Table 2. XPRESSpipe sub-module statistics for dataset GSE65778.
| Process | Command | Wallclock Time | Max RAM |
|---|---|---|---|
| Curate STAR reference | curateReference | 00h 38m 34s | 34.03 GB |
| Truncate GTF | modifyGTF -t | 00h 03m 40s | 03.27 GB |
| Read Pre-processing | trim | 00h 08m 50s | 00.48 GB |
| Alignment / Post-processing | align | 07h 57m 44s | 38.03 GB |
| Read Quantification | count -c htseq | 03h 13m 04s | 00.16 GB |
| Isoform Abundance | count -c cufflinks | 00h 56m 44s | 02.36 GB |
| Differential Expression (n = 9) | diffxpress | 00h 07m 50s | 00.65 GB |
| Read Distributions | readDistribution | 00h 05m 00s | 00.28 GB |
| Metagene Analysis | metagene | 01h 45m 35s | 35.52 GB |
| Gene Coverage (n = 1) | geneCoverage | 01h 24m 00s | 19.32 GB |
| Periodicity | periodicity | 01h 08m 22s | 54.16 GB |
| Library Complexity | complexity | 01h 02m 57s | 01.52 GB |
| rRNA probe | rrnaProbe | 00h 00m 55s | 00.15 GB |
| Pipeline | riboseq | 16h 46m 19s | 54.16 GB |
| Attribute | Value | ||
| Total Raw Input | 257 GB | ||
| Total Output | 500 GB | ||
| Allocated Virtual CPUs | 32 | ||
| Minimum Allocated Memory | 62.50 GB | ||
The geneCoverage module was performed using a high-coverage gene. While some memory footprints are large in this test case, steps will scale based on available user resources. Input raw FASTQ files were uncompressed. The metagene and geneCoverage sub-modules used a conservative BAM file multiprocessing limit to avoid out-of-memory errors. XPRESSpipe v0.3.1 was used to generate these statistics.