I recently came across this error while making contain files.
mothur > make.contigs(file=stability.files, processors=8)
Using 8 processors.
Processing file pair /Users/genecis/Desktop/mothur/sample_10_R1.fastq - /Users/genecis/Desktop/mothur/sample_10_R2.fastq (files 1 of 15) <<<<<
Making contigs…
[WARNING]: reading expected a name with @ as a leading character, ignoring read.
[WARNING]: reading G?+%?.W5? expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read for fasta and G?+%?.W5? for quality, ignoring.[WARNING]: Lengths do not match for sequence . Read 37 characters for fasta and 4 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? FASTQ format - Wikipedia
[WARNING]: reading expected a name with @ as a leading character, ignoring read.
[WARNING]: reading ?2?VJ??n?Oｻwew٠?EJI? expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read for fasta and ?2?VJ??n?Oｻwew٠?EJI? for quality, ignoring.[WARNING]: Lengths do not match for sequence . Read 37 characters for fasta and 14 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? FASTQ format - Wikipedia
?f6 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
Rzy?0??D9??V?E?J??S???8r??Njہ??K?#?Y͍???0R??w?PgD?a?? is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
d^?~8???[$???˒"f"?J?MƋ~i?"???zū6??bzm?? is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
j.?4?U5?V??!?5 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
?z|Y贁?Sq?W-?Z?^???l?n?_6U???M???=?? is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
?U|??H??w?? is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
?+???m?_??QZʑ`)? is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
zsh: segmentation fault ./mothur
My log file for this command is empty.