Hi all,
I have pair-end data that I am currently analysing using Trinity.
I am now running the following script provided by Trinity to estimate abundance:
run_RSEM_align_n_estimate.pl --seqType fq --SS_lib_type RF --left seq1.fq --right seq2.fq --thread_count 16 --prefix /output/RSEM --transcripts Trinity.fasta
and although I get all the output files, I get errors in the log:
Warning: Exhausted best-first chunk memory for read X; skipping read
(or around 11000 reads)
# reads processed: 188565323
# reads with at least one reported alignment: 82758840 (43.89%)
# reads that failed to align: 105806483 (56.11%)
Reported 225985477 paired-end alignments to 1 output stream(s)
[bam_sort_core] merging from 335 files...
From my understanding, you can play with the following setting in Bowtie (--chunkmbs) to increase memory requirements for alignment.
But is there any possibility to do so using the perl script provided in Trinity (run_RSEM_align_n_estimate.pl)? Or should I analyse my data with RSEM directly, as it offers a --bowtie-chunkmbs option?
I have pair-end data that I am currently analysing using Trinity.
I am now running the following script provided by Trinity to estimate abundance:
run_RSEM_align_n_estimate.pl --seqType fq --SS_lib_type RF --left seq1.fq --right seq2.fq --thread_count 16 --prefix /output/RSEM --transcripts Trinity.fasta
and although I get all the output files, I get errors in the log:
Warning: Exhausted best-first chunk memory for read X; skipping read
(or around 11000 reads)
# reads processed: 188565323
# reads with at least one reported alignment: 82758840 (43.89%)
# reads that failed to align: 105806483 (56.11%)
Reported 225985477 paired-end alignments to 1 output stream(s)
[bam_sort_core] merging from 335 files...
From my understanding, you can play with the following setting in Bowtie (--chunkmbs) to increase memory requirements for alignment.
But is there any possibility to do so using the perl script provided in Trinity (run_RSEM_align_n_estimate.pl)? Or should I analyse my data with RSEM directly, as it offers a --bowtie-chunkmbs option?
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