Hi I am running the following on my MiniKNOW (albacore) fast5 files from a direct RNA seq run but Poreplex errors out:
poreplex -i . -o /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/ --trim-adapter --keep-unsplit -p 38
It states no basecalled files are found... but these are basecalled fast5 files - direct output from my MinION run. Here is the log file:
2018-10-01 13:51:53,768 Starting poreplex version 0.1
2018-10-01 13:51:53,768 Command line: /home/sdunaj/.local/bin/poreplex -i . -o /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/ --trim-adapter --keep-unsplit -p 38 --b
asecall
2018-10-01 13:51:53,768 == Analysis settings ======================================
2018-10-01 13:51:53,768 Input: .
2018-10-01 13:51:53,769 Output: /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/
2018-10-01 13:51:53,769 Processes: 38
2018-10-01 13:51:53,769 Presets: rna-r941.cfg
2018-10-01 13:51:53,769 Basecall on-the-fly: Yes (albacore 2.3.3)
2018-10-01 13:51:53,769 Trim 3' adapter: Yes
2018-10-01 13:51:53,769 Filter concatenated read: No
2018-10-01 13:51:53,769 Separate by barcode: No
2018-10-01 13:51:53,769 Real-time alignment: No
2018-10-01 13:51:53,769 FASTQ in output: Yes
2018-10-01 13:51:53,769 FAST5 in output: No
2018-10-01 13:51:53,769 Basecall table in output: No
2018-10-01 13:51:53,769 ===========================================================
2018-10-01 13:51:53,769
2018-10-01 13:53:55,750 Finished.
Hi I am running the following on my MiniKNOW (albacore) fast5 files from a direct RNA seq run but Poreplex errors out: poreplex -i . -o /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/ --trim-adapter --keep-unsplit -p 38
It states no basecalled files are found... but these are basecalled fast5 files - direct output from my MinION run. Here is the log file:
2018-10-01 13:51:53,768 Starting poreplex version 0.1 2018-10-01 13:51:53,768 Command line: /home/sdunaj/.local/bin/poreplex -i . -o /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/ --trim-adapter --keep-unsplit -p 38 --b asecall 2018-10-01 13:51:53,768 == Analysis settings ====================================== 2018-10-01 13:51:53,768 Input: . 2018-10-01 13:51:53,769 Output: /prod/Nanopore_Seq_Data/20181001_Sept17_18_2018_Trimmed_Fastq/ 2018-10-01 13:51:53,769 Processes: 38 2018-10-01 13:51:53,769 Presets: rna-r941.cfg 2018-10-01 13:51:53,769 Basecall on-the-fly: Yes (albacore 2.3.3) 2018-10-01 13:51:53,769 Trim 3' adapter: Yes 2018-10-01 13:51:53,769 Filter concatenated read: No 2018-10-01 13:51:53,769 Separate by barcode: No 2018-10-01 13:51:53,769 Real-time alignment: No 2018-10-01 13:51:53,769 FASTQ in output: Yes 2018-10-01 13:51:53,769 FAST5 in output: No 2018-10-01 13:51:53,769 Basecall table in output: No 2018-10-01 13:51:53,769 =========================================================== 2018-10-01 13:51:53,769 2018-10-01 13:53:55,750 Finished.
Thank you!