index-summary app only returns header line
rdavison opened this issue · 3 comments
Hi, I am using the 1.2.4 version of this package, and it seems like no matter what I do, the index-summary
app always returns only a header line. Is this the correct behavior?
For example, here is the output when I run index-summary
:
$ index-summary /run/
# Version: v1.2.4
That's the result that I get when the run
directory looks like this:
$ ls -l /run/
total 954148
-rw-rw-r-- 1 1001 1001 4608006 Jul 18 03:32 AlignmentMetricsOut.bin
-rw-rw-r-- 1 1001 1001 108605960 Jul 18 03:32 BasecallingMetricsOut.bin
drwxrwxr-x 2 1001 1001 4096 Aug 1 18:59 C5.1
-rw-rw-r-- 1 1001 1001 19493378 Jul 17 23:36 CorrectedIntMetricsOut.bin
-rw-rw-r-- 1 1001 1001 10035202 Jul 17 23:36 EmpiricalPhasingMetricsOut.bin
-rw-rw-r-- 1 1001 1001 1280006 Jul 17 23:36 ErrorMetricsOut.bin
-rw-rw-r-- 1 1001 1001 473547937 Jul 17 23:36 EventMetricsOut.bin
-rw-rw-r-- 1 1001 1001 56450 Jul 17 23:37 ExtendedTileMetricsOut.bin
-rw-rw-r-- 1 1001 1001 13923843 Jul 17 23:37 ExtractionMetricsOut.bin
-rw-rw-r-- 1 1001 1001 43552774 Jul 17 23:37 FWHMGridMetricsOut.bin
-rw-rw-r-- 1 1001 1001 11139075 Jul 17 23:37 ImageMetricsOut.bin
-rw-rw-r-- 1 1001 1001 2630409 Jul 17 23:37 InsertSizeMetricsOut.bin
drwxrwxr-x 224 1001 1001 8192 Sep 6 22:38 InterOp
-rw-rw-r-- 1 1001 1001 31366 Jul 17 23:37 OpticalMetricsOut.bin
-rw-rw-r-- 1 1001 1001 12738475 Jul 17 23:37 OpticalModelMetricsOut.bin
-rw-rw-r-- 1 1001 1001 5437835 Jul 17 23:37 PFGridMetricsOut.bin
-rw-rw-r-- 1 1001 1001 15316227 Jul 17 23:37 QMetrics2030Out.bin
-rw-rw-r-- 1 1001 1001 31981 Jul 17 23:37 QMetricsByLaneOut.bin
-rw-rw-r-- 1 1001 1001 13923853 Jul 17 23:37 QMetricsOut.bin
-rw-rw-r-- 1 1001 1001 240186333 Jul 17 23:37 RegistrationMetricsOut.bin
-rw-rw-r-- 1 1001 1001 605 Jul 17 23:43 RunCompletionStatus.xml
-rw-rw-r-- 1 1001 1001 79277 Jul 17 23:43 RunInfo.xml
-rw-rw-r-- 1 1001 1001 127554 Jul 17 23:38 RunInfoMetricsOut.bin
-rw-rw-r-- 1 1001 1001 2647 Jul 17 23:43 RunParameters.xml
-rw-rw-r-- 1 1001 1001 77791 Jul 17 23:43 SampleSheet.csv
-rw-rw-r-- 1 1001 1001 39 Jul 17 23:38 SummaryRunMetricsOut.bin
-rw-rw-r-- 1 1001 1001 141126 Jul 17 23:38 TileMetricsOut.bin
And the InterOp
directory is as follows:
$ ls -l /run/InterOp/
total 954856
-rw-rw-r-- 1 1001 1001 4608006 Jul 18 03:32 AlignmentMetricsOut.bin
-rw-rw-r-- 1 1001 1001 108605960 Jul 18 03:32 BasecallingMetricsOut.bin
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:37 C1.1
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:37 C10.1
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:37 C100.1
...snip...
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:38 C97.1
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:38 C98.1
drwxrwxr-x 2 1001 1001 4096 Sep 6 22:38 C99.1
-rw-rw-r-- 1 1001 1001 19493378 Jul 17 23:36 CorrectedIntMetricsOut.bin
-rw-rw-r-- 1 1001 1001 10035202 Jul 17 23:36 EmpiricalPhasingMetricsOut.bin
-rw-rw-r-- 1 1001 1001 1280006 Jul 17 23:36 ErrorMetricsOut.bin
-rw-rw-r-- 1 1001 1001 473547937 Jul 17 23:36 EventMetricsOut.bin
-rw-rw-r-- 1 1001 1001 56450 Jul 17 23:37 ExtendedTileMetricsOut.bin
-rw-rw-r-- 1 1001 1001 13923843 Jul 17 23:37 ExtractionMetricsOut.bin
-rw-rw-r-- 1 1001 1001 43552774 Jul 17 23:37 FWHMGridMetricsOut.bin
-rw-rw-r-- 1 1001 1001 11139075 Jul 17 23:37 ImageMetricsOut.bin
-rw-rw-r-- 1 1001 1001 2630409 Jul 17 23:37 InsertSizeMetricsOut.bin
-rw-rw-r-- 1 1001 1001 31366 Jul 17 23:37 OpticalMetricsOut.bin
-rw-rw-r-- 1 1001 1001 12738475 Jul 17 23:37 OpticalModelMetricsOut.bin
-rw-rw-r-- 1 1001 1001 5437835 Jul 17 23:37 PFGridMetricsOut.bin
-rw-rw-r-- 1 1001 1001 15316227 Jul 17 23:37 QMetrics2030Out.bin
-rw-rw-r-- 1 1001 1001 31981 Jul 17 23:37 QMetricsByLaneOut.bin
-rw-rw-r-- 1 1001 1001 13923853 Jul 17 23:37 QMetricsOut.bin
-rw-rw-r-- 1 1001 1001 240186333 Jul 17 23:37 RegistrationMetricsOut.bin
-rw-rw-r-- 1 1001 1001 127554 Jul 17 23:38 RunInfoMetricsOut.bin
-rw-rw-r-- 1 1001 1001 39 Jul 17 23:38 SummaryRunMetricsOut.bin
-rw-rw-r-- 1 1001 1001 141126 Jul 17 23:38 TileMetricsOut.bin
Hi, @ezralanglois, I saw that you were the most recent contributor. I wasn't sure if you received a notification about this issue. Just wondering if you had any perspective on this?
index-summary
requires the IndexMetricsOut.bin
. This is the only InterOp metric not produced by RTA. It is produced by bcl2fastq or bclconvert. And you have to move it into the InterOp directory yourself if you want it to be found.
If it is missing, then this behavior is expected.
Thanks for the quick response! This is helpful. I'll close this issue if this resolves our problem. Thank you.