**10**wrote:

Hello, I have ran into to various problems in the HISAT-StringTie pipeline and have traced it back to incomplete SAM file output from the initial mapping. I generated the indicies myself (job out complete and gave 8 .ht2 files of binary content). My read files are called in .gz archive file format and contain reads in the expected format. The job "successfully" completes (output below) but my out sam files look like this (the entire file is in this format- I have also ran this minus the ERCC seqs and get the same output):

```
@HD VN:1.0 SO:unsorted
@SQ SN:ERCC-00002 LN:1061
@SQ SN:ERCC-00003 LN:1023
@SQ SN:ERCC-00004 LN:523
@SQ SN:ERCC-00009 LN:984
@SQ SN:ERCC-00012 LN:994
@SQ SN:ERCC-00013 LN:808
@SQ SN:ERCC-00014 LN:1957
@SQ SN:ERCC-00016 LN:844
@SQ SN:ERCC-00017 LN:1136
@SQ SN:ERCC-00019 LN:644
```

I cannot find a similar problem but perhaps you might be able to point me in the right direction?

Thanks in advance

I'm running the command:

```
hisat2 -p 8 --dta -x indexes/genome_ERCC92_tran -1 readfiles/readfile_r1.fastq.gz
-2 readfiles/readfile_r2.fastq.gz
-U readfiles/readfile_r0.fastq.gz
-S 21divv1.sam
```

with memory request

```
#$ -pe smp-verbose 8
#$ -l h_vmem=125G
#$ -l himem=true
```

My job file shows:

```
182087500 reads; of these:
171955418 (94.44%) were paired; of these:
45539147 (26.48%) aligned concordantly 0 times
93921035 (54.62%) aligned concordantly exactly 1 time
32495236 (18.90%) aligned concordantly >1 times
----
45539147 pairs aligned concordantly 0 times; of these:
2017830 (4.43%) aligned discordantly 1 time
----
43521317 pairs aligned 0 times concordantly or discordantly; of these:
87042634 mates make up the pairs; of these:
77335867 (88.85%) aligned 0 times
6644882 (7.63%) aligned exactly 1 time
3061885 (3.52%) aligned >1 times
10132082 (5.56%) were unpaired; of these:
2937197 (28.99%) aligned 0 times
4468634 (44.10%) aligned exactly 1 time
2726251 (26.91%) aligned >1 times
77.33% overall alignment rate
```