[2023-03-18 21:07:03,638] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:07:03,638] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:07:03,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference
[2023-03-18 21:07:05,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:07:05,389] [INFO] Task started: Prodigal
[2023-03-18 21:07:05,389] [INFO] Running command: cat /var/lib/cwl/stgd3bc9a56-cb6b-4349-8b91-0f3555f7618a/OceanDNA-a480.fa | prodigal -d OceanDNA-a480/cds.fna -a OceanDNA-a480/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:07:08,938] [INFO] Task succeeded: Prodigal
[2023-03-18 21:07:08,939] [INFO] Task started: HMMsearch
[2023-03-18 21:07:08,939] [INFO] Running command: hmmsearch --tblout OceanDNA-a480/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/reference_markers.hmm OceanDNA-a480/protein.faa > /dev/null
[2023-03-18 21:07:09,126] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:07:09,126] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd3bc9a56-cb6b-4349-8b91-0f3555f7618a/OceanDNA-a480.fa]
[2023-03-18 21:07:09,134] [INFO] Query marker FASTA was written to OceanDNA-a480/markers.fasta
[2023-03-18 21:07:09,136] [INFO] Task started: Blastn
[2023-03-18 21:07:09,136] [INFO] Running command: blastn -query OceanDNA-a480/markers.fasta -db /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/reference_markers.fasta -out OceanDNA-a480/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:07:11,924] [INFO] Task succeeded: Blastn
[2023-03-18 21:07:11,925] [INFO] Selected 2 target genomes.
[2023-03-18 21:07:11,925] [INFO] Target genome list was writen to OceanDNA-a480/target_genomes.txt
[2023-03-18 21:07:11,929] [INFO] Task started: fastANI
[2023-03-18 21:07:11,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3bc9a56-cb6b-4349-8b91-0f3555f7618a/OceanDNA-a480.fa --refList OceanDNA-a480/target_genomes.txt --output OceanDNA-a480/fastani_result.tsv --threads 1
[2023-03-18 21:07:12,506] [INFO] Task succeeded: fastANI
[2023-03-18 21:07:12,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:07:12,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:07:12,517] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:07:12,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:07:12,517] [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	76.6576	53	233	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:07:12,517] [INFO] DFAST Taxonomy check result was written to OceanDNA-a480/tc_result.tsv
[2023-03-18 21:07:12,517] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:07:12,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:07:12,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/checkm_data
[2023-03-18 21:07:12,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:07:12,520] [INFO] Task started: CheckM
[2023-03-18 21:07:12,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a480/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a480/checkm_input OceanDNA-a480/checkm_result
[2023-03-18 21:07:30,475] [INFO] Task succeeded: CheckM
[2023-03-18 21:07:30,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:07:30,477] [INFO] ===== Completeness check finished =====
[2023-03-18 21:07:30,478] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:07:30,478] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a480/markers.fasta)
[2023-03-18 21:07:30,479] [INFO] Task started: Blastn
[2023-03-18 21:07:30,479] [INFO] Running command: blastn -query OceanDNA-a480/markers.fasta -db /var/lib/cwl/stgcb5f40c8-541b-4e75-92b9-be5256f51da3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a480/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:07:31,026] [INFO] Task succeeded: Blastn
[2023-03-18 21:07:31,027] [INFO] Selected 5 target genomes.
[2023-03-18 21:07:31,027] [INFO] Target genome list was writen to OceanDNA-a480/target_genomes_gtdb.txt
[2023-03-18 21:07:31,033] [INFO] Task started: fastANI
[2023-03-18 21:07:31,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3bc9a56-cb6b-4349-8b91-0f3555f7618a/OceanDNA-a480.fa --refList OceanDNA-a480/target_genomes_gtdb.txt --output OceanDNA-a480/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:07:31,793] [INFO] Task succeeded: fastANI
[2023-03-18 21:07:31,797] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:07:31,797] [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	98.2687	150	233	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001510295.1	s__Nitrosopelagicus sp001510295	78.0461	74	233	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	77.7871	58	233	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	77.6311	77	233	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627235.1	s__Nitrosopelagicus sp001627235	77.4801	99	233	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.70	95.15	0.86	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-18 21:07:31,797] [INFO] GTDB search result was written to OceanDNA-a480/result_gtdb.tsv
[2023-03-18 21:07:31,797] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:07:31,798] [INFO] DFAST_QC result json was written to OceanDNA-a480/dqc_result.json
[2023-03-18 21:07:31,798] [INFO] DFAST_QC completed!
[2023-03-18 21:07:31,798] [INFO] Total running time: 0h0m28s