I was ran Mothur on HPC and received the following warning messages and errors (see below). Have any of you experienced that before? Your assistance is much appreciated. Thanks!
Jean-Rene
mothur > count.seqs(name=current, group=current)
[WARNING]: no file was saved for group parameter.
[WARNING]: no file was saved for name parameter.
You have no current namefile or sharedfile and the name or shared parameter is required, unless inflating or deflating an existing count file.
[ERROR]: did not complete count.seqs.
[WARNING]: 200 of your sequences generated alignments that eliminated too many bases
“[WARNING]: HWI-M03127_118_AHCMU_1_1109_22309_14727 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_1108_24018_23579 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_2113_16892_10466 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_2101_8000_5393 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_1110_19686_9112 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_2101_20688_27281 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_1112_21504_28039 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_2103_21763_19913 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_1103_13571_18979 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: HWI-M03127_118_AHCMU_1_2114_26879_17869 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.”
[WARNING]: Your count file does not have group info, all reads will be assigned to mothurGroup.
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