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hattori-lab / SACRA

SACRA (Split Amplified Chimeric Read Algorithm) is the algorithm for correcting chimeric long-reads generated by MDA.
MIT License
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syntax error near unexpected token `(' #6

Closed aguygarner closed 3 years ago

aguygarner commented 3 years ago

Hi, I am running Sacra on some reads corrected using NECAT. The output of NECAT makes the read names as follows with parentheses in them.

ontsa_id14509(0_10814_10864_10814_109_220.000000)(469_10822_10140_10864_57_51_46.646883):222-417

On the last step of running SACRA on this data I get the following error. cns_final.fasta.blasttab.depth.pcratio.faidx.split10.sh: line 1: syntax error near unexpected token (' cns_final.fasta.blasttab.depth.pcratio.faidx.split10.sh: line 1:samtools faidx cns_final.fasta ontsa_id14509(0_10814_10864_10814_109_220.000000)(469_10822_10140_10864_57_51_46.646883):222-417 >> cns_final.fasta.blasttab.depth.pcratio.faidx.split10.fasta'

Is there a simple work around to move forward with this or do I need to figure out how to change my read names?

aguygarner commented 3 years ago

it seems that single quotes in this command on line 148 of SACRA.sh resolves this issue echo "samtools faidx '$i' '$j' >> $n.fasta" >> $n.sh

YuyaKiguchi commented 3 years ago

Hi aguygarner,

Thank you for your information. I think it's because samtools could not handle unusual characters like "(". Please remove "(" from the header of your fasta or add single quotes as you suggested.

Yuya