[2023-03-19 02:16:59,673] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,673] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference
[2023-03-19 02:17:00,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,766] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,767] [INFO] Running command: cat /var/lib/cwl/stg4ef3dac3-1037-4f5e-9ac4-ef5beb0a36c8/OceanDNA-b17676.fa | prodigal -d OceanDNA-b17676/cds.fna -a OceanDNA-b17676/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:36,847] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:36,847] [INFO] Task started: HMMsearch
[2023-03-19 02:17:36,847] [INFO] Running command: hmmsearch --tblout OceanDNA-b17676/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/reference_markers.hmm OceanDNA-b17676/protein.faa > /dev/null
[2023-03-19 02:17:37,115] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:37,116] [INFO] Found 6/6 markers.
[2023-03-19 02:17:37,154] [INFO] Query marker FASTA was written to OceanDNA-b17676/markers.fasta
[2023-03-19 02:17:37,155] [INFO] Task started: Blastn
[2023-03-19 02:17:37,155] [INFO] Running command: blastn -query OceanDNA-b17676/markers.fasta -db /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/reference_markers.fasta -out OceanDNA-b17676/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:37,690] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:37,691] [INFO] Selected 36 target genomes.
[2023-03-19 02:17:37,692] [INFO] Target genome list was writen to OceanDNA-b17676/target_genomes.txt
[2023-03-19 02:17:37,710] [INFO] Task started: fastANI
[2023-03-19 02:17:37,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ef3dac3-1037-4f5e-9ac4-ef5beb0a36c8/OceanDNA-b17676.fa --refList OceanDNA-b17676/target_genomes.txt --output OceanDNA-b17676/fastani_result.tsv --threads 1
[2023-03-19 02:18:05,842] [INFO] Task succeeded: fastANI
[2023-03-19 02:18:05,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:18:05,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:18:05,847] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:18:05,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:18:05,847] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.673	75	1980	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.6466	73	1980	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.5868	53	1980	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:18:05,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17676/tc_result.tsv
[2023-03-19 02:18:05,848] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:18:05,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:18:05,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/checkm_data
[2023-03-19 02:18:05,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:18:05,979] [INFO] Task started: CheckM
[2023-03-19 02:18:05,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17676/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17676/checkm_input OceanDNA-b17676/checkm_result
[2023-03-19 02:19:30,215] [INFO] Task succeeded: CheckM
[2023-03-19 02:19:30,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:19:30,221] [INFO] ===== Completeness check finished =====
[2023-03-19 02:19:30,221] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:19:30,221] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17676/markers.fasta)
[2023-03-19 02:19:30,222] [INFO] Task started: Blastn
[2023-03-19 02:19:30,222] [INFO] Running command: blastn -query OceanDNA-b17676/markers.fasta -db /var/lib/cwl/stg9e50bf24-1928-43da-ad61-1f9407ceeea3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17676/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:19:30,984] [INFO] Task succeeded: Blastn
[2023-03-19 02:19:30,986] [INFO] Selected 21 target genomes.
[2023-03-19 02:19:30,987] [INFO] Target genome list was writen to OceanDNA-b17676/target_genomes_gtdb.txt
[2023-03-19 02:19:30,999] [INFO] Task started: fastANI
[2023-03-19 02:19:30,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ef3dac3-1037-4f5e-9ac4-ef5beb0a36c8/OceanDNA-b17676.fa --refList OceanDNA-b17676/target_genomes_gtdb.txt --output OceanDNA-b17676/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:19:49,365] [INFO] Task succeeded: fastANI
[2023-03-19 02:19:49,371] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:19:49,371] [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_018672475.1	s__GCA-2724215 sp018672475	99.8176	1901	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	conclusive
GCA_015660315.1	s__GCA-2724215 sp015660315	93.0789	1183	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	77.9439	734	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841115.1	s__GCA-2724215 sp009841115	76.8372	375	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009840005.1	s__GCA-2724215 sp009840005	76.7646	366	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009845645.1	s__GCA-2724215 sp009845645	76.6101	210	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	76.5914	272	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	75.5721	62	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	75.4708	88	1980	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:19:49,372] [INFO] GTDB search result was written to OceanDNA-b17676/result_gtdb.tsv
[2023-03-19 02:19:49,373] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:19:49,375] [INFO] DFAST_QC result json was written to OceanDNA-b17676/dqc_result.json
[2023-03-19 02:19:49,375] [INFO] DFAST_QC completed!
[2023-03-19 02:19:49,375] [INFO] Total running time: 0h2m50s