Question: AfterQC what is the reason killed
0
gravatar for esraesmeray1990
8 days ago by
esraesmeray19900 wrote:

When i run afterQC tool for my WTS raw data suddenly it just wrote killed . there is not any warning etc. what could be the reason?

esra@asus:/media/esra/Seagate Expansion Drive/try-1$ pypy /home/esra/AfterQC/after.py -1 R1.fq.gz -2 R_2.fq.gz
R1.fq.gz options:
{'read1_file': 'R1.fq.gz', 'read2_file': 'R2.fq.gz', 'index1_file': None, 'index2_file': None, 'input_dir': None, 'good_output_folder': 'good', 'bad_output_folder': None, 'report_output_folder': None, 'read1_flag': 'R1', 'read2_flag': 'R2', 'index1_flag': 'I1', 'index2_flag': 'I2', 'trim_front': 9, 'trim_tail': 0, 'trim_pair_same': True, 'qualified_quality_phred': 15, 'unqualified_base_limit': 60, 'poly_size_limit': 35, 'allow_mismatch_in_poly': 2, 'n_base_limit': 5, 'seq_len_req': 35, 'debubble': False, 'debubble_dir': 'debubble', 'draw': True, 'barcode': False, 'barcode_length': 12, 'barcode_flag': 'barcode', 'barcode_verify': 'CAGTA', 'store_overlap': False, 'overlap_output_folder': None, 'qc_only': False, 'qc_sample': 200000, 'qc_kmer': 8, 'no_correction': False, 'mask_mismatch': False, 'no_overlap': False, 'gzip': False, 'compression': 2, 'version': '0.9.6', 'trim_front2': 9, 'trim_tail2': 0}

Killed
alignment sequence • 87 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by esraesmeray19900

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ADD REPLYlink written 8 days ago by WouterDeCoster35k

thank you, i am new as you can understand :)

ADD REPLYlink written 8 days ago by esraesmeray19900

Is it possible you ran out of memory/RAM?

Try to run it again and monitor it using e.g. htop

ADD REPLYlink written 8 days ago by WouterDeCoster35k

I think its about memory. i tried htop. but it was okay before. I am using 250 gb SSD but as i know Afterqc needs just 4 gb? how should i run afterqc?

and now i took that outpıut:

Traceback (most recent call last):
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 228, in <module>
    main()
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 222, in main
    processOptions(options)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 175, in processOptions
    filter.run()
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/preprocesser.py", line 620, in run
    self.writeReads(r1, r2, i1, i2, good_read1_file, good_read2_file, good_index1_file, good_index2_file, None)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/preprocesser.py", line 214, in writeReads
    r1_file.writeLines(r1)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/fastq.py", line 92, in writeLines
    self.__file.write(line+"\n")
  File "/usr/lib/pypy/lib-python/2.7/gzip.py", line 241, in write
    self.fileobj.write(self.compress.compress(data))
ADD REPLYlink written 3 days ago by esraesmeray19900

250 gb SSD but as i know Afterqc needs just 4 gb

You are confusing RAM with hard disk.

Your error message is incomplete.

ADD REPLYlink modified 3 days ago • written 3 days ago by WouterDeCoster35k

my laptop's RAM is 8 gb also so i think it shouldnt be poblem about RAM

ADD REPLYlink modified 2 days ago • written 2 days ago by esraesmeray19900

did it create an error file or log file in your directory with any more information?

How big are your fastq files, and what are your system resources?

ADD REPLYlink written 8 days ago by jrj.healey9.8k

No it didnt. I think problem is about memory. but it was okay before I am using 250 gb SSD now, but as i know Afterqc needs just 4 gb? how should i run afterqc?

and now i took that output:

Traceback (most recent call last):
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 228, in <module>
    main()
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 222, in main
    processOptions(options)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/bin/after.py", line 175, in processOptions
    filter.run()
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/preprocesser.py", line 620, in run
    self.writeReads(r1, r2, i1, i2, good_read1_file, good_read2_file, good_index1_file, good_index2_file, None)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/preprocesser.py", line 214, in writeReads
    r1_file.writeLines(r1)
  File "/home/esra/anaconda3/pkgs/afterqc-0.9.7-py27_2/share/afterqc-0.9.7-2/fastq.py", line 92, in writeLines
    self.__file.write(line+"\n")
  File "/usr/lib/pypy/lib-python/2.7/gzip.py", line 241, in write
    self.fileobj.write(self.compress.compress(data))
ADD REPLYlink written 3 days ago by esraesmeray19900
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