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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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Error: can not read sequence #269

Closed mdiricks closed 4 years ago

mdiricks commented 4 years ago

Hi, Trying to run nullarbor but I get following error message: ERROR: Isolate 'B-2' - can not read sequence #1 of 1 files: 'C:\Users\diric\Desktop\Totest\B-2_lib603_miseq_r0047_251bp_R1.fastq.gz' My samples file is B-2 C:\Users\diric\Desktop\Totest\B-2_lib603_miseq_r0047_251bp_R1.fastq.gz C:\Users\diric\Desktop\Totest\B-2_lib603_miseq_r0047_251bp_R2.fastq.gz H-239 C:\Users\diric\Desktop\Totest\H-239_lib653_miseq_r0049_251bp_R1.fastq.gz C:\Users\diric\Desktop\Totest\H-239_lib653_miseq_r0049_251bp_R2.fastq.gz

I´m working with ubuntu subsystem for windows. Using the /mnt/c/Users/diric/... also does not work. Any suggestions?

tseemann commented 4 years ago

WSL/Unix doesn't understand C:\ I think the input.tab will need to refer to the /mnt/c/Users/diric/ folder. Did you put TAB characters between the columns? Spaces will not work.

mdiricks commented 4 years ago

I automated the samples.tab file generation and now I don´t get the error anymore.