Input file does not exist

[Mic L]

Hi,   

I have recieved the following error with running the code below code:

  ...

  bowtie2 -x /home/galaxy/Downloads/kumaran/Bactrocera_tryoni -1 /home/galaxy/Downloads/kumaran/reads/CLI-R-B1/CLI-R_S7_L004_R1_001.fastq.gz -2 /home/galaxy/Downloads/kumaran/reads/CLI-R-B1/CLI-R_S7_L004_R2_001.fastq.gz  --rg-id CLI-R_S7_L004 --rg SM:CLI-R_S7_L004 --rg LB:CLI-R_S7_L004 --rg PL:ILLUMINA | samtools view -bS - | samtools sort - /home/galaxy/Downloads/kumaran/reads/CLI-R-B1//home/galaxy/Downloads/kumaran/alignments/CLI-R_S7_L004.sorted

  Completed Task = 'run_bwa' 

  Task enters queue = 'mergeBams' 

  Traceback (most recent call last):

    File "/home/galaxy/PycharmProjects/chip-seq/pipeline.py", line 48, in <module>

      pipeline_run([mergeBams], multithread = 5)

    File "/home/galaxy/.local/lib/python2.7/site-packages/ruffus/task.py", line 5916, in pipeline_run

      raise job_errors

  ruffus.ruffus_exceptions.RethrownJobError: 

            

  Original exception:

      Exception #1

'<class 'ruffus.ruffus_exceptions.RethrownJobError'>

 

 Exceptions generating parameters for

 

 task = 'mergeBams'

 

      Original exception:

      

 Exception #1

   'ruffus.ruffus_exceptions.MissingInputFileError(    

     

     

     No way to run job: Input file '/home/galaxy/Downloads/kumaran/reads/C5-B1-32237239//home/galaxy/Downloads/kumaran/alignments/C5-B1_S5_L001.sorted' does not exist)' raised in ...

   Task = def mergeBams(...)

This is is the code:

  from ruffus import *

  from collections import defaultdict

  from glob import glob

  import os

  data_files = glob("/home/galaxy/Downloads/kumaran/reads/*/*.fastq.gz")

  sambam_dir = "/home/galaxy/Downloads/kumaran/alignments"

  fastq_metadata = defaultdict(dict)

  ref = "/home/galaxy/Downloads/kumaran/Bactrocera_tryoni"

  def make_rg(metadata):

      return " --rg-id %s --rg SM:%s --rg LB:%s --rg PL:ILLUMINA" % (metadata, metadata, metadata)

  @collate(data_files, regex(r"([^/]+)(_R1|_R2)\_001.fastq.gz"),

 [r"%s/\1.sorted" % sambam_dir, r"%s/\1.bwaPE.Success" % sambam_dir])

  def run_bwa(inputs, outputs):

      """

      Aligns two paired-end fastq files to a reference genome to produce a sam file.

      """

      seq1, seq2 = sorted(inputs)

      output, flag_file = outputs

      rg = make_rg(os.path.basename(os.path.splitext(os.path.splitext(output)[0])[0]))

      cmd = "bowtie2 -x %s -1 %s -2 %s %s | samtools view -bS - | samtools sort - %s" \

   % (ref, seq1, seq2, rg, output)

      print cmd

      # if not os.system(cmd):

      #     #   It worked: Create completion flag_file

      #     open(flag_file, "w")

  # Merge all the sorted BAM alignments.

  @merge(run_bwa, regex(r"([^/]+).sorted.bam"), r"\1/all_reads_aligned.sorted.bam")

  def mergeBams(sortedBams, output):

      bams = ' '.join(sortedBams)

      print bams, output

What did I do wrong?

Mic