AfterQC what is the reason killed

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

sequence alignment

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written 7.6 years ago by MS •

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written 7.6 years ago by WouterDeCoster

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

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written 7.6 years ago by MS •

Is it possible you ran out of memory/RAM?

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

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written 7.6 years ago by WouterDeCoster

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))

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written 7.6 years ago by MS •

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

You are confusing RAM with hard disk.

Your error message is incomplete.

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written 7.6 years ago by WouterDeCoster

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

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written 7.6 years ago by MS •

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?

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written 7.6 years ago by Joe

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))

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written 7.6 years ago by MS •

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