Open FabianGrammes opened 7 years ago
Hi! When we see issues like this it usually has to do with the /tmp directory being used. Do you have sufficient space there? You can use the -T option to reset the location of the processing directory to a location that may have more space.
Hello,
I am unsure if this is the exact same, but I believe it is similar. I am getting this error code:
2018-01-26 14:28:08,973 [ INFO] - Processing sorted SAM/BAM with molecular tag sequence in read name (assumes sorted)
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
2018-01-26 14:28:10,736 [ ERROR] -
I have tried it with and without changing the -T option. I have plenty of hard drive and RAM space.
Hi @peterwc; I never got nudup.py
to run on my cluster either and I have also plenty of RAM and space. Not even even with small test files. Anyway in case you havn't found a solution I've wrote my own script which you can try: https://gitlab.com/fabian.grammes/RRBS_kit
; script rrbs_dedup.py
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... :-(
Hey @FabianGrammes, I believe I followed the comments from one of the other threads on here. It works after a bit. Overall, its a great program and runs well on linux machines.
Peter
Hi all, I am seeing a similar issue on our cluster, though I am using a local scratch as the tmp directory. In my case the named pipe hangs indefinitely on the adding the molecular tag to the read name. I also see several defunct samtools processes in the background. Using top
:
top - 20:18:58 up 29 days, 6:54, 1 user, load average: 14.69, 15.27, 14.74
Tasks: 321 total, 15 running, 302 sleeping, 0 stopped, 4 zombie
%Cpu(s): 57.7 us, 0.9 sy, 0.0 ni, 41.3 id, 0.0 wa, 0.0 hi, 0.1 si, 0.0 st
KiB Mem : 39622716+total, 37905289+free, 4447912 used, 12726356 buff/cache
KiB Swap: 0 total, 0 free, 0 used. 38831289+avail Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
2435148 cjfields 20 0 168184 2508 1600 R 0.3 0.0 0:00.05 top -u cjfields
2420613 cjfields 20 0 125980 2428 1708 S 0.0 0.0 0:00.01 /usr/bin/bash
2433627 cjfields 20 0 193756 10008 3608 S 0.0 0.0 0:00.08 python /home/groups/hpcbio/apps/NuGen/nudup/nudup.py -T /scratch -f DMVF015_SubQ_AGTGAG_L00M_R2_001.fastq -o DMVF015_SubQ_AG+
2433699 cjfields 20 0 0 0 0 Z 0.0 0.0 0:00.00 [samtools] <defunct>
2433700 cjfields 20 0 0 0 0 Z 0.0 0.0 0:00.00 [samtools] <defunct>
2434124 cjfields 20 0 192216 2672 1088 S 0.0 0.0 0:00.00 sshd: cjfields@pts/3
2434125 cjfields 20 0 125820 2180 1676 S 0.0 0.0 0:00.00 -system-specific
2435140 cjfields 20 0 0 0 0 Z 0.0 0.0 0:00.00 [samtools] <defunct>
2435141 cjfields 20 0 0 0 0 Z 0.0 0.0 0:00.00 [samtools] <defunct>
2435142 cjfields 20 0 107952 380 276 S 0.0 0.0 0:00.00 cat /scratch/nudup_X1lDc6/named_pipe /scratch/nudup_qjxxlN/named_pipe
2435143 cjfields 20 0 107932 636 512 S 0.0 0.0 0:00.00 tee /scratch/nudup_H5q7vH/named_pipe
If I kill the process it exits as below:
$ python $NUGEN_NODUP_HOME/nudup.py -T /scratch -f DMVF015_SubQ_AGTGAG_L00M_R2_001.fastq -o DMVF015_SubQ_AGTGAG.nugen_dedup DMVF015_SubQ_AGTGAG.sam_stripped.sam
2018-09-18 18:50:43,447 [ INFO] - Deduplicating NuGEN single end reads...
2018-09-18 18:50:55,173 [ INFO] - Using molecular tag sequence from Index FASTQ read
2018-09-18 18:50:55,173 [ INFO] - Appending molecular tag sequence to SAM/BAM read name
^CTraceback (most recent call last):
File "/home/groups/hpcbio/apps/NuGen/nudup/nudup.py", line 1110, in <module>
w.main(umi_start=args.start, umi_length=args.length)
File "/home/groups/hpcbio/apps/NuGen/nudup/nudup.py", line 1003, in main
w = self.process_unsynced_sam(umi_start, umi_length)
File "/home/groups/hpcbio/apps/NuGen/nudup/nudup.py", line 939, in process_unsynced_sam
logger.debug('Add molecular tag sequence to sam: %s', umi_nohead_sam)
File "/home/groups/hpcbio/apps/NuGen/nudup/nudup.py", line 170, in __exit__
time.sleep(self._POLL_TIME)
KeyboardInterrupt
For this kind of error, the problem concerns the tmp directory. Using the
-T $TMPDIR
option to redirect the tmp directory to $TMPDIR is not enough. The issue can be fixed by adding the following line to~/.bash_profile
file:export TMPDIR="somewhere_you_redirect_the_tmp_directory"
Originally posted by @boro2013 in https://github.com/nugentechnologies/nudup/issues/19#issuecomment-458194227
Hi, trying to run
nudup.py
I get the following error messageThe script progresses from there but the resulting
.bam
files are empty. I'm running it using anaconda/1.9.1 and samtools/1.3. Any help is welcome.