[2023-03-15 20:34:26,743] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg00342682-2115-46bc-8ffc-5764a09c3235/dqc_reference
[2023-03-15 20:34:28,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,461] [INFO] Running command: cat /var/lib/cwl/stg479345c1-5cf3-444d-9ae1-615327a774a3/OceanDNA-a449.fa | prodigal -d OceanDNA-a449/cds.fna -a OceanDNA-a449/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:31,515] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:31,515] [INFO] Task started: HMMsearch
[2023-03-15 20:34:31,516] [INFO] Running command: hmmsearch --tblout OceanDNA-a449/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00342682-2115-46bc-8ffc-5764a09c3235/dqc_reference/reference_markers.hmm OceanDNA-a449/protein.faa > /dev/null
[2023-03-15 20:34:31,687] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:31,688] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg479345c1-5cf3-444d-9ae1-615327a774a3/OceanDNA-a449.fa]
[2023-03-15 20:34:31,694] [INFO] Query marker FASTA was written to OceanDNA-a449/markers.fasta
[2023-03-15 20:34:31,694] [INFO] Task started: Blastn
[2023-03-15 20:34:31,694] [INFO] Running command: blastn -query OceanDNA-a449/markers.fasta -db /var/lib/cwl/stg00342682-2115-46bc-8ffc-5764a09c3235/dqc_reference/reference_markers.fasta -out OceanDNA-a449/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:33,915] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:33,916] [INFO] Selected 0 target genomes.
[2023-03-15 20:34:33,916] [INFO] Target genome list was writen to OceanDNA-a449/target_genomes.txt
[2023-03-15 20:34:33,916] [ERROR] File is empty. [OceanDNA-a449/target_genomes.txt]
[2023-03-15 20:34:33,916] [ERROR] Task failed. No target genome found.
[2023-03-15 20:34:33,916] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:33,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00342682-2115-46bc-8ffc-5764a09c3235/dqc_reference/checkm_data
[2023-03-15 20:34:33,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:33,971] [INFO] Task started: CheckM
[2023-03-15 20:34:33,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a449/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a449/checkm_input OceanDNA-a449/checkm_result
[2023-03-15 20:34:54,983] [INFO] Task succeeded: CheckM
[2023-03-15 20:34:54,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.99%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 20:34:54,985] [INFO] ===== Completeness check finished =====
[2023-03-15 20:34:54,985] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:34:54,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a449/markers.fasta)
[2023-03-15 20:34:54,986] [INFO] Task started: Blastn
[2023-03-15 20:34:54,986] [INFO] Running command: blastn -query OceanDNA-a449/markers.fasta -db /var/lib/cwl/stg00342682-2115-46bc-8ffc-5764a09c3235/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a449/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:56,498] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:56,498] [INFO] Selected 6 target genomes.
[2023-03-15 20:34:56,499] [INFO] Target genome list was writen to OceanDNA-a449/target_genomes_gtdb.txt
[2023-03-15 20:34:56,676] [INFO] Task started: fastANI
[2023-03-15 20:34:56,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg479345c1-5cf3-444d-9ae1-615327a774a3/OceanDNA-a449.fa --refList OceanDNA-a449/target_genomes_gtdb.txt --output OceanDNA-a449/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:34:57,656] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:57,661] [INFO] Found 6 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-15 20:34:57,661] [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_000402075.1	s__Nitrosopelagicus sp000402075	96.6993	104	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	95.01	95.01	0.87	0.87	2	inconclusive
GCA_013390745.1	s__Nitrosopelagicus sp013390745	96.3066	100	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_018263495.1	s__Nitrosopelagicus sp018263495	95.8172	92	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_013390375.1	s__Nitrosopelagicus sp000484935	89.929	107	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.75	96.12	0.83	0.80	4	-
GCA_013390785.1	s__Nitrosopelagicus sp013390785	88.3415	87	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390765.1	s__Nitrosopelagicus sp013390765	87.9141	75	108	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:34:57,662] [INFO] GTDB search result was written to OceanDNA-a449/result_gtdb.tsv
[2023-03-15 20:34:57,662] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:34:57,662] [INFO] DFAST_QC result json was written to OceanDNA-a449/dqc_result.json
[2023-03-15 20:34:57,662] [INFO] DFAST_QC completed!
[2023-03-15 20:34:57,662] [INFO] Total running time: 0h0m31s