[2023-03-18 04:16:54,168] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference
[2023-03-18 04:16:55,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,826] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,826] [INFO] Running command: cat /var/lib/cwl/stgd6ec906f-5052-486b-a42f-eb059f211266/OceanDNA-a831.fa | prodigal -d OceanDNA-a831/cds.fna -a OceanDNA-a831/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:01,328] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:01,328] [INFO] Task started: HMMsearch
[2023-03-18 04:17:01,328] [INFO] Running command: hmmsearch --tblout OceanDNA-a831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/reference_markers.hmm OceanDNA-a831/protein.faa > /dev/null
[2023-03-18 04:17:01,434] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:01,435] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd6ec906f-5052-486b-a42f-eb059f211266/OceanDNA-a831.fa]
[2023-03-18 04:17:01,443] [INFO] Query marker FASTA was written to OceanDNA-a831/markers.fasta
[2023-03-18 04:17:01,444] [INFO] Task started: Blastn
[2023-03-18 04:17:01,444] [INFO] Running command: blastn -query OceanDNA-a831/markers.fasta -db /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/reference_markers.fasta -out OceanDNA-a831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:01,862] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:01,862] [INFO] Selected 3 target genomes.
[2023-03-18 04:17:01,863] [INFO] Target genome list was writen to OceanDNA-a831/target_genomes.txt
[2023-03-18 04:17:01,883] [INFO] Task started: fastANI
[2023-03-18 04:17:01,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ec906f-5052-486b-a42f-eb059f211266/OceanDNA-a831.fa --refList OceanDNA-a831/target_genomes.txt --output OceanDNA-a831/fastani_result.tsv --threads 1
[2023-03-18 04:17:02,969] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:02,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:02,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:02,974] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:02,974] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:02,974] [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
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.529	284	350	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.0749	295	350	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.881	282	350	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:02,974] [INFO] DFAST Taxonomy check result was written to OceanDNA-a831/tc_result.tsv
[2023-03-18 04:17:02,974] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:02,974] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:02,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/checkm_data
[2023-03-18 04:17:02,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:02,978] [INFO] Task started: CheckM
[2023-03-18 04:17:02,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a831/checkm_input OceanDNA-a831/checkm_result
[2023-03-18 04:17:23,157] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:23,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:23,159] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:23,160] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:23,160] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a831/markers.fasta)
[2023-03-18 04:17:23,161] [INFO] Task started: Blastn
[2023-03-18 04:17:23,161] [INFO] Running command: blastn -query OceanDNA-a831/markers.fasta -db /var/lib/cwl/stg6e0eb391-5941-43e3-b846-0f429de8d6ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:23,559] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:23,559] [INFO] Selected 5 target genomes.
[2023-03-18 04:17:23,559] [INFO] Target genome list was writen to OceanDNA-a831/target_genomes_gtdb.txt
[2023-03-18 04:17:23,622] [INFO] Task started: fastANI
[2023-03-18 04:17:23,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6ec906f-5052-486b-a42f-eb059f211266/OceanDNA-a831.fa --refList OceanDNA-a831/target_genomes_gtdb.txt --output OceanDNA-a831/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:17:25,241] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:25,245] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:17:25,245] [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_002730325.1	s__Nitrosopumilus sp002730325	98.1089	321	350	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018263505.1	s__Nitrosopumilus sp018263505	84.6028	286	350	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002317795.1	s__Nitrosopumilus sp002317795	82.7367	298	350	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510275.1	s__Nitrosopumilus sp001510275	82.3544	268	350	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911135.1	s__Nitrosopumilus sp013911135	81.9974	281	350	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:17:25,246] [INFO] GTDB search result was written to OceanDNA-a831/result_gtdb.tsv
[2023-03-18 04:17:25,246] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:17:25,246] [INFO] DFAST_QC result json was written to OceanDNA-a831/dqc_result.json
[2023-03-18 04:17:25,247] [INFO] DFAST_QC completed!
[2023-03-18 04:17:25,247] [INFO] Total running time: 0h0m31s