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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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lions problems #1

Closed b12loroc closed 6 years ago

b12loroc commented 6 years ago

I have a problem with LIONS. scripts/ChimericReadTool/chimericReadSearch.py Line 728:

"results = processReads(samfile_path, exonTrees, repeatTrees, chimericBedFile)"

& 114

"repeat_results1 = repeatTrees[str(chr)].findRange([start1,end1])"

my resource file are in the same format than lions example and chromosome name is the same in the three files

ababaian commented 6 years ago

This may be an issue with pysam; can you post which version you are using.

b12loroc commented 6 years ago

1) bowtie/2.2.9 7) libxml2/2.7.8 13) samtools/1.4 2) bowtie/1.0 8) openssl/1.0.2f 14) bedtools/2.26.0 3) bowtie/2.2.4 9) latex/3.14 15) bzip2/1.0.6 4) tophat/2.0.13 10) java/jre-8u60 16) lion/171220 5) cufflinks/2.2.1 11) R/3.2.3 6) python/anaconda-3_440 12) gcc/4.9.1

This my module lion

2018-02-06 11:02 GMT+01:00 Artem Babaian notifications@github.com:

This may be an issue with pysam; can you post which version you are using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ababaian/LIONS/issues/1#issuecomment-363372352, or mute the thread https://github.com/notifications/unsubscribe-auth/Af3ejCTUOGMb8U74WqO_1RaQz_IApcmNks5tSCNOgaJpZM4R5Ud_ .

b12loroc commented 6 years ago

pysam 0.13 version

2018-02-06 12:28 GMT+01:00 Carmen Maria Lopez Rodriguez b12loroc@gmail.com :

1) bowtie/2.2.9 7) libxml2/2.7.8 13) samtools/1.4 2) bowtie/1.0 8) openssl/1.0.2f 14) bedtools/2.26.0 3) bowtie/2.2.4 9) latex/3.14 15) bzip2/1.0.6 4) tophat/2.0.13 10) java/jre-8u60 16) lion/171220 5) cufflinks/2.2.1 11) R/3.2.3 6) python/anaconda-3_440 12) gcc/4.9.1

This my module lion

2018-02-06 11:02 GMT+01:00 Artem Babaian notifications@github.com:

This may be an issue with pysam; can you post which version you are using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ababaian/LIONS/issues/1#issuecomment-363372352, or mute the thread https://github.com/notifications/unsubscribe-auth/Af3ejCTUOGMb8U74WqO_1RaQz_IApcmNks5tSCNOgaJpZM4R5Ud_ .

b12loroc commented 6 years ago

Good afternoon Artem, i run lions by a bam file, this file was aligned by STAR, i do not use -tophat2, would this be a problem? how do you input a paired sample with two fastq files in Lions? for example, input list with paired reads in two files. Or is necessary to use an interleaved file??? Cheers Thank you Sorry for any inconvenience caused! Carmen María López Rodríguez

2018-02-06 13:35 GMT+01:00 Carmen Maria Lopez Rodriguez b12loroc@gmail.com :

pysam 0.13 version

2018-02-06 12:28 GMT+01:00 Carmen Maria Lopez Rodriguez < b12loroc@gmail.com>:

1) bowtie/2.2.9 7) libxml2/2.7.8 13) samtools/1.4 2) bowtie/1.0 8) openssl/1.0.2f 14) bedtools/2.26.0 3) bowtie/2.2.4 9) latex/3.14 15) bzip2/1.0.6 4) tophat/2.0.13 10) java/jre-8u60 16) lion/171220 5) cufflinks/2.2.1 11) R/3.2.3 6) python/anaconda-3_440 12) gcc/4.9.1

This my module lion

2018-02-06 11:02 GMT+01:00 Artem Babaian notifications@github.com:

This may be an issue with pysam; can you post which version you are using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ababaian/LIONS/issues/1#issuecomment-363372352, or mute the thread https://github.com/notifications/unsubscribe-auth/Af3ejCTUOGMb8U74WqO_1RaQz_IApcmNks5tSCNOgaJpZM4R5Ud_ .

b12loroc commented 6 years ago

I have run Lions again. My input files this time were your samples (H1rep1,Gmrep...), paired reads in fastq format. Alignment with Tophat gave me the next error: [2018-02-07 13:20:31] Generating SAM header for hg38_illumina Traceback (most recent call last): File "/mnt/backup/soft/tophat/programs/x86_64/2.0.13/tophat", line 4088, in <module> sys.exit(main()) File "/mnt/backup/soft/tophat/programs/x86_64/2.0.13/tophat", line 3942, in main params.read_params = check_reads_format(params, reads_list) File "/mnt/backup/soft/tophat/programs/x86_64/2.0.13/tophat", line 1840, in check_reads_format freader=FastxReader(zf.file, params.read_params.color, zf.fname) File "/mnt/backup/soft/tophat/programs/x86_64/2.0.13/tophat", line 1585, in __init__ while hlines>0 and self.lastline[0] not in "@>" : IndexError: string index out of range Thanks