Dataset Information
| Number | 12 |
|---|---|
| Name | SRR11532725:reverse |
| Created | Wednesday Mar 18th 14:25:37 2026 GMT+5:30 |
| Filesize | 6.4 MB |
| Dbkey | ? |
| Format | fastqsanger.gz |
| File contents | contents |
Tool Parameters
| Input Parameter | Value |
|---|---|
| select input type | accession_number |
| Accession | SRR11532725 |
I received the below error when running for the above input data. Kindly suggest.
Why Trimmomatic Might Fail
Trimmomatic is a Java‐based read‑trimming tool. When it “did not finish successfully” Galaxy usually captures the stderr output and shows a generic Tool failed message.
Typical reasons for a failure are:
| Category | What usually goes wrong | How it shows up in the log |
|---|---|---|
| Input files | • Wrong file type (e.g., FASTA instead of FASTQ) • Corrupted or empty file • Mismatched read‑pair files (different number of reads) |
Error: Input file is not a valid FASTQ file, java.io.IOException: Stream closed |
| Adapter / reference files | • Path to adapter list not supplied or does not exist • Wrong format (FASTA instead of plain text list) |
FileNotFoundException or IllegalArgumentException |
| Java memory / JVM options | • Not enough RAM for the dataset (especially large paired‑end libraries) | java.lang.OutOfMemoryError: Java heap space |
| Command‑line arguments | • Invalid parameter values (e.g., negative trim length) • Missing required option |
IllegalArgumentException |
| Disk space / I/O | • No free space in Galaxy’s temporary directory • Permissions problems on the output location |
No space left on device, Permission denied |
| Tool version mismatch | • Using an outdated Trimmomatic wrapper that expects a different version of the JAR | Version‑specific error messages |
Because you only see the generic “Trimmomatic did not finish successfully” message, we need to look at the tool log to know which of the above (or something else) triggered the failure.