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TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
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NCLscan error: "does not appear to be a valid novoindex. Code 9" #15

Closed Swadha22 closed 5 years ago

Swadha22 commented 5 years ago

Hi, I have been trying to use NCLscan Version 1.6 for one of my projects. I am getting this same error again and again: "does not appear to be a valid novoindex. Code 9" I have the licence of NOVOCRAFT software for one month trial. Do you know why I am getting this type of error and what should I do to fix this?

I have attached the output file with this email. NCLscan_novoindex_error.txt

Any help will be appreciated. Thanks in advance, Swadha

chiangtw commented 5 years ago

Hi,

This error message is probably due to the "empty" index file. (You may check the file "[Project_name].JS2.fa" to see if it is empty.)

For further help, please provide the output of the following command: 

ls -lhtr /path/to/NCLscan_output_dir

Thanks for the report!

tw

Swadha22 commented 5 years ago

Hey, Thanks a lot for getting back! Yes, it looks like that file is empty. Here is the list of output files below:

total 39G -rw-r--r-- 1 roylab roylab 3.0G Sep 17 13:43 test_NCLscan.main.bwa.bam -rw-r--r-- 1 roylab roylab 6.5G Sep 17 13:48 test_NCLscan.main.bwa.unmapped.sam -rw-r--r-- 1 roylab roylab 232M Sep 17 13:50 test_NCLscan.main.bwa.unmapped.sam.id -rw-r--r-- 1 roylab roylab 2.8G Sep 17 13:53 test_NCLscan.main.bwa.unmapped_1.fastq -rw-r--r-- 1 roylab roylab 2.8G Sep 17 13:55 test_NCLscan.main.bwa.unmapped_2.fastq -rw-r--r-- 1 roylab roylab 3.2G Sep 17 14:53 test_NCLscan.main.sam -rw-r--r-- 1 roylab roylab 2.3G Sep 17 14:58 test_NCLscan.main.unmapped.sam -rw-r--r-- 1 roylab roylab 179M Sep 17 14:58 test_NCLscan.main.unmapped.sam.id -rw-r--r-- 1 roylab roylab 2.2G Sep 17 15:00 test_NCLscan.main.unmapped_1.fastq -rw-r--r-- 1 roylab roylab 2.2G Sep 17 15:03 test_NCLscan.main.unmapped_2.fastq -rw-r--r-- 1 roylab roylab 1.9G Sep 17 15:18 test_NCLscan.main.unmapped.fa -rw-r--r-- 1 roylab roylab 1.9G Sep 17 15:19 test_NCLscan.unmapped.fa -rw-r--r-- 1 roylab roylab 104M Sep 17 15:32 test_NCLscan.rG.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:32 test_NCLscan.un.psl -rw-r--r-- 1 roylab roylab 104M Sep 17 15:32 test_NCLscan.rG.non_un.psl -rw-r--r-- 1 roylab roylab 171K Sep 17 15:32 test_NCLscan.chi0.bed -rw-r--r-- 1 roylab roylab 291K Sep 17 15:33 test_NCLscan.unmapped.2.fa -rw-r--r-- 1 roylab roylab 307K Sep 17 15:33 test_NCLscan.coding.2.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:33 test_NCLscan.lncRNA.2.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:33 test_NCLscan.chrM.2.psl -rw-r--r-- 1 roylab roylab 628 Sep 17 15:33 test_NCLscan.colinear.psl -rw-r--r-- 1 roylab roylab 171K Sep 17 15:33 test_NCLscan.chi.bed -rw-r--r-- 1 roylab roylab 9.2K Sep 17 15:33 test_NCLscan.preJS.bed -rw-r--r-- 1 roylab roylab 8.8K Sep 17 15:33 test_NCLscan.preJS.info -rw-r--r-- 1 roylab roylab 8.6K Sep 17 15:33 test_NCLscan.preJS.info2 -rw-r--r-- 1 roylab roylab 5.6K Sep 17 15:33 test_NCLscan.JS.info_1 -rw-r--r-- 1 roylab roylab 4.0K Sep 17 15:33 test_NCLscan.JS.info_2 -rw-r--r-- 1 roylab roylab 2.1K Sep 17 15:33 test_NCLscan.JS.info -rw-r--r-- 1 roylab roylab 1.4K Sep 17 15:33 test_NCLscan.JS.cleaned.info -rw-r--r-- 1 roylab roylab 32K Sep 17 15:33 test_NCLscan.preJS.seq -rw-r--r-- 1 roylab roylab 32K Sep 17 15:33 test_NCLscan.preJS.seq2 -rw-r--r-- 1 roylab roylab 18K Sep 17 15:33 test_NCLscan.JS.seq_1 -rw-r--r-- 1 roylab roylab 15K Sep 17 15:33 test_NCLscan.JS.seq_2 -rw-r--r-- 1 roylab roylab 8.6K Sep 17 15:33 test_NCLscan.JS.seq12 -rw-r--r-- 1 roylab roylab 5.4K Sep 17 15:33 test_NCLscan.JS.seq -rw-r--r-- 1 roylab roylab 5.4K Sep 17 15:33 test_NCLscan.JS.fa -rw-r--r-- 1 roylab roylab 1.1M Sep 17 15:33 test_NCLscan.JS.ndx -rw-r--r-- 1 roylab roylab 2.5G Sep 17 15:37 test_NCLscan.main_1.JS.sam -rw-r--r-- 1 roylab roylab 2.5G Sep 17 15:40 test_NCLscan.main_2.JS.sam -rw-r--r-- 1 roylab roylab 5.0G Sep 17 15:41 all.test_NCLscan.JS.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:41 all.test_NCLscan.JS.Parsered.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 tmp.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.JS.clear.fa -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.JS.GRCh37.