miARma Readcount Analysis problem

[Adrian Kasztelan]

Hi,

I obtained such error when trying to run analysis:

sh: line 1: 27741 Segmentation fault: 11 featureCounts -s 0 -t miRNA -g transcript_id -T 2 -a Examples/basic_examples/miRNAs/data/ath_miR_annot.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//nat_bw1_readcount_results/5_ADXS_1_12_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//Bowtie1_results/5_ADXS_1_12_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//miARma_logfile.25509.log SEQCOUNT ERROR :: system args failed: 35584 (mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//nat_bw1_readcount_results/ ;featureCounts -s 0 -t miRNA -g transcript_id -T 2 -a Examples/basic_examples/miRNAs/data/ath_miR_annot.gtf -o Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//nat_bw1_readcount_results/5_ADXS_1_12_cut_nat_bw1.tab Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//Bowtie1_results/5_ADXS_1_12_cut_nat_bw1.bam 2>> Examples/basic_examples/miRNAs/Known_miRNAs/results_Ath//miARma_logfile.25509.log) at lib/CbBio/RNASeq/Readcount.pm line 202.

For several bam files it goes without any problem until the error occurs. I have successfully pass through example from miARma website without such issue.

Could you please help me?

Best regards, Adrian

[Adrian Kasztelan]

I finally had passed through it. Please close the topic.

[Vasu Saini]

May I ask how did you solve this issue?

I am getting a similar error

[Eduardo Andres Leon]

Dear Vasu, please include you log files (stat and log file), please

‌

[Vasu Saini]

That error has been resolved.

Thanks

Apparently it was due to an older version of subread