readlink: illegal option -f
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Attempting to run the TEMP2 script:
(TEMP2_TE) Seans-MacBook-Pro:test sbresnahan$ TEMP2 readlink: illegal option -- f usage: readlink [-n] [file ...] usage: dirname path /usr/local/bin/TEMP2: line 10: /echo0: No such file or directory /usr/local/bin/TEMP2: line 11: /echo0: No such file or directory /usr/local/bin/TEMP2: line 12: /echo0: No such file or directory /usr/local/bin/TEMP2: line 13: /echo0: No such file or directory /usr/local/bin/TEMP2: line 14: /echo0: No such file or directory /usr/local/bin/TEMP2: line 15: /echo0: No such file or directory
Attempting to run TEMP2 insertion
(TEMP2_TE) Seans-MacBook-Pro:test sbresnahan$ TEMP2 insertion -l test.1.fastq.gz -r test.2.fastq.gz -I bwa_index/chr2L -g chr2L.fa -R transposon.fa -t rmsk.bed -o test_output -c 2 readlink: illegal option -- f usage: readlink [-n] [file ...] usage: dirname path bash: /TEMP2_insertion.sh: No such file or directory
It seems you are executing TEMP2 in Mac OS, which doesn't support "-f" option for "readlink". Currently, we've only tested TEMP2 on the Linux x86_64 system, maybe you can give it a try.