ERROR: '+' expected
Opened this issue · 5 comments
Hello. I keep getting the same error when running my RNA-seq data with fastp. The error implies that there is a '+' missing, but I don't see that in my fastq file. Please help.
Here is an example:
Command:
fastp --in1 R2_FKRN240086271-1A_2253CMLT4_L7_1.fq --out1 fastp_R2_1_trimmed.fq --in2 R2_FKRN240086271-1A_2253CMLT4_L7_2.fq --out2 fastp_R2_2_trimmed.fq
Error message:
Expected '+', got @LH00281:101:2253CMLT4:7:1153:17937:24071 2:N:0:GAAGACTAGC+TAGGAAGAGC
ERROR: '+' expected
I found the line in the fastq file where this error message is pointing to, and don't see any '+' missing:
I uploaded here 1M reads each of my forward and reverse files: https://1drv.ms/f/s!AlHK-h6IM1EWl-o0nQvUh8iCeZ5VYA?e=AF7xpe
I ran the following command:
fastp --in1 R2_F_1M.fq --out1 fastp_R2_1_trimmed.fq --in2 R2_R_1M.fq --out2 fastp_R2_2_trimmed.f
And got the following message:
Expected '+', got TCTTCGCCGACCTTCGCCGGCCTCAGCGCCACCGGGCGCAGCAGGAAAGACGGCACGTGGTCGCCCAGTCCAATGACGGGCGGCCCATCGTCTTCATGATGGCGCGGGCGGCGCTCACGACGGTCTGCGACAGGCGCCCCGGCCGGCGCC
ERROR: '+' expected
Not sure if this information is helpful: I am using a MacBook Pro with Apple M3 Pro chip.
I just wanted to provide an update that I ran the exact same code using the exact same data, but on my institution's clusters (instead of my personal MacBook), and it worked perfectly.
I checked your data, seems that the file R2_R_1M.fq is with bad format
@LH00281:101:2253CMLT4:7:1105:33021:5553 2:N:0:GAAGACTAGC+TAGGAAGAGC
TGCTACTATTGCTATCGCAGCTCTTTCTTCATGTGCAATGACCGTACCTGTGGCTGCTACGAGCAACCCAATCGGCAGTAAAGTAGGCACTTCCACCGGTTCCGGTTTTTTGGGAGTTCTTATCTTCTCGCCTGATACCGGCATTCAACA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@LH00281:101:2253CMLT4:7:1105:33377:5553 2:N:0:GIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@LH00281:101:2253CMLT4:7:1167:24751:12668 1:N:0:GAAGACTAGC+TAGGAAGAGC
TCTTCGCCGACCTTCGCCGGCCTCAGCGCCACCGGGCGCAGCAGGAAAGACGGCACGTGGTCGCCCAGTCCAATGACGGGCGGCCCATCGTCTTCATGATGGCGCGGGCGGCGCTCACGACGGTCTGCGACAGGCGCCCCGGCCGGCGCC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIII-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
and the two files have different line numbers:
wc -l *.fq
4000000 R2_F_1M.fq
3999297 R2_R_1M.fq