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5.3 years ago
MS
▴
30
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
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thank you, i am new as you can understand :)
Is it possible you ran out of memory/RAM?
Try to run it again and monitor it using e.g.
htopI 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:
You are confusing RAM with hard disk.
Your error message is incomplete.
my laptop's RAM is 8 gb also so i think it shouldnt be poblem about RAM
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?
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: