[khmer] InvalidFASTQFileFormat

[Shaolin Wang]

I am new, please help, I got InvalidFASTQFileFormat error, the sequence
looks fine, even after I remove that sequence, it still shows the error,
and the error always show on line 16181.

[17:27:40]sw4ed at hpcserver:~/Meta/SoilMeta> load-into-counting.py -T 4 -k 20
 -N 4 -x 4e9 Sample_2024-1F_1.kh Sample_2024-1F_1.trimmed.fastq

PARAMETERS:
 - kmer size =    20            (-k)
 - n hashes =     4             (-N)
 - min hashsize = 4e+09         (-x)

Estimated memory usage is 1.6e+10 bytes (n_hashes x min_hashsize)
--------
Saving hashtable to Sample_2024-1F_1.kh
Loading kmers from sequences in ['Sample_2024-1F_1.trimmed.fastq']
making hashtable
consuming input Sample_2024-1F_1.trimmed.fastq
terminate called after throwing an instance of
'khmer::read_parsers::InvalidFASTQFileFormat'
  what():  InvalidFASTQFileFormat: illegal sequence letters:
@HISEQ700708:147:D278GACXX:2:1101:6816:3815 2:N:0:ATCACG
Aborted (core dumped)

[17:44:12]sw4ed at hpcserver:~/Meta/SoilMeta> sed -n '16181,16188p'
Sample_2024-1F_1.trimmed.fastq
@HISEQ700708:147:D278GACXX:2:1101:6816:3815 2:N:0:ATCACG
ATTGTCTGCGCGTTACGATATTATCAAGAATCGCGACTGGTTATGGTCTCTTACTGCTACAACACTGAACACTAAGACCAAATATGCTAACATTGGCAAC
+
CCCFFFFFHHHHHIJJJJIJJJJJJJJJJJJJJJJJJJJJIJIIIJIHHHHHFFFFFFFFEEEDDDDDDDDDDCDDDDDDDDDDEEDEDDDDDDDDDDDD
@HISEQ700708:147:D278GACXX:2:1101:6919:3932 1:N:0:ATCACG
TATTCAGGAAAACCTGCCGCAGACGCTTGGGGTCGCAGGAGATTTCCGGAATGTCTTCGTCATTGTCGATATAGTCCAGTCGAATACCGTCCTGGGCCAG
+
@C at FFFDFFHGFHIGIIJIIIJJJJGIJIJJIFEFHIIGGDHFHHHHFF<ACAEDDCDD=?A?DD at CBDDBDDCC
@CDCDD at B?C at CCB<@DD>C?BDDB


-- 
Shaolin Wang, Ph.D
Research Scientist
Department of Psychiatry & Neurobiology Science
University of Virginia
1670 Discovery Drive, Suite 110
Charlottesville, VA 22911
 Phone: 434-982-0243
Fax:434-973-7031
E-mail: swang at virginia.edu <sw4ed at eservices.virginia.edu>
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