[2023-03-18 02:48:47,735] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,735] [INFO] DQC Reference Directory: /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference
[2023-03-18 02:48:49,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,548] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,548] [INFO] Running command: cat /var/lib/cwl/stg30fa289a-76de-4a6e-a623-62fe43441688/OceanDNA-a240.fa | prodigal -d OceanDNA-a240/cds.fna -a OceanDNA-a240/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:55,437] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:55,438] [INFO] Task started: HMMsearch
[2023-03-18 02:48:55,438] [INFO] Running command: hmmsearch --tblout OceanDNA-a240/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/reference_markers.hmm OceanDNA-a240/protein.faa > /dev/null
[2023-03-18 02:48:55,585] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:55,586] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg30fa289a-76de-4a6e-a623-62fe43441688/OceanDNA-a240.fa]
[2023-03-18 02:48:55,594] [INFO] Query marker FASTA was written to OceanDNA-a240/markers.fasta
[2023-03-18 02:48:55,595] [INFO] Task started: Blastn
[2023-03-18 02:48:55,595] [INFO] Running command: blastn -query OceanDNA-a240/markers.fasta -db /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/reference_markers.fasta -out OceanDNA-a240/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:56,015] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:56,015] [INFO] Selected 1 target genomes.
[2023-03-18 02:48:56,016] [INFO] Target genome list was writen to OceanDNA-a240/target_genomes.txt
[2023-03-18 02:48:56,017] [INFO] Task started: fastANI
[2023-03-18 02:48:56,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg30fa289a-76de-4a6e-a623-62fe43441688/OceanDNA-a240.fa --refList OceanDNA-a240/target_genomes.txt --output OceanDNA-a240/fastani_result.tsv --threads 1
[2023-03-18 02:48:56,300] [INFO] Task succeeded: fastANI
[2023-03-18 02:48:56,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:48:56,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:48:56,352] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:48:56,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:48:56,352] [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 zosterae	strain=NM25	GCA_003175215.1	718286	718286	type	True	76.4166	56	273	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:48:56,352] [INFO] DFAST Taxonomy check result was written to OceanDNA-a240/tc_result.tsv
[2023-03-18 02:48:56,352] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:48:56,352] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:48:56,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/checkm_data
[2023-03-18 02:48:56,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:48:56,356] [INFO] Task started: CheckM
[2023-03-18 02:48:56,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a240/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a240/checkm_input OceanDNA-a240/checkm_result
[2023-03-18 02:49:17,217] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:17,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:17,219] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:17,219] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:17,219] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a240/markers.fasta)
[2023-03-18 02:49:17,220] [INFO] Task started: Blastn
[2023-03-18 02:49:17,220] [INFO] Running command: blastn -query OceanDNA-a240/markers.fasta -db /var/lib/cwl/stga14cdf97-4bc1-47e2-be4d-cba69e5d12e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a240/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:17,631] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:17,632] [INFO] Selected 5 target genomes.
[2023-03-18 02:49:17,632] [INFO] Target genome list was writen to OceanDNA-a240/target_genomes_gtdb.txt
[2023-03-18 02:49:17,638] [INFO] Task started: fastANI
[2023-03-18 02:49:17,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg30fa289a-76de-4a6e-a623-62fe43441688/OceanDNA-a240.fa --refList OceanDNA-a240/target_genomes_gtdb.txt --output OceanDNA-a240/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:18,502] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:18,506] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:49:18,506] [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_002698885.1	s__Nitrosopelagicus sp002698885	85.1145	140	273	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	78.4725	76	273	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647405.1	s__Nitrosopelagicus sp018647405	78.4648	105	273	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_001510295.1	s__Nitrosopelagicus sp001510295	77.9814	74	273	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512865.1	s__Nitrosopelagicus sp902512865	77.8749	59	273	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:49:18,506] [INFO] GTDB search result was written to OceanDNA-a240/result_gtdb.tsv
[2023-03-18 02:49:18,507] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:18,507] [INFO] DFAST_QC result json was written to OceanDNA-a240/dqc_result.json
[2023-03-18 02:49:18,507] [INFO] DFAST_QC completed!
[2023-03-18 02:49:18,507] [INFO] Total running time: 0h0m31s