# Error in Qualimap RNA-seq QC

**URL:** https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549
**Category:** usegalaxy.org support
**Tags:** troubleshooting, quality-control
**Created:** [October 2, 2020, 12:45am UTC](https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549 "2020-10-02T00:45:43Z")
**Posts on this page:** 1
**Showing post:** 10

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### Author: ![David](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/david/32/7031_2.png) [@David](https://help.galaxyproject.org/u/David)
#### Post date: [June 4, 2021, 5:28pm UTC](https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549/10 "2021-06-04T17:28:00Z")

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@clsven  
UPDATE: The smaller datasets completed running ok in the .org instance, although it took much more time to start/complete. The bigger one is still running on .org.  
**Also there are interesting differences about the org/eu runs:**

- Eu

has `Command Line` and `Tool Standard Output` text; `Tool Standard Error` empty:

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/74beb08c333dfb618af7bcfd0d359db2681568a2.png)

- Org

has `Command Line` empty, but has `Tool Standard Output` and `Tool Standard Error` text:

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/7/7cf7846a893f50bd38f8fd36d8e02a4eeb28d21c.png)

Output values are the same:

- Eu

| Reference size | 12,567,654 |
| --- | --- |
| Number of reads | 267,167 |
| Mapped reads | 267,167 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Supplementary alignments | 1,737 / 0.65% |
| Read min/max/mean length | 30 / 151 / 94.83 |
| Overlapping read pairs | 0 / 0% |
| Duplicated reads (flagged) | 0 / 0% |
| Duplicated reads (estimated) | 48,903 / 18.3% |
| Duplication rate | 16.42% |
| Clipped reads | 143,727 / 53.8% |

- Org

| Reference size | 12,567,654 |
| --- | --- |
| Number of reads | 267,167 |
| Mapped reads | 267,167 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Supplementary alignments | 1,737 / 0.65% |
| Read min/max/mean length | 30 / 151 / 94.83 |
| Overlapping read pairs | 0 / 0% |
| Duplicated reads (flagged) | 0 / 0% |
| Duplicated reads (estimated) | 48,903 / 18.3% |
| Duplication rate | 16.42% |
| Clipped reads | 143,727 / 53.8% |

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_[View the full topic](https://help.galaxyproject.org/t/error-in-qualimap-rna-seq-qc/4549)._