Trimmomatic Error

Question

[Princy]

Hello everyone,

I was doing Trimmomatic on paired fastq file, but this is giving an error.

 head SO_5494_LR_20_MS_01_S27_R2_001.fq
@NS500223:167:H3T5HBGXY:1:11101:21506:1055 2:N:0:GCCAATAT+NGANCTCG
ATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAA###################################################################################################################################################
--
@NS500223:167:H3T5HBGXY:1:11101:3745:1056 2:N:0:GCCAATAT+NGANCTCG
AGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAA###################################################################################################################################################
--

While doing Trimmomatic it is giving this error,

Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: --
        at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:68)
        at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:156)
        at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:265)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

How can I remove -- this from my fastq file?

[lieven.sterck]

how where they 'added' to that file in the first place? That is indeed not standard fastq format.

(looks like it's the output of grep or such)

Answer 1

[lieven.sterck]

cat <your_file>  |  sed 's/^\-\-$//g'  > new_file

should do it (but do first test on a small section or such, not to destroy your original file)

EDIT: added an extra slash before g

[Princy]

Thanks for reply, but this error is showing

 cat SO_5494_LR_20_MS_01_R1.fastq | sed 's/^\-\-$/g' > new_file
    sed: -e expression #1, char 10: unterminated `s' command

[GenoMax]

There is one additional character missing. Try:

cat SO_5494_LR_20_MS_01_R1.fastq | sed 's/^\-\-$//g' > new_file

[Princy]

Hi, Thanks, it's working fine, but the file should look like this, Head file

@NS500223:167:H3T5HBGXY:1:11101:11031:1058 2:N:0:ACAGTGAT+NGATCTCG
GAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAAA##################################################################################################################################################
@NS500223:167:H3T5HBGXY:1:11101:20535:1059 2:N:0:ACAGTGAT+NGATCTCG
TCTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAAA##################################################################################################################################################
@NS500223:167:H3T5HBGXY:1:11101:12124:1059 2:N:0:ACAGTGAT+NGATCTCG
CTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

There is an extra space before @NS500223

Head file

@NS500223:167:H3T5HBGXY:1:11101:21506:1055 2:N:0:GCCAATAT+NGANCTCG
ATGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAA###################################################################################################################################################

@NS500223:167:H3T5HBGXY:1:11101:3745:1056 2:N:0:GCCAATAT+NGANCTCG
AGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
AAA###################################################################################################################################################

[GenoMax]

cat SO_5494_LR_20_MS_01_R1.fastq | sed -e 's/^\-\-$//g'  -e '/^$/d' > new_file