[2023-03-19 04:11:06,926] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg80af3f1e-6b46-4589-af74-a74a3281c61b/dqc_reference
[2023-03-19 04:11:08,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,641] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,641] [INFO] Running command: cat /var/lib/cwl/stg6b889f4c-c413-4e32-8f51-b87d03e65169/OceanDNA-a96.fa | prodigal -d OceanDNA-a96/cds.fna -a OceanDNA-a96/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:11,867] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:11,868] [INFO] Task started: HMMsearch
[2023-03-19 04:11:11,868] [INFO] Running command: hmmsearch --tblout OceanDNA-a96/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80af3f1e-6b46-4589-af74-a74a3281c61b/dqc_reference/reference_markers.hmm OceanDNA-a96/protein.faa > /dev/null
[2023-03-19 04:11:11,989] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:11,990] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6b889f4c-c413-4e32-8f51-b87d03e65169/OceanDNA-a96.fa]
[2023-03-19 04:11:11,995] [INFO] Query marker FASTA was written to OceanDNA-a96/markers.fasta
[2023-03-19 04:11:11,996] [INFO] Task started: Blastn
[2023-03-19 04:11:11,996] [INFO] Running command: blastn -query OceanDNA-a96/markers.fasta -db /var/lib/cwl/stg80af3f1e-6b46-4589-af74-a74a3281c61b/dqc_reference/reference_markers.fasta -out OceanDNA-a96/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:14,083] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:14,083] [INFO] Selected 0 target genomes.
[2023-03-19 04:11:14,084] [INFO] Target genome list was writen to OceanDNA-a96/target_genomes.txt
[2023-03-19 04:11:14,084] [ERROR] File is empty. [OceanDNA-a96/target_genomes.txt]
[2023-03-19 04:11:14,084] [ERROR] Task failed. No target genome found.
[2023-03-19 04:11:14,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:14,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80af3f1e-6b46-4589-af74-a74a3281c61b/dqc_reference/checkm_data
[2023-03-19 04:11:14,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:14,133] [INFO] Task started: CheckM
[2023-03-19 04:11:14,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a96/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a96/checkm_input OceanDNA-a96/checkm_result
[2023-03-19 04:11:34,762] [INFO] Task succeeded: CheckM
[2023-03-19 04:11:34,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.44%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 04:11:34,763] [INFO] ===== Completeness check finished =====
[2023-03-19 04:11:34,764] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:11:34,764] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a96/markers.fasta)
[2023-03-19 04:11:34,766] [INFO] Task started: Blastn
[2023-03-19 04:11:34,766] [INFO] Running command: blastn -query OceanDNA-a96/markers.fasta -db /var/lib/cwl/stg80af3f1e-6b46-4589-af74-a74a3281c61b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a96/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:35,468] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:35,468] [INFO] Selected 5 target genomes.
[2023-03-19 04:11:35,469] [INFO] Target genome list was writen to OceanDNA-a96/target_genomes_gtdb.txt
[2023-03-19 04:11:35,530] [INFO] Task started: fastANI
[2023-03-19 04:11:35,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b889f4c-c413-4e32-8f51-b87d03e65169/OceanDNA-a96.fa --refList OceanDNA-a96/target_genomes_gtdb.txt --output OceanDNA-a96/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:11:36,291] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:36,296] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:11:36,296] [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_013390765.1	s__Nitrosopelagicus sp013390765	81.7235	57	126	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390785.1	s__Nitrosopelagicus sp013390785	81.1126	82	126	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390745.1	s__Nitrosopelagicus sp013390745	81.0047	89	126	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578515.1	s__Nitrosopelagicus sp902578515	79.7991	59	126	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	96.49	96.49	0.54	0.54	2	-
GCA_902606965.1	s__Nitrosopelagicus sp902606965	79.6401	58	126	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:11:36,296] [INFO] GTDB search result was written to OceanDNA-a96/result_gtdb.tsv
[2023-03-19 04:11:36,296] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:11:36,297] [INFO] DFAST_QC result json was written to OceanDNA-a96/dqc_result.json
[2023-03-19 04:11:36,297] [INFO] DFAST_QC completed!
[2023-03-19 04:11:36,297] [INFO] Total running time: 0h0m29s