Error in make.group

Commands in mothur
1

Hi All,

My name is Maya, and I am new to mothur. I am using version 1.37.4

I got my sequences as a list of fasta files for each of my samples from the sequencing center. I am trying to make a group file by using the command: make.group.

When I try it with one or two files it works fine, but when I try with the whole set of samples (90 samples) I get an error.
This is the error I get:
[ERROR]: Could not open C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences\C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences\mergegroups

This is the command I used:
make.group(fasta=Maya1.165.fasta-Maya2.166.fasta-Maya3.167.fasta-Maya4.186.fasta-Maya5.196.fasta-Maya6.210.fasta-Maya7.211.fasta-Maya8.sub1.fasta-Maya9.212.fasta-Maya10.232.fasta-Maya11.248.fasta-Maya12.249.fasta-Maya13.250.fasta-Maya14.316.fasta-Maya15.317.fasta-Maya16.sub2…fasta-Maya17.322.fasta-Maya18.339.fasta-Maya19.352.fasta-Maya20.356.fasta-Maya21.357.fasta-Maya22.360.fasta-Maya23.370.fasta-Maya24.sub3.fasta-Maya25.371.fasta-Maya26.372.fasta-Maya27.373.fasta-Maya28.374.fasta-Maya29.375.fasta-Maya30.376.fasta-Maya31.378.fasta-Maya32.sea.water.fasta-Maya33.379.fasta-Maya34.380.fasta-Maya35.381.fasta-Maya36.382.fasta-Maya37.384.fasta-Maya38.385.fasta-Maya39.386.fasta-Maya40.N1.DNA.fasta-Maya41.389.fasta-Maya42.390.fasta-Maya43.391.fasta-Maya44.393.fasta-Maya45.394.fasta-Maya46.396.fasta-Maya47.402.fasta-Maya48.N2.DNA.fasta-Maya49.403.fasta-Maya50.404.fasta-Maya51.405.fasta-Maya52.406.fasta-Maya53.412.fasta-Maya54.417.fasta-Maya55.418.fasta-Maya56.N1.RNA.fasta-Maya57.419.fasta-Maya58.370c.fasta-Maya59.371c.fasta-Maya60.372c.fasta-Maya61.373c.fasta-Maya62.374c.fasta-Maya63.375c.fasta-Maya64.N2.RNA.fasta-Maya65.376c.fasta-Maya66.378c.fasta-Maya67.379c.fasta-Maya68.380c.fasta-Maya69.381c.fasta-Maya70.382c.fasta-Maya71.384c.fasta-Maya72.N1.no.template.fasta-Maya73.385c.fasta-Maya74.386c.fasta-Maya75.389c.fasta-Maya76.390c.fasta-Maya77.391c.fasta-Maya78.393c.fasta-Maya79.394c.fasta-Maya80.N2.no.template.fasta-Maya81.396c.fasta-Maya82.402c.fasta-Maya83.403c.fasta-Maya84.404c.fasta-Maya85.405c.fasta-Maya86.406c.fasta-Maya87.412c.fasta-Maya88.417c.fasta-Maya89.418c.fasta-Maya90.419c.fasta, groups=165-166-167-186-196-210-211-sub1-212-232-248-249-250-316-317-sub2-322-339-352-356-357-360-370-sub3-371-372-373-374-375-376-378-sea.water-379-380-381-382-384-385-386-N1.DNA-389-390-391-393-394-396-402-N2.DNA-403-404-405-406-412-417-418-N1.RNA-419-370c-371c-372c-373c-374c-375c-N2.RNA-376c-378c-379c-380c-381c-382c-384c-N1.no.template-385c-386c-389c-390c-391c-393c-394c-N2.no.template-396c-402c-403c-404c-405c-406c-412c-417c-418c-419c)

Thanks!

2

Thanks for reporting this issue. It looks like mothur is appending the output directory twice. Can you try running the command without the output redirect?

3

Hi,

Thank you for your reply!

Can you please explain what you mean by “without the output redirect”? you mean when I do the “set.dir” command?

BTW, I didn’t write it above, but after the program displays this error, it is thinking and at the end sends the message:

“Output File Names:
C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences\C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences\mergegroups”

But this file is not created.

Thanks again!

4

Hi all,
I have the same problem. Working good with two fasta files and stuck with 8. :roll:

Best regards,
Ilia

5

I think when you use the set.dir(output=XXX) command and then use more than 3 groups, mothur is appending XXX twice to the new file name it creates “merge.groups”. This does not happen with less than 3 groups. The new name becomes “XXX\XXX\merge.groups”. Since there is no way to create a file in location “C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences\C:\Users\Maya\Documents\MiSeq140_Maya_12437\sequences” no output file is created. Can you try running the make.groups command with out the set.dir command?

