[BUG/HELP]

[guildelhaye]

Hi Alex,
here's a message from Laura who's unable to report a bug here.

Hi Alex,
I tried to run Helena’s sequences in my computer as she was having problems, I encountered an error and I used some of the scripts below:
457 cd otu_pipeline_Alex
458 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
459 pull its_glue
460 ./scripts/pipe_two.cluster_classify.sh -d ../UNITE_usearchRefdatabase -f ../out/its/ALL_ITS.fa -o ../out/otu
461 pull its_glue
462 git pull
463 git reset --hard
464 git pull
465 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
466 ./scripts/CREATE_ENV.sh
467 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
468 ./pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
469 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
470 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
471 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
472 ./pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o ../out -x
473 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out -x
474 ./pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out -x
475 ./scripts/pipe_one.trace_its.sh -t ‘../TCC_1F_4’ -f _1F -r _4R -o ../out
476 git pull
477 ./scripts/CREATE_ENV.sh
478 chmod +x ./scripts/CREATE_ENV.sh
479 chmod +x ./scripts/pipe_one.trace_its.sh
480 chmod +x ./pipe_one.trace_its.sh
481 chmod +x ./scripts/pipe_two.classify_cluster.sh
482 chmod +x ./pipe_two.classify_cluster.sh
483 ./scripts/CREATE_ENV.sh
484 ls
485 cd Desktop
486 ls
487 cd otu_pipeline_Alex
488 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
489 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
490 ls
491 cd its_glue
492 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
493 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
494 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
495 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
496 CREATE_ENV.sh
497 /Users/laura/Desktop/otu_pipeline_Alex/its_glue/scripts/CREATE_ENV.sh
498 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
499 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o ../out
500 ./scripts/pipe_one.trace_its.sh -t ../TCC_1F_4 -f _1F -r _4R -o /Users/laura/Desktop/otu_pipeline_Alex/out
501 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o /Users/laura/Desktop/otu_pipeline_Alex/out
502 ./scripts/pipe_one.trace_its.sh -t ../ITS_sequences -f -f -r -r -o /Users/laura/Desktop/otu_pipeline_Alex/out
503 history

And now I get this:

running Tracy...
ls: ../TCC_1F_4/_4R.: No such file or directory
ERROR: 0 trace files detected using given -r tag

Can you remember how did you solve this problem?

Thanks!

Laura

[blex-max]

Unfortunately, there is both not enough and too much information here for me to help. Which one command out of these is giving the error? Also, please could you zip up a couple of pairs of traces and upload them here for me to look at?

Please use the template when submitting bugs, and please title them. It makes the repository much easier to manage.