[2023-03-18 08:42:34,373] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:42:34,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:42:34,373] [INFO] DQC Reference Directory: /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference
[2023-03-18 08:42:35,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:42:35,489] [INFO] Task started: Prodigal
[2023-03-18 08:42:35,489] [INFO] Running command: cat /var/lib/cwl/stgda1de2f2-8bae-429b-89f5-16a07a53ee39/OceanDNA-a464.fa | prodigal -d OceanDNA-a464/cds.fna -a OceanDNA-a464/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:39,128] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:39,129] [INFO] Task started: HMMsearch
[2023-03-18 08:42:39,129] [INFO] Running command: hmmsearch --tblout OceanDNA-a464/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/reference_markers.hmm OceanDNA-a464/protein.faa > /dev/null
[2023-03-18 08:42:39,249] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:39,250] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgda1de2f2-8bae-429b-89f5-16a07a53ee39/OceanDNA-a464.fa]
[2023-03-18 08:42:39,258] [INFO] Query marker FASTA was written to OceanDNA-a464/markers.fasta
[2023-03-18 08:42:39,259] [INFO] Task started: Blastn
[2023-03-18 08:42:39,259] [INFO] Running command: blastn -query OceanDNA-a464/markers.fasta -db /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/reference_markers.fasta -out OceanDNA-a464/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:39,677] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:39,677] [INFO] Selected 2 target genomes.
[2023-03-18 08:42:39,678] [INFO] Target genome list was writen to OceanDNA-a464/target_genomes.txt
[2023-03-18 08:42:39,679] [INFO] Task started: fastANI
[2023-03-18 08:42:39,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1de2f2-8bae-429b-89f5-16a07a53ee39/OceanDNA-a464.fa --refList OceanDNA-a464/target_genomes.txt --output OceanDNA-a464/fastani_result.tsv --threads 1
[2023-03-18 08:42:40,192] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:40,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:40,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:40,197] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:40,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:42:40,197] [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	77.0439	58	212	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	76.9575	51	212	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:42:40,197] [INFO] DFAST Taxonomy check result was written to OceanDNA-a464/tc_result.tsv
[2023-03-18 08:42:40,197] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:40,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:40,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/checkm_data
[2023-03-18 08:42:40,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:40,209] [INFO] Task started: CheckM
[2023-03-18 08:42:40,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a464/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a464/checkm_input OceanDNA-a464/checkm_result
[2023-03-18 08:42:55,883] [INFO] Task succeeded: CheckM
[2023-03-18 08:42:55,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:42:55,885] [INFO] ===== Completeness check finished =====
[2023-03-18 08:42:55,885] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:42:55,885] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a464/markers.fasta)
[2023-03-18 08:42:55,886] [INFO] Task started: Blastn
[2023-03-18 08:42:55,886] [INFO] Running command: blastn -query OceanDNA-a464/markers.fasta -db /var/lib/cwl/stg208d341a-f376-4996-a6d3-bd0969dab034/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a464/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:56,270] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:56,271] [INFO] Selected 5 target genomes.
[2023-03-18 08:42:56,271] [INFO] Target genome list was writen to OceanDNA-a464/target_genomes_gtdb.txt
[2023-03-18 08:42:56,277] [INFO] Task started: fastANI
[2023-03-18 08:42:56,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgda1de2f2-8bae-429b-89f5-16a07a53ee39/OceanDNA-a464.fa --refList OceanDNA-a464/target_genomes_gtdb.txt --output OceanDNA-a464/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:42:57,196] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:57,200] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:42:57,200] [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_001627235.1	s__Nitrosopelagicus sp001627235	96.2012	189	212	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.70	95.15	0.86	0.83	5	conclusive
GCF_000812185.1	s__Nitrosopelagicus brevis	84.397	195	212	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	-
GCA_902511735.1	s__Nitrosopelagicus sp902511735	84.1734	118	212	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	83.3568	177	212	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCA_902512865.1	s__Nitrosopelagicus sp902512865	83.2576	94	212	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 08:42:57,200] [INFO] GTDB search result was written to OceanDNA-a464/result_gtdb.tsv
[2023-03-18 08:42:57,200] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:42:57,201] [INFO] DFAST_QC result json was written to OceanDNA-a464/dqc_result.json
[2023-03-18 08:42:57,201] [INFO] DFAST_QC completed!
[2023-03-18 08:42:57,201] [INFO] Total running time: 0h0m23s