Self Test Script Fail - [samopen] no @SQ lines in the header.

[stone84]

Hi to all,

I've to issues When I execute the Self Test of Pipe. The first part of it, the "mutation detection test" finishes without problem.
After this, cpipe continue the test with the recall precision test. At this point, at the stage "Stage align_bwa [NA12878CHR22_L001] " the test fails with this report:

_========= Stage align_bwa [NA12878CHR22_L001] ===================
[bam_header_read] EOF marker is absent. The input is probably truncated.
[M::main_mem] read 509156 sequences (50000164 bp)...
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Cleaned up file align/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam to .bpipe/trash/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam
ERROR: Command failed with exit status = 1 : 

set -o pipefail;  /home/pmirabelli/cpipe2017/cpipe/tools/bwa/0.7.5a/bwa mem -M -t 5 -k 19                           -R "@RG\tID:NA12878CHR22_L001\tPL:illumina\tPU:1\tLB:null\tSM:NA12878CHR22"
                            /home/pmirabelli/cpipe2017/cpipe/hg19/ucsc.hg19.fasta /home/pmirabelli/cpipe2017/cpipe/batches/recall_precision_test/data/NA12878CHR22_L001_R1.fastq.gz /home/pmirabelli/cpipe2017/cpipe/batches/recall_precision_test/data/NA12878CHR22_L001_R2.fastq.gz | 
                          /home/pmirabelli/cpipe2017/cpipe/tools/samtools/0.1.19/samtools view -F 0x100 -bSu - | /home/pmirabelli/cpipe2017/cpipe/tools/samtools/0.1.19/samtools sort - align/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001_

How I can fix these error? How can be correct the absence of the header?

Thanks