Hello,
I have installed psiclass on conda.
I have used HISAT2 to align the directional RNA-Seq reads.
When running
psiclass --lb slist -p 6 --stranded fr
I get this error
/home/arolab/miniconda3/bin/junc ../M32-5-Exp2-T0.bam -a --stranded fr > ./splice/psiclass_bam_0.raw_splice
/home/arolab/miniconda3/bin/junc ../M32-5-T8H.bam -a --stranded fr > ./splice/psiclass_bam_1.raw_splice
/home/arolab/miniconda3/bin/junc ../M32-5-T8S.bam -a --stranded fr > ./splice/psiclass_bam_2.raw_splice
/home/arolab/miniconda3/bin/junc ../MT-Exp2-T0.bam -a --stranded fr > ./splice/psiclass_bam_3.raw_splice
/home/arolab/miniconda3/bin/junc ../MT-T8H.bam -a --stranded fr > ./splice/psiclass_bam_4.raw_splice
/home/arolab/miniconda3/bin/junc ../MT-T8S.bam -a --stranded fr > ./splice/psiclass_bam_5.raw_splice
/home/arolab/miniconda3/bin/junc ../P19-T8H.bam -a --stranded fr > ./splice/psiclass_bam_7.raw_splice
/home/arolab/miniconda3/bin/junc ../P19-T0.bam -a --stranded fr > ./splice/psiclass_bam_6.raw_splice
/home/arolab/miniconda3/bin/junc ../P19-T8S.bam -a --stranded fr > ./splice/psiclass_bam_8.raw_splice
/home/arolab/miniconda3/bin/junc -a --stranded fr > ./splice/psiclass_bam_9.raw_splice
/home/arolab/miniconda3/bin/trust-splice ./splice/psiclass_splice.list ../M32-5-Exp2-T0.bam > ./splice/psiclass_bam.trusted_splice
Terminated
it only generates these files in the splice folder
-rw-rw-r-- 1 arolab arolab 7430864 abr 18 14:43 psiclass_bam_0.raw_splice
-rw-rw-r-- 1 arolab arolab 8138092 abr 18 14:42 psiclass_bam_1.raw_splice
-rw-rw-r-- 1 arolab arolab 7903662 abr 18 14:44 psiclass_bam_2.raw_splice
-rw-rw-r-- 1 arolab arolab 8282401 abr 18 14:54 psiclass_bam_3.raw_splice
-rw-rw-r-- 1 arolab arolab 9182378 abr 18 14:57 psiclass_bam_4.raw_splice
-rw-rw-r-- 1 arolab arolab 8162269 abr 18 14:57 psiclass_bam_5.raw_splice
-rw-rw-r-- 1 arolab arolab 6900554 abr 18 14:59 psiclass_bam_6.raw_splice
-rw-rw-r-- 1 arolab arolab 7663008 abr 18 14:59 psiclass_bam_7.raw_splice
-rw-rw-r-- 1 arolab arolab 7600777 abr 18 15:00 psiclass_bam_8.raw_splice
-rw-rw-r-- 1 arolab arolab 23 abr 18 14:54 psiclass_bam_9.raw_splice
-rw-rw-r-- 1 arolab arolab 27 abr 18 15:00 psiclass_bam.trusted_splice
-rw-rw-r-- 1 arolab arolab 350 abr 18 15:00 psiclass_splice.list
Hello, I have installed psiclass on conda. I have used HISAT2 to align the directional RNA-Seq reads. When running psiclass --lb slist -p 6 --stranded fr
I get this error /home/arolab/miniconda3/bin/junc ../M32-5-Exp2-T0.bam -a --stranded fr > ./splice/psiclass_bam_0.raw_splice /home/arolab/miniconda3/bin/junc ../M32-5-T8H.bam -a --stranded fr > ./splice/psiclass_bam_1.raw_splice /home/arolab/miniconda3/bin/junc ../M32-5-T8S.bam -a --stranded fr > ./splice/psiclass_bam_2.raw_splice /home/arolab/miniconda3/bin/junc ../MT-Exp2-T0.bam -a --stranded fr > ./splice/psiclass_bam_3.raw_splice /home/arolab/miniconda3/bin/junc ../MT-T8H.bam -a --stranded fr > ./splice/psiclass_bam_4.raw_splice /home/arolab/miniconda3/bin/junc ../MT-T8S.bam -a --stranded fr > ./splice/psiclass_bam_5.raw_splice /home/arolab/miniconda3/bin/junc ../P19-T8H.bam -a --stranded fr > ./splice/psiclass_bam_7.raw_splice /home/arolab/miniconda3/bin/junc ../P19-T0.bam -a --stranded fr > ./splice/psiclass_bam_6.raw_splice /home/arolab/miniconda3/bin/junc ../P19-T8S.bam -a --stranded fr > ./splice/psiclass_bam_8.raw_splice /home/arolab/miniconda3/bin/junc -a --stranded fr > ./splice/psiclass_bam_9.raw_splice /home/arolab/miniconda3/bin/trust-splice ./splice/psiclass_splice.list ../M32-5-Exp2-T0.bam > ./splice/psiclass_bam.trusted_splice Terminated
it only generates these files in the splice folder -rw-rw-r-- 1 arolab arolab 7430864 abr 18 14:43 psiclass_bam_0.raw_splice -rw-rw-r-- 1 arolab arolab 8138092 abr 18 14:42 psiclass_bam_1.raw_splice -rw-rw-r-- 1 arolab arolab 7903662 abr 18 14:44 psiclass_bam_2.raw_splice -rw-rw-r-- 1 arolab arolab 8282401 abr 18 14:54 psiclass_bam_3.raw_splice -rw-rw-r-- 1 arolab arolab 9182378 abr 18 14:57 psiclass_bam_4.raw_splice -rw-rw-r-- 1 arolab arolab 8162269 abr 18 14:57 psiclass_bam_5.raw_splice -rw-rw-r-- 1 arolab arolab 6900554 abr 18 14:59 psiclass_bam_6.raw_splice -rw-rw-r-- 1 arolab arolab 7663008 abr 18 14:59 psiclass_bam_7.raw_splice -rw-rw-r-- 1 arolab arolab 7600777 abr 18 15:00 psiclass_bam_8.raw_splice -rw-rw-r-- 1 arolab arolab 23 abr 18 14:54 psiclass_bam_9.raw_splice -rw-rw-r-- 1 arolab arolab 27 abr 18 15:00 psiclass_bam.trusted_splice -rw-rw-r-- 1 arolab arolab 350 abr 18 15:00 psiclass_splice.list
could you tell me how to fix it
thanks