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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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arf is empty #104

Closed yy549159265 closed 2 years ago

yy549159265 commented 2 years ago

my log


current dir:    /home/yuanshuai20/DP/Transcribe/srna/mirdeep_output
mapper command: ../mirdeep2-master/src/mapper.pl ../exon.intron.filter/all.fa -c -v -n -l 17 -p ../gene_index/MG8 -t all_aligned.arf

timestamp: 28_11_2022_t_19_39_10

discarding short reads fastaparse.pl ../exon.intron.filter/all.fa -a 17 > dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/reads_no_short.fa 2>dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/reads_too_short mapping reads to genome index bowtie -p 1 -f -n 0 -e 80 -l 18 -a -m 20 --best --strata ../gene_index/MG8 --al dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/all.fa_mapped --un dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/all.fa_not_mapped dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/reads_no_short.fa dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/mappings.bwt 2>bowtie.log

convert_bowtie_output.pl dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/mappings.bwt > dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/mappings.arf trimming unmapped nts in the 3' ends parse_mappings.pl dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/mappings.arf -j > dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/mappings_trim.arf

remove tmp dir rmtree(dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10)

fastaparse.pl ../exon.intron.filter/all.fa -a 17 > dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/reads_no_short.fa 2>dir_mapper_seq_all.fa_1488199162_28_11_2022_t_19_39_10/reads_too_short


I fount reads_no_short.fa is empty.It leads to my bowtie comparison that arf is null.How can I solve it? Thank you
yy549159265 commented 2 years ago

bowtie-log

Warning: Could not find any reads in "dir_mapper_seq_all.fa_3951745085_28_11_2022_t_19_41_57/reads_no_short.fa"
# reads processed: 0
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
No alignments
yy549159265 commented 2 years ago

I found the answer. I didn't give *.pl permission