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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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BoundsException #82

Open YIGUIz opened 4 days ago

YIGUIz commented 4 days ago

Hi, An error was reported: Java.lang.ArrayIndexOutOfBoundsException: Index 9 out of bounds for length 9.

rnabloom:2.0.1

openjdk version "1.8.0_181" OpenJDK Runtime Environment (build 1.8.0_181-b13) OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)

set -x; /usr/bin/time -v singularity exec /public/home/b20223040336/Workspace/long_read_rna/02code/singularity_images/rnabloom\:2.0.1--hdfd78af_1 rnabloom -t 30 -ntcard -long hypothalamus_34_qc_FL_reads.fq.gz hypothalamus_3_qc_FL_reads.fq.gz hypothalamus_4_qc_FL_reads.fq.gz hypothalamus_1_qc_FL_reads.fq.gz hypothalamus_2_qc_FL_reads.fq.gz hypothalamus_16_qc_FL_reads.fq.gz -sef hypothalamus_3_R1.clean.fq.gz hypothalamus_4_R1.clean.fq.gz hypothalamus_3_R2.clean.fq.gz hypothalamus_4_R2.clean.fq.gz -fpr 0.005 -indel 20 -p 0.75 -Q 15 -overlap 100 -length 150

report error: image

image

Thank you so much for your help.

kmnip commented 3 days ago

Your overlapping step (with minimap2) should generate a PAF format output with 12 columns, but it did not, hence the error. I think it ran out of memory because you have a lot of reads.

Can you use less reads and try again? May be just 2 long-read FASTQs instead of 6? Also, remove these settings: -indel 20 -p 0.75 -overlap 100