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.linearJS -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.JS.GRCh37.2.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.tmp.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.tmp2.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.2.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:44 test_NCLscan.2.info.fa -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.2.info.GRCh37.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.2.chi.bed -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 temp.list -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.chi2.bed -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.chi3.bed -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.PreJS2.bed -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.PreJS2.info -rw-r--r-- 1 roylab roylab 2 Sep 17 15:45 test_NCLscan.PreJS2.info2 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.info_1 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.info_2 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.cleaned.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.preIdx -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS1.preIdx -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS1.Idx -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.Idx -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.PreJS2.seq -rw-r--r-- 1 roylab roylab 2 Sep 17 15:45 test_NCLscan.PreJS2.seq2 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.seq_1 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.seq_2 -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.seq -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.prefa -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.fa -rw-r--r-- 1 roylab roylab 1.1M Sep 17 15:45 test_NCLscan.JS2.ndx -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.main.JS2.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.1.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.1.result -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.ncl.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.JS2.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.result -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.JS2.result.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.result.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.2b.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.4.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.3.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.preResult -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.main_1.um3.fastq -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.main_2.um3.fastq -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.main.um3.fa -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.um3.fa -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.rG.um3.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.coding.um3.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.lncRNA.um3.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.chrM.um3.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.um3.colinear.psl -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.main.JS2b.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.1b.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.1b.result -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.JS2b.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.result.sam -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 all.test_NCLscan.b.result -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.3b.info -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.result.tmp -rw-r--r-- 1 roylab roylab 0 Sep 17 15:45 test_NCLscan.4b.info

Thanks Swadha

chiangtw commented 5 years ago

Hi,

It seems that most of the candidates of NCL events are not on the annotated exon boundaries.

You may check the following two NCL candidates files:

-rw-r--r-- 1 roylab roylab 171K Sep 17 15:33 test_NCLscan.chi.bed
-rw-r--r-- 1 roylab roylab 9.2K Sep 17 15:33 test_NCLscan.preJS.bed

The second(test_NCLscan.preJS.bed) is derived from the first(test_NCLscan.chi.bed) by correcting to the annotated exon boundaries.

Simply check the file size, we see that it decreases from 171k to 9.2k. And such decrease of NCL candidates then leads the pipeline to fails.

Thanks tw