junction_saturation.py error -- ValueError: tid -1 out of range 0<=tid<25

Michael zhou

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Apr 28, 2014, 4:54:34 PM4/28/14

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I am trying to run command line one by one, all other functions seem to work (except 2 more functions which are still running, so far so good. )

when i tried junction annotion, no error message, but output is 0

when I tried junction saturation, got the ValueError: tid -1 out of range 0<=tid<25.

I did try these 2 functions on the sample data from the website, it worked.

Anyone has any ideas?

Thanks a lot for your help.

############# error message ####################

$RSeQC/junction_saturation.py -i ${x}.sorted.bam -r $r efSeqBed -o ${x}.sorted.bam

reading reference bed file: /home/hz783373/ngs5/onc_ngs5/MichaelHZ/ database/Homo_sapiens/UCSC/hg19/hg19_RefSeq.bed ... Done! Total 21 9696 known splicing junctions.

Load BAM file ... Traceback (most recent call last):

File "/home/hz783373/ngs5/onc_ngs5/MichaelHZ/software/RSeQC-2.3.9/ scripts/junction_saturation.py", line 99, in <module>

main()

File "/home/hz783373/ngs5/onc_ngs5/MichaelHZ/software/RSeQC-2.3.9/ scripts/junction_saturation.py", line 85, in main

obj.saturation_junction(outfile=options.output_prefix, refgene=o ptions.refgene_bed, sample_start=options.percentile_low_bound,sample _end=options.percentile_up_bound,sample_step=options.percentile_step ,min_intron=options.minimum_intron_size,recur=options.minimum_splice _read, q_cut = options.map_qual)

File "/home/hz783373/ngs5/onc_ngs5/MichaelHZ/bin/lib/python2.7/sit e-packages/RSeQC-2.3.9-py2.7-linux-x86_64.egg/qcmodule/SAM.py", line 3670, in saturation_junction

chrom = self.samfile.getrname(aligned_read.tid).upper()

File "csamtools.pyx", line 644, in csamtools.Samfile.getrname (lib /pysam/csamtools.c:6891)

ValueError: tid -1 out of range 0<=tid<25

Liguo Wang

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Apr 28, 2014, 8:55:55 PM4/28/14

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Hi Mike,

Make sure the chromosome IDs (chr1, chr2, chrX, etc) are consistent between your alignment BAM file and the gene model BED files.

Liguo

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Michael zhou

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Apr 29, 2014, 11:53:33 AM4/29/14

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Hi Liguo,

I checked both reference genome (i use ucsc hg19) and hg19_RefSeq.bed, both use "chr". I assume my .bam files are also use this. So they should be consistant. Any other possibilities for the error? Thanks a lot.

Michael

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Michael zhou

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Jun 4, 2014, 9:24:34 AM6/4/14

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hi liguo,

here is my .bam output

HWI-1KL155:43:H088BADXX:2:1114:13792:19720 163 chr2 20199715 42 50M = 20199801 136 CTCAAACTTACTGGAAGATCTGTGTGGGTCTAATTCAGGCATTCACAAAG CCCFFFFFHHHHHEHIHIGGHDHHCGHIDHHGIJGIJIJJJIJJJJIJJI AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP

HWI-1KL155:43:H088BADXX:1:2213:7424:98962 83 chr2 20199743 42 50M = 20199610 -183TCTAATTCAGGCATTCACAAAGTCTTCTTTACTAAAATCATCCAGCTTTA IHIJIGHJHGEJIGGIHJGJIHDIIJJJJIIFFJIGGDHDHGFFFDD@?B AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP

HWI-1KL155:43:H088BADXX:2:1114:13792:19720 83 chr2 20199801 42 50M = 20199715 -136ACTACAGAAAAGTTCCAGGCCAAGTTTTAACTGGAAAAAGATCAGTTCAT FEGG?IHC9JGIGJGGHGC+JJJJJJJJFFCGJJIGJHHHHDDFFFDCCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP

HWI-1KL155:43:H088BADXX:1:1103:5121:92473 99 chr2 20199819 42 50M = 20199945 176 GCCAAGTTTTAACTGGAAAAAGATCAGTTCATCCTATCACACCAAATAGT B@BFDDDEHGFHHHIJJ?IH>EFHF9CHHHEIJJICHI@DHJJJJJJCGI AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP

HWI-1KL155:43:H088BADXX:1:1103:5121:92473 147 chr2 20199945 42 50M = 20199819 -176GGATAAGGACCCTACATTTAGTTAGTTTTTCTCATATCCCCCACTCCCTA C8AG@DC=8FB?<B@HHD9D<GG?FGGF??HEEHGHFHAHBCA@BDD=1? AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP

here i s the bed file i use: /hg19_RefSeq.bed

chr1 175913966 176176370 NM_022457 0 - 175914288 176176114 0 20 340,4

5,161,125,118,117,82,109,144,136,115,58,77,60,69,120,77,98,60,663, 0,2364,42112,43457,44531,82741,98355,98879,101350,136

321,140945,171793,190179,191657,204175,218038,218984,231079,239802,261741,

chr1 175913966 176176370 NM_001001740 0 - 175914288 176176114 0 19 340,4

5,161,125,118,117,82,109,144,136,115,58,77,69,120,65,98,60,663, 0,2364,42112,43457,44531,82741,98355,98879,101350,136321,1409

What is the reason I can not get any result?

Thanks.

Michael

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Liguo Wang

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Jun 4, 2014, 2:58:49 PM6/4/14

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The format has no problem. If the program finished normally, I cannot understand why you didn't get any results. Be sure the bam and bed files are matched:

1) chromosome name

2) genome version (hg19 or hg18)

3) there are reads in BAM files covering your genes. It cannot give you results if your BAM file contains reads aligned to chr2, and your input genes are all from chr1. ( But I guess what you sent is just example)

You try to run this program using other bam files to see if it works.

Liguo

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Indugu Nagaraju

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Jun 3, 2016, 7:10:17 PM6/3/16

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Hi

I am getting same error meassage when I run junction_saturation.py.

Michael how you solved this issue. The chromosome names in bam file and reference file are same.

log file

Load BAM file ... Traceback (most recent call last):

File "/usr/local/bin/junction_saturation.py", line 5, in <module>

pkg_resources.run_script('RSeQC==2.4', 'junction_saturation.py')

File "/opt/qiime/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 499, in run_script

self.require(requires)[0].run_script(script_name, ns)

File "/opt/qiime/matplotlib-1.3.1-release/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg/pkg_resources.py", line 1239, in run_script

execfile(script_filename, namespace, namespace)

File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.4-py2.7-linux-x86_64.egg/EGG-INFO/scripts/junction_saturation.py", line 99, in <module>

main()

File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.4-py2.7-linux-x86_64.egg/EGG-INFO/scripts/junction_saturation.py", line 85, in main

obj.saturation_junction(outfile=options.output_prefix, refgene=options.refgene_bed, sample_start=options.percentile_low_bound,sample_end=options.percentile_up_bound,sample_step=options.percentile_step,min_intron=options.minimum_intron_size,recur=options.minimum_splice_read, q_cut = options.map_qual)

File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.4-py2.7-linux-x86_64.egg/qcmodule/SAM.py", line 3670, in saturation_junction

chrom = self.samfile.getrname(aligned_read.tid).upper()

File "csamtools.pyx", line 644, in csamtools.Samfile.getrname (lib/pysam/csamtools.c:7386)

ValueError: tid -1 out of range 0<=tid<25

Thank you

Raju

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