[2023-03-15 15:55:16,234] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,912] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,912] [INFO] Running command: cat /var/lib/cwl/stg2cba5025-78a7-4be1-97e0-bd40495d8d15/OceanDNA-b23974.fa | prodigal -d OceanDNA-b23974/cds.fna -a OceanDNA-b23974/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:25,055] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:25,055] [INFO] Task started: HMMsearch
[2023-03-15 15:55:25,055] [INFO] Running command: hmmsearch --tblout OceanDNA-b23974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/reference_markers.hmm OceanDNA-b23974/protein.faa > /dev/null
[2023-03-15 15:55:25,205] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:25,206] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2cba5025-78a7-4be1-97e0-bd40495d8d15/OceanDNA-b23974.fa]
[2023-03-15 15:55:25,221] [INFO] Query marker FASTA was written to OceanDNA-b23974/markers.fasta
[2023-03-15 15:55:25,221] [INFO] Task started: Blastn
[2023-03-15 15:55:25,221] [INFO] Running command: blastn -query OceanDNA-b23974/markers.fasta -db /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/reference_markers.fasta -out OceanDNA-b23974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:25,864] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:25,865] [INFO] Selected 20 target genomes.
[2023-03-15 15:55:25,865] [INFO] Target genome list was writen to OceanDNA-b23974/target_genomes.txt
[2023-03-15 15:55:25,890] [INFO] Task started: fastANI
[2023-03-15 15:55:25,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cba5025-78a7-4be1-97e0-bd40495d8d15/OceanDNA-b23974.fa --refList OceanDNA-b23974/target_genomes.txt --output OceanDNA-b23974/fastani_result.tsv --threads 1
[2023-03-15 15:55:39,179] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:39,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:39,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:39,186] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:39,186] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:39,186] [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
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.435	88	319	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.435	88	319	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.435	88	319	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.2207	94	319	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.1867	96	319	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.0509	112	319	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.0275	113	319	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:39,186] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23974/tc_result.tsv
[2023-03-15 15:55:39,186] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:39,187] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:39,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/checkm_data
[2023-03-15 15:55:39,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:39,191] [INFO] Task started: CheckM
[2023-03-15 15:55:39,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23974/checkm_input OceanDNA-b23974/checkm_result
[2023-03-15 15:56:03,141] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:03,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:03,144] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:03,144] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:03,144] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23974/markers.fasta)
[2023-03-15 15:56:03,145] [INFO] Task started: Blastn
[2023-03-15 15:56:03,145] [INFO] Running command: blastn -query OceanDNA-b23974/markers.fasta -db /var/lib/cwl/stg829e5f3a-8d76-43ec-9df7-cba38d6a190f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:04,028] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:04,028] [INFO] Selected 8 target genomes.
[2023-03-15 15:56:04,029] [INFO] Target genome list was writen to OceanDNA-b23974/target_genomes_gtdb.txt
[2023-03-15 15:56:04,033] [INFO] Task started: fastANI
[2023-03-15 15:56:04,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cba5025-78a7-4be1-97e0-bd40495d8d15/OceanDNA-b23974.fa --refList OceanDNA-b23974/target_genomes_gtdb.txt --output OceanDNA-b23974/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:07,929] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:07,935] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:07,935] [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_000152745.1	s__Oceanicaulis sp000152745	86.2501	298	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_000420265.1	s__Oceanicaulis alexandrii	83.3709	283	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCF_003046365.1	s__Oceanicaulis sp003046365	83.0475	278	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_008630495.1	s__Oceanicaulis satelles	77.9712	130	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657295.1	s__Oceanicaulis sp001657295	77.7778	128	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	77.6309	140	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	77.435	88	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_017161425.1	s__Marinicauda algicola	77.0275	113	319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:07,935] [INFO] GTDB search result was written to OceanDNA-b23974/result_gtdb.tsv
[2023-03-15 15:56:07,935] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:07,937] [INFO] DFAST_QC result json was written to OceanDNA-b23974/dqc_result.json
[2023-03-15 15:56:07,937] [INFO] DFAST_QC completed!
[2023-03-15 15:56:07,937] [INFO] Total running time: 0h0m52s