Error during ORF prediction step

[PSSUN]

when I try to run example, here comes an error during ORF prediction step. I ues command:

run-all-rpbp-instances c-elegans-test.yaml --overwrite --num-cpus 2 --logging-level INFO --keep-intermediate-files

the error is:

[bam_index_build2] fail to open the BAM file. ^[[?62;cINFO root 2018-03-19 23:38:45,537 : samtools view -h /home/malab1/sps/04_software/rp-bp/c-elegans-chrI-example/without-rrna-mapping/c-elegans-rep-1.test-unique.bam > /dev/null INFO root 2018-03-19 23:38:45,537 : calling open: No such file or directory

it seems that lack of file: c-elegans-rep-1.test-unique.bam

cd without-rrna-mapping && ls the result is: c-elegans-rep-1.testAligned.sortedByCoord.out.bam c-elegans-rep-1.testLog.final.out
c-elegans-rep-1.testLog.progress.out c-elegans-rep-1.test_STARgenome c-elegans-rep-1.test.bam
c-elegans-rep-1.testLog.out
c-elegans-rep-1.testSJ.out.tab

c-elegans-rep-1.test-unique.bam not exist

[eboileau]

The unique part of the file name comes from the fact that you are removing multimapping reads.

This is likely a problem when creating the bamtools index samtools index -b c-elegans-rep-1.test.bam. In fact, you don't seem to have the file c-elegans-rep-1.test.bam.bai. Have you checked the output/logs of STAR, and in particular c-elegans-rep-1.test.bam? Without more information, it is unclear why this is happening. Are you able to create the index directly? Although unlikely, it may be a difference with samtools versions, in particular with the -b parameter. The latest version I am currently using is 1.6.

You can also use --logging-level DEBUG and --log-file out.log to get the logging information.

[PSSUN]

Thank you for your answer, after I update the version of samtools to 1.6, this problem was solved. But here comes another error,

INFO root 2018-03-21 09:09:56,777 : estimate-metagene-profile-bayes-factors /home/malab1/sps/04_software/rp-bp/c-elegans-chrI-example/metagene-profiles/c-elegans-rep-1.test-unique.metagene-profile.csv.gz /home/malab1/sps/04_software/rp-bp/c-elegans-chrI-example/metagene-profiles/c-elegans-rep-1.test-unique.metagene-periodicity-bayes-factors.csv.gz --num-cpus 2 --periodic-models --nonperiodic-models --periodic-offset-start -20 --periodic-offset-end 0 --metagene-profile-length 21 --seed 8675309 --chains 2 --iterations 500 --logging-level INFO --stdout-logging-level NOTSET --file-logging-level NOTSET --log-file out.log --stderr-logging-level NOTSET INFO root 2018-03-21 09:09:56,778 : calling ... estimate-metagene-profile-bayes-factors: error: argument --periodic-models: expected at least one argument

It's seems that argument --periodic-models and --nonperiodic-models have no input file

[eboileau]

Hi, this appears to be related to (closed) issue #72 , and part of this is not relevant anymore (for instance pickle-stan is now part of riboseq-utils, latest version). See also #41, this could be related, you should avoid paths with spaces in them, although this should be handled by OSX.

The models are installed in an OS-specific location (in particular, user_data_dir from the appdirs package), determined during installation, unless this has been changed, in which case this can be specified via the configuration file with

models_base: /path/to/rp-bp/models

The default location is typically $HOME/.local/share/rpbp/rpbp_models/. Please use the following command to check if the files exist:

$ find $HOME/.local/share/rpbp \( -name "*stan" -o -name "*pkl" \)

If they do not exist, then it is likely that a problem occurred while installing the program. If installed with --verbose, you should be able to see if there was a problem compiling the models. Please consult the docs for installation.

[PSSUN]

Thank you for your answer,I reinstalled rpbp and solved this problem.