:35,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg42489047-60d2-4725-9780-2b414e2b9e26/OceanDNA-b23945.fa --refList OceanDNA-b23945/target_genomes_gtdb.txt --output OceanDNA-b23945/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:14:42,373] [INFO] Task succeeded: fastANI
[2023-03-17 23:14:42,380] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:14:42,380] [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_900103475.1	s__Maricaulis salignorans	82.2983	631	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	79.0419	439	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_016817355.1	s__Maricaulis parjimensis	78.9661	408	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	78.9293	421	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	78.8532	419	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_017642925.1	s__Maricaulis sp017642925	78.8503	468	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	78.8199	332	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_905480005.1	s__Maricaulis sp905480005	78.6446	370	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	78.6042	429	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694345.1	s__Maricaulis sp002694345	78.5411	258	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222865.1	s__Maricaulis sp018222865	77.1732	205	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:14:42,383] [INFO] GTDB search result was written to OceanDNA-b23945/result_gtdb.tsv
[2023-03-17 23:14:42,383] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:14:42,386] [INFO] DFAST_QC result json was written to OceanDNA-b23945/dqc_result.json
[2023-03-17 23:14:42,386] [INFO] DFAST_QC completed!
[2023-03-17 23:14:42,386] [INFO] Total running time: 0h1m25s