search

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
27 stars 13 forks source link

Could not find Bowtie2 index file presist #22

Closed WalterHK closed 3 years ago

WalterHK commented 3 years ago

Hello,

     I have encountered a closed issue in which the solution is to use the most update LIONS and all fastq should be compressed. However, I still have the same problem. Followings are the code for executing lions_opt.sh

./lions_opt.sh \ -P /home/mytools/LIONS/WTRNA_para/WTRNA.ctrl \ -b /home/mytools/LIONS \ -p WTRNAseq \ -i /home/mytools/LIONS/WTRNA_para/input.list --callsettings oncoexaptation --index /home/mytools/LIONS/resources/hg19/genome/hg19 --geneset /home/mytools/LIONS/resources/hg19/annotation/refSeq_hg19.ucsc --repeatmasker /homemytools/LIONS/resources/hg19/repeat/rm_hg19.ucsc --systemctrl /homemytools/LIONS/controls/system.sysctrl --bowtie bowtie2 --alignbypass 1 --threads 40

Following are the error codes: Checking for Bowtie Bowtie verison: 2.2.6.0 Checking for Bowtie index file (genome).. Error: Could not find Bowtie 2 index file (bowtie2.*.bt2l) du: cannot access _acceptedhits.bam: No such file or directory /home/mytools/LIONS/scripts/eastLion.sh: line 194: [: -ge unary operator expected Alignment probably didnt work

    Since I using hg19 which size is less than 4G, bt2l should not be generated.

    Thank you for your help.

Best, Walter

ababaian commented 3 years ago

Sorry I will get to this later in the evening when the tyke is asleep. or did you resolve this?

WalterHK commented 3 years ago

Thank you for your instant response, the problem is mine since I declare something wrong in the parameter file.

ababaian commented 3 years ago

I apologize in advance this isn't the most user-friendly software. I was a PhD student learning software development on the fly.

WalterHK commented 3 years ago

May I ask if the program takes 6 hours to complete alignments, how long the post alignment work needs?

ababaian commented 3 years ago

About the same time, the python scripts need to go through read by read to calculate statistics.