6

Hi, I’m starting to learn mothur and I think I’m having a related problem. I’m using mothur version 1.36.1

Here is the command/result I used:

mothur > make.group(fasta=2_IG_ost.fasta-27_S_no.fasta-9_ID_ost.fasta-4_TG_ost.fasta-28_ID_no.fasta-31_S_no.fasta-16_IG_ost.fasta-15_ID_ost.fasta-32_IG_no.fasta-21_IG_ost.fasta-33_ID_no.fasta-34_TD_no.fasta-25_IG_ost.fasta-29_ID_no.fasta-5_S_ost.fasta-7_IG_ost.fasta-14_ID_ost.fasta-18_TG_ost.fasta-6_S_ost.fasta-20_ID_ost.fasta-1_S_ost.fasta-10_S_ost.fasta-3_IG_ost.fasta-17_IG_ost.fasta-24_S_ost.fasta-19_S_ost.fasta-26_ID_no.fasta-11_S_ost.fasta-12_ID_ost.fasta-13_TD_ost.fasta-30_S_no.fasta, groups=2_IG_ost-27_S_no-9_ID_ost-4_TG_ost-28_ID_no-31_S_no-16_IG_ost-15_ID_ost-32_IG_no-21_IG_ost-33_ID_no-34_TD_no-25_IG_ost-29_ID_no-5_S_ost-7_IG_ost-14_ID_ost-18_TG_ost-6_S_ost-20_ID_ost-1_S_ost-10_S_ost-3_IG_ost-17_IG_ost-24_S_ost-19_S_ost-26_ID_no-11_S_ost-12_ID_ost-13_TD_ost-30_S_no)


Output File Names: mergegroups

Here are the first 10 lines (opened with R cuz I didn’t know any other way… but I’m open to pointers!):

readLines(“mergegroups”, n = 10)
[1] “M00987_100_000000000-AGJ3W_1_1101_14599_1390\t2_IG_ost”
[2] “M00987_100_000000000-AGJ3W_1_1101_13121_1793\t2_IG_ost”
[3] “M00987_100_000000000-AGJ3W_1_1101_13587_2091\t2_IG_ost”
[4] “M00987_100_000000000-AGJ3W_1_1101_13638_2108\t2_IG_ost”
[5] “M00987_100_000000000-AGJ3W_1_1101_13685_2310\t2_IG_ost”
[6] “M00987_100_000000000-AGJ3W_1_1101_10598_2459\t2_IG_ost”
[7] “M00987_100_000000000-AGJ3W_1_1101_20812_2888\t2_IG_ost”
[8] “M00987_100_000000000-AGJ3W_1_1101_12485_3215\t2_IG_ost”
[9] “M00987_100_000000000-AGJ3W_1_1101_14007_3253\t2_IG_ost”
[10] “M00987_100_000000000-AGJ3W_1_1101_14061_3389\t2_IG_ost”

I was expecting “sequenceID” space “2_IG_ost”. There is no space… there’s a slash and a t. I never fussed with input and output directories (I just copied the mothur executable into the directory I was using.

Should I be worried that this file is not .groups? Is this format (no space) OK?

Please forgive me if this has been asked a thousand times already… I’m really new to all this.

Sincerely, Carey

7

Hi, I just did exactly the same command with mothur version 1.37.4 and got exactly the same result:

readLines(“mergegroups”, n = 10)
[1] “M00987_100_000000000-AGJ3W_1_1101_14599_1390\t2_IG_ost”
[2] “M00987_100_000000000-AGJ3W_1_1101_13121_1793\t2_IG_ost”
[3] “M00987_100_000000000-AGJ3W_1_1101_13587_2091\t2_IG_ost”
[4] “M00987_100_000000000-AGJ3W_1_1101_13638_2108\t2_IG_ost”
[5] “M00987_100_000000000-AGJ3W_1_1101_13685_2310\t2_IG_ost”
[6] “M00987_100_000000000-AGJ3W_1_1101_10598_2459\t2_IG_ost”
[7] “M00987_100_000000000-AGJ3W_1_1101_20812_2888\t2_IG_ost”
[8] “M00987_100_000000000-AGJ3W_1_1101_12485_3215\t2_IG_ost”
[9] “M00987_100_000000000-AGJ3W_1_1101_14007_3253\t2_IG_ost”
[10] “M00987_100_000000000-AGJ3W_1_1101_14061_3389\t2_IG_ost”

8

Hi, here is a follow-up on my newbie error. The output is the last post is correct: “\t” corresponds to a space. Pulling up the files in bash correctly displays the spaces. However, I still have no explanation for why the file name is “mergegroups”, but it might not really matter.