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tjiangHIT / rMETL

rMETL - realignment-based Mobile Element insertion detection Tool for Long read
MIT License
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Unable to complete detection stage #3

Open ggstatgen opened 5 years ago

ggstatgen commented 5 years ago

Hi

I'm having problems to complete the first stage ('detection'). The code terminates with an exception.

A bit of info to help you diagnose the issue.

My command is as follows

python <CODE>/rMETL/rMETL.py detection -t 40 -x pacbio <DATA>/alignment/alignments.hg38hengli.ngmlr.sorted.bam <DATA>/REF/GRCh38_hengli_recommended/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna <OUT>/rMETL <OUT>/rMETL

This is the beginning of the STDOUT from rMETL:

2019-03-11 17:23:36,749 [INFO] The bam file is legal.
2019-03-11 17:23:37,039 [INFO] Loading reference genome...
2019-03-11 17:24:06,195 [INFO] The total number of chromsomes: 195
2019-03-11 17:24:06,536 [INFO] Resolving the chromsome chrUn_KI270742v1.
2019-03-11 17:24:06,538 [INFO] Resolving the chromsome chr14_GL000225v1_random.
2019-03-11 17:24:06,539 [INFO] Resolving the chromsome chr1.
2019-03-11 17:24:06,548 [INFO] Resolving the chromsome chr9.
2019-03-11 17:24:06,550 [INFO] Resolving the chromsome chrUn_KI270438v1.
2019-03-11 17:24:06,550 [INFO] Resolving the chromsome chr16_KI270728v1_random.
2019-03-11 17:24:06,559 [INFO] Resolving the chromsome chr2.
2019-03-11 17:24:06,560 [INFO] Resolving the chromsome chrUn_KI270744v1.
2019-03-11 17:24:06,560 [INFO] Resolving the chromsome chr16.
2019-03-11 17:24:06,565 [INFO] Resolving the chromsome chr4_GL000008v2_random.
2019-03-11 17:24:06,568 [INFO] Resolving the chromsome chr20
...

and this is how it terminates:

2019-03-11 17:24:10,626 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270381v1.
2019-03-11 17:24:10,635 [INFO] Resolving the chromsome chrUn_KI270392v1.
2019-03-11 17:24:10,636 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270392v1.
2019-03-11 17:24:10,638 [INFO] Resolving the chromsome chrUn_KI270371v1.
2019-03-11 17:24:10,638 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270371v1.
2019-03-11 17:24:10,640 [INFO] Resolving the chromsome chrUn_KI270372v1.
2019-03-11 17:24:10,640 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270372v1.
2019-03-11 17:24:10,641 [INFO] Resolving the chromsome chrUn_KI270375v1.
2019-03-11 17:24:10,641 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270375v1.
2019-03-11 17:24:10,645 [INFO] Resolving the chromsome chrUn_KI270385v1.
2019-03-11 17:24:10,645 [INFO] 0 MEI signal locuses in the chromsome chrUn_KI270385v1.
2019-03-11 17:34:59,547 [ERROR] Merging ME signatures failed!
2019-03-11 17:34:59,547 [ERROR] RETCODE 1
2019-03-11 17:34:59,547 [ERROR] STDOUT b'cat: <DATA>/rMETL/signatures/*: No such file or directory\n'
2019-03-11 17:34:59,547 [ERROR] STDERR None
2019-03-11 17:34:59,547 [ERROR] Exiting

Any help would be greatly appreciated.

tjiangHIT commented 5 years ago

Thank you for using rMETL and your bug report. This error is raised by no directory which called /rMETL. I strongly recommend that you can make directoris manually at first. By the way, pls use the latest version. I'll close this issue for now. Feel free to reopen if you have further questions :)

SegoleneDiry commented 4 years ago

Hi, I have the same problem when I run the following command : rMETL detection ../align/mysample.bam /reference/hg38/ref.fa transposons/temp/ transposons/mysample/ -s 2 -x ont However I manually created the directories transposons/temp/ and transposons/mysample/ before running the command.

Here is the end of the STDOUT with error 

2020-08-27 14:23:38,952 [INFO] 0 MEI/MED signal loci in the chromsome chrUn_KI270745v1.
2020-08-27 14:23:38,952 [INFO] 0 MEI/MED signal loci in the chromsome chrUn_KI270748v1.
2020-08-27 14:23:38,952 [INFO] Resolving chromsome chrUn_KI270752v1.
2020-08-27 14:23:38,953 [INFO] 0 MEI/MED signal loci in the chromsome chrUn_KI270752v1.
2020-08-27 14:23:38,955 [INFO] Resolving chromsome chrUn_KI270753v1.
2020-08-27 14:23:38,955 [INFO] 0 MEI/MED signal loci in the chromsome chrUn_KI270753v1.
2020-08-27 14:23:38,955 [INFO] Resolving chromsome chrUn_KI270755v1.
2020-08-27 14:23:38,955 [INFO] 0 MEI/MED signal loci in the chromsome chrUn_KI270755v1.
2020-08-27 14:23:38,956 [INFO] Resolving chromsome chrY_KI270740v1_random.
2020-08-27 14:23:38,956 [INFO] 0 MEI/MED signal loci in the chromsome chrY_KI270740v1_random.
2020-08-27 14:23:39,218 [ERROR] Merging ME signatures failed!
2020-08-27 14:23:39,218 [ERROR] RETCODE 1
2020-08-27 14:23:39,218 [ERROR] STDOUT b"cat: 'transposons/temp/signatures/*': No such file or directory\n"
2020-08-27 14:23:39,218 [ERROR] STDERR None
2020-08-27 14:23:39,218 [ERROR] Exiting

Could you help me? Thanks,

tjiangHIT commented 4 years ago

Hello @SegoleneDiry rMETL is designed for python2. Please check your python version. Some suggestions:

Hope this can help!

Tao

SegoleneDiry commented 4 years ago

Thank you Tao for your answer. Indeed, I was working with Python3... so, I will try with Python2