Dear mothur developers, and users,
I apologize for taking your time but I have encountered an error that I could not solve by myself. I have checked the forum, and also other pages, but I did not find any similar problem. I’m new to mothur, so please be patient with me. The situation is the following:
I use mothur v.1.44.3, our server has 99GB RAM, 5 cores, and 2TB disk space assigned for this project. When I run chimera.vsearch, the command generates the fasta and count_table files for each group successfully, however after only creates empty output files (…vsearch.pick.count_table, …vsearch.chimeras, …vsearch.accnos). Since for me the chimera.vsearch takes long time to run, more than a day or two, when I checked the mothur I saw that an error messages printed only on the screen: "
Removing group: EA1A201803 because all sequences have been removed." (please, check the attached screenshot).
My command is the following:
chimera.vsearch(fasta=/home/tendre/metagenomics_kati/data/2018/precluster/2018.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=/home/tendre/metagenomics_kati/data/2018/precluster/2018.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate= T, outputdir=/home/tendre/metagenomics_kati/data/2018/chimera)
I have no idea where to search for the solution or where is this problem originates from. Please, help me to solve it.
I attach my log file, in which chimera.vsearch starts from the 662nd line (https://ufile.io/hb3mbf53).