I am using the 1.36.1 version of mothur and I am getting a segmentation fault when running make.contigs on fastq.gz files:
Processing file pair trimmed_2_R1.fastq.gz - trimmed_2_R2.fastq.gz (files 2 of 374) <<<<<
M03742_14_000000000-BNJ5K_1_1102_16619_1766 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
As far as I am aware, this version of mothur should be able to cope with missing sequences (which are as a result of removing sequences prior to inputting into mothur).
Many thanks in advance for your help on this issue,