These are chat archives for dereneaton/ipyrad

14th
Jul 2017
bbarker505
@bbarker505
Jul 14 2017 03:40
@jenarch Hi Jenny, thank you very much for your advice. I did this but am now getting an error message of ([Errno 2] No such file or directory) after I put a wildcard *.fastq in my sorted reads path (the program told me to do this). I made sure that the path is correct, so have no clue what the deal is.
Jenny Archibald
@jenarch
Jul 14 2017 13:48
@dereneaton. Thanks for the info! It has been stuck at 62% for at least 4 days of the 7+ days it has been on step 6. I cannot run top on it, but our cluster gives CPU stats and says it is only using 1 of 48 dedicated CPUs. That seems even lower than you'd expect if it were on the little node, doesn't it?
Jenny Archibald
@jenarch
Jul 14 2017 13:56

@bbarker505 I am not certain, but if you paste the param line for the path to your data, and also paste an example of the path to one of your data files - we may be able to spot a problem. Although it sounds like you may have already checked that?
For example, for one of my recent runs, param 4 is:

/panfs/pfs.local/work/bi/jkarch/cam/data/*.fq                               ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files

and the actual path to one data file is:

/panfs/pfs.local/work/bi/jkarch/cam/data/CC_IHC_6m_R1_.fq
joqb
@joqb
Jul 14 2017 15:19
HELP @eaton-lab for some obscure reason my json file got emptied when trying to restart the step 6!! I still have all the files would there be a smart way to recover the content of the json file as from what I could see it's mainly compiling all the stats per individual per step?
Deren Eaton
@dereneaton
Jul 14 2017 15:48
yes if the files are all still there then I'm sure it can be recovered.
It will require a little trickery with the Python API
I'll have too do a little testing and get back to you with some example code...
joqb
@joqb
Jul 14 2017 15:54
Thanks @dereneaton that would be really cool and give me some hope this analysis will finally be over with.
Isaac Overcast
@isaacovercast
Jul 14 2017 19:32
@bbarker505 The *.fastq prompt is just a suggestion. You have to match the file type of your raw data files. So you may need to change this to *.fq.gz or *.fastq.gz or *.fq or whatever, depending on the format of your data.
Bohao Fang
@fangbohao_twitter
Jul 14 2017 20:17
Hi @isaacovercast. what the meaning of
"ERROR sample [NOR-SKF-GA-30_R1] failed in step [ref_build_and_muscle_chunk]; error: AttributeError('module' object has no attribute 'AlignmentFile')"
in step3?
I read it from "ipyrad_log.txt"
Deren Eaton
@dereneaton
Jul 14 2017 21:16

Hi @fangbohao_twitter, this is a bug with the current installation which we're working quickly to try to fix. Right now it installs pysam v.0.6, whereas it should install pysam v.0.10 or higher. One way to work around this for now is to run the following conda commands in this order

conda remove ipyrad pysam samtools bcftools htslib 
conda install pysam=0.10.0 -c bioconda
conda install ipyrad -c ipyrad -f

This workaround will be temporary until we get the versions updated correctly so that they can all be installed from the ipyrad channel instead of requiring the bioconda channel.

@jobq, the above fix should work for you as well.