CyVerse test using `analyze-neon-greatplains-16s.R`

[KaiZhuPhD]

In testing analyze-neon-greatplains-16s.R on CyVerse, the following chunk:

filter_trackReads <- qualityFilter16S(
  fl_nm, in_subdir = "1_trimmed", out_subdir = "2_filtered",
  meta = meta, truncLen = 220, maxEE = 8, multithread = TRUE
)

The error message is

Using user-provided truncLen: 220
Error in names(answer) <- names1 : 
  'names' attribute [86] must be the same length as the vector [75]
In addition: Warning messages:
1: In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule,  :
  scheduled cores 2, 11 did not deliver results, all values of the jobs will be affected
2: In mclapply(seq_len(n), do_one, mc.preschedule = mc.preschedule,  :
  scheduled cores 6, 10, 13, 14, 7, 9, 15 encountered errors in user code, all values of the jobs will be affected

[claraqin]

Hi Kai,

This error happens when the multithreading in the dada2 function filterAndTrim demands too much memory. (See this issue thread in dada2: https://github.com/benjjneb/dada2/issues/273 .) To get around this, you can either request more memory on CyVerse, reduce the number of threads by setting multithread to a specific number, or set multithread = FALSE, which disables multithreading. Let me know if any of these works for you.

Clara

[KaiZhuPhD]

line 110, can't find the otu_table object; also, phyloseq() function should reference phyloseq::phyloseq() package.

[KaiZhuPhD]

Testing was done successfully. Remaining issues:

• line 128 and below, tidyverse functions--either load tidyverse (but will create conflicts with other packages) or each time use tidyr:: to call functions.
• Create plots subfolder.