index-summary app only returns header line

[rdavison]

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

[rdavison]

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?

[ezralanglois]

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.

[rdavison]

Thanks for the quick response! This is helpful. I'll close this issue if this resolves our problem. Thank you.