Trying to get pipeline to work

[jalalsiddiqui]

I am trying to reproduce the analysis with HEK293T cells. The script used is as below:

perl samPairingCalling.test.pl
-i /fs/project/PAS1348/PARIS_stuff/pipeline_setup/HEK293T_1/HEK293T_1_trim_nodup_bc01_starSSAligned_prim_N.out_sorted.sam
-j /fs/project/PAS1348/PARIS_stuff/pipeline_setup/HEK293T_1/HEK293T_1_aligned_dr_Chimeric.out.junction
-s /fs/project/PAS1348/PARIS_stuff/pipeline_setup/HEK293T_1/HEK293T_1_aligned_dr_Chimeric.out.sam
-o /fs/project/PAS1348/PARIS_stuff/pipeline_setup/HEK293T_1/HEK293T_1_alt.geometric
-g /fs/project/PAS1348/PARIS_stuff/indexes/genome_alignment/GRCh38.p12/GRCh38.p12.genome.fa
-z /fs/project/PAS1348/PARIS_stuff/indexes/genome_alignment/GRCh38.p12/chrNameLength.txt
-t /fs/project/PAS1348/PARIS_stuff/pipeline_setup/HEK293T_1/paris_alt/gencode.v31.transcripts.fa
-l 15 -p 2 -c geometric

It appears that only the samPairingCalling.test.pl file works. However we have some potential issues that will need to be worked out before proceeding further.

The file step11_altsampaircalling.sh.e8007729 or error file has these types of errors:

Use of uninitialized value in split at samPairingCalling.test.pl line 1236

Warning! unexpected CIGAR string: 7M752N34M19S!

Input error: Chromosome chrX found in non-sequential lines. This suggests that the input file is not sorted correctly.

Differing number of BED fields encountered at line: 631157. Exiting...

***** WARNING: File tmp.68347.cluster.neg.bed has inconsistent naming convention for record:
GL000008.2 6535 6549 806307 1 -

There are more than one of these types of errors but I want to know how we can address this before proceeding further.