Luigi Error NGS pipeline ?

Question

[pinn]

Hi, can anyone help me , why it is showing error ?

$ python Luigipipeline.py --local-scheduler Custom_Genome_Pipeline

Output:

====== Running BWA ======
INFO: [pid 18146] Worker Worker(salt=235547989, workers=1, host=Curium, username=likith_reddy, pid=18146) done Bwa_Mem(sample=SRR098401testsickle_1.fastq)
DEBUG: 1 running tasks, waiting for next task to finish
INFO: Informed scheduler that task Bwa_Mem_SRR098401testsic_c845cfe3a6 has status DONE
DEBUG: Asking scheduler for work...
DEBUG: Pending tasks: 11
INFO: [pid 18146] Worker Worker(salt=235547989, workers=1, host=Curium, username=likith_reddy, pid=18146) running Convert_Sam_Bam(sample=SRR098401testsickle_1.fastq)
ERROR: [pid 18146] Worker Worker(salt=235547989, workers=1, host=Curium, username=likith_reddy, pid=18146) failed Convert_Sam_Bam(sample=SRR098401testsickle_1.fastq)
Traceback (most recent call last):
File "/home/likith_reddy/.local/lib/python2.7/site-packages/luigi/worker.py", line 194, in run
new_deps = self._run_get_new_deps()
File "/home/likith_reddy/.local/lib/python2.7/site-packages/luigi/worker.py", line 131, in _run_get_new_deps
task_gen = self.task.run()
File "Luigipipeline.py", line 60, in run
"sam/"+self.sample+".sam"])
File "Luigipipeline.py", line 15, in run_cmd
p = subprocess.Popen(cmd, shell=False, universal_newlines=True, stdout=subprocess.PIPE)
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
DEBUG: 1 running tasks, waiting for next task to finish
INFO: Informed scheduler that task Convert_Sam_Bam_SRR098401testsic_c845cfe3a6 has status FAILED
DEBUG: Asking scheduler for work...
DEBUG: Done
DEBUG: There are no more tasks to run at this time
DEBUG: There are 11 pending tasks possibly being run by other workers
DEBUG: There are 11 pending tasks unique to this worker
DEBUG: There are 11 pending tasks last scheduled by this worker
INFO: Worker Worker(salt=235547989, workers=1, host=Curium, username=likith_reddy, pid=18146) was stopped. Shutting down Keep-Alive thread
INFO:
===== Luigi Execution Summary =====

Scheduled 13 tasks of which:

    2 ran successfully:
        2 Bwa_Mem(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)
    2 failed:
        2 Convert_Sam_Bam(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)
    9 were left pending, among these:
        9 had failed dependencies:
            2 Call_Variant(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)
            2 Convert_Bcf_Vcf(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)
            1 Custom_Genome_Pipeline()
            2 Index_Bam(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)
            2 Sort_Bam(sample=SRR098401testsickle_1.fastq,SRR098401testsickle_2.fastq)

This progress looks :( because there were failed tasks

[Devon Ryan]

Apparently your Convert_Sam_Bam command has issues.

[pinn]

thanks for your reply

[cpad0112]

check also this: OSError: [Errno 2] No such file or directory