get.mimarkspackage

Hi,

I’m trying to run the get.mimarkspackage command with the file option
get.mimarkspackage(file=test_mimarks.file)

but I get the following warning
[WARNING]: can’t find S12_TGCGGCATCGAA_L001_R1_001.fastq, ignoring.
[WARNING]: can’t find S12_TGCGGCATCGAA_L001_R2_001.fastq, ignoring pair.
[WARNING]: can’t find S21_CTCCTGAAAGTT_L001_R1_001.fastq, ignoring.
[WARNING]: can’t find S21_CTCCTGAAAGTT_L001_R2_001.fastq, ignoring pair.
[WARNING]: can’t find S23_GATAGCTGTCTT_L001_R1_001_.fastq, ignoring.
[WARNING]: can’t find S23_GATAGCTGTCTT_L001_R2_001_.fastq, ignoring pair.

and the output .tsv file has no sample names in the *sample_name column. What am I doing wrong? I’m using v.1.35.1.

Mothur can’t find your files. http://www.mothur.org/wiki/Frequently_asked_questions#Mothur_can.27t_find_my_input_files

Hi!
I have the same problem. I’m trying to make the tsv file with the file= option (same file as the stability.files used at the beginning of the MISeq SOP). Mothur makes the .tsv file without any error message, but the columns in the tsv file are empty.

The get.mimarkspackage command creates a template for you for you to fill in with your data about your experiment. It should look like:

#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages.
#Please fill all the required fields indicated with '*'
#Unknown or inapplicable fields can be assigned 'missing' value.
#You may add extra custom fields to this template. Make sure all the fields are separated by tabs.
#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs.
#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE.
#MIMARKS.survey.host-associated.4.0
#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock} {Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36)} {descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {descriptor of the local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"} {The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, "Homo sapiens".} {The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W}
#{text} {text} {text} {text} {controlled vacabulary} Template:Timestamp Template:Term Template:Term Template:Term {{term}:{term}:{text}} Template:None {{float} {float}}
*sample_name *description *sample_title *seq_methods *organism *collection_date *env_biome *env_feature *env_material *geo_loc_name *host *lat_lon
F003D000_AATGGTAC.CCGTCAATTCMTTTRAGT 
F003D002_AACCTGGC.CCGTCAATTCMTTTRAGT 
F003D004_TTCGTGGC.CCGTCAATTCMTTTRAGT 
F003D006_TTCTTGAC.CCGTCAATTCMTTTRAGT 
F003D008_TTCGCGAC.CCGTCAATTCMTTTRAGT 
F003D142_TCCAGAAC.CCGTCAATTCMTTTRAGT 
F003D144_AAGGCCTC.CCGTCAATTCMTTTRAGT 
F003D146_TGACCGTC.CCGTCAATTCMTTTRAGT 
F003D148_AGGTTGTC.CCGTCAATTCMTTTRAGT 
F003D150_TGGTGAAC.CCGTCAATTCMTTTRAGT 
MOCK.GQY1XT001_AACCGTGTC.CCGTCAATTCMTTTRAGT

Where the sample_name column is filled in, but the remaining columns are blank for you to fill in.

I have the same problem… Mothur find the file, everything work without any error message, but the sample_name column is empty.