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Gregor-Mendel-Institute / nanoPARE

RNA 5' analysis tools for use with the nanoPARE protocol
GNU General Public License v3.0
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Unable to run endMap.sh on provided sample data #2

Closed MikeAxtell closed 5 years ago

MikeAxtell commented 5 years ago

Trying to test with provided example data, but failing in a way I can't figure out. Successfully ran ./nanoPARE_setup.sh. Then tried to run endMap.sh as follows: ./endMap.sh --cpus 2 --ram 10 -L 1 All 'results' files are empty. Within the corresponding 'temp' directory I see: -rw-rw---- 1 mja18 mja18_collab 18M Apr 30 09:33 flower_1.1.fastq -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:33 flower_1.2.fastq -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:34 flower_1.5P.minus.bedgraph -rw-rw---- 1 mja18 mja18_collab 19 Apr 30 09:34 flower_1_5P_minus_untemp.bedgraph -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:34 flower_1.5P.plus.bedgraph -rw-rw---- 1 mja18 mja18_collab 19 Apr 30 09:34 flower_1_5P_plus_untemp.bedgraph -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:34 flower_1_cleaned.1.fastq -rw-rw---- 1 mja18 mja18_collab 2.4K Apr 30 09:34 flower_1.sam -rw-rw---- 1 mja18 mja18_collab 473 Apr 30 09:34 flower_1.star.log -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:34 flower_1.uG.minus.bedgraph -rw-rw---- 1 mja18 mja18_collab 0 Apr 30 09:34 flower_1.uG.plus.bedgraph -rw-rw---- 1 mja18 mja18_collab 17 Apr 30 09:34 length.table drwxrws--- 4 mja18 mja18_collab 4.0K Apr 30 09:34 star In particular I noticed that the 'flower_1_cleaned.1.fastq' file is empty. I believe this is the file fed to STAR.

A few error messages, from python, come through during the run: File "/storage/home/mja18/work/nanoPARE/scripts/python_scripts/fastq_drop_short_reads.py", line 37 print "Finished cleaning." ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Finished cleaning.")?

than a few lines later: cat: flower_1_cleaned.fastq: No such file or directory

Python version Python 3.6.3 :: Anaconda, Inc.

Any suggestions? I can send more details if you need them. Thanks in advance for your advice.

maschon0 commented 5 years ago

This is caused by an earlier version of the pipeline being written for Python 2.7, and a couple of pre-final Python scripts snuck into the release version. I just pushed an update to the two Python scripts responsible for this issue and was able to run ./endMap.sh --cpus 2 --ram 10 -L 1 on our cluster.
Software versions for testing:
--Python 3.6.6 --cutadapt 1.18 --STAR 2.6.1c --samtools 1.9 --bedtools 2.27.1

Does this fix the problem?

MikeAxtell commented 5 years ago

Great, thanks. Confirmed fixed.