search

mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
63 stars 18 forks source link

Fails at stage 3 #9

Closed StoltzfusJ closed 6 years ago

StoltzfusJ commented 6 years ago

When I run: perl run_rcorrector.pl -1 /1RNAseq/read_1.fastq.gz -2 /1RNAseq/read_2.fastq.gz -od /1RNAseq/rCorrector_out/ -t 2 -verbose I get the following: Put the kmers into bloom filter jellyfish bc -m 23 -s 100000000 -C -t 2 -o tmp_d8b9e7e64de6664e34a42a1e89d74e8e.bc <(gzip -cd /1RNAseq/read_1.fastq.gz) <(gzip -cd /1RNAseq/read_2.fastq.gz) Count the kmers in the bloom filter jellyfish count -m 23 -s 100000 -C -t 2 --bc tmp_d8b9e7e64de6664e34a42a1e89d74e8e.bc -o tmp_d8b9e7e64de6664e34a42a1e89d74e8e.mer_counts <(gzip -cd /1RNAseq/read_1.fastq.gz) <(gzip -cd /1RNAseq/read_2.fastq.gz) Dump the kmers jellyfish dump -L 2 tmp_d8b9e7e64de6664e34a42a1e89d74e8e.mer_counts > tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump Error correction /1RNAseq/Programs/Rcorrector-1.0.2/rcorrector -od /1RNAseq/rCorrector_out/ -t 2 -verbose -p /1RNAseq/read_1.fastq.gz /1RNAseq/read_2.fastq.gz -c tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump Failed at stage 3. I've tried this with multiple samples and always get a "failed at stage 3" error. I've run the input reads through FASTQC, and things look good. Any help would be appreciated.

mourisl commented 6 years ago

Do you have the write access to the /1RNAseq/ folder? Since there is no "." in front of it, it points to the root directory which we usually don't have access right. If this is not the case, can you show me a few lines of the fastq file?

Thanks

StoltzfusJ commented 6 years ago

Hi,

Thank you for your reply. In answer to your questions:

Here are the permissions for the directories: drwxr-xr-x 4 jonathanstoltzfus root 4096 Jun 9 15:21 1RNAseq drwxr-xr-x 2 jonathanstoltzfus jonathanstoltzfus 4096 Jun 8 13:23 rCorrector_out

Here are the first few lines of one of the fastq files: @K00315:112:HTGNJBBXX:6:1101:1357:1595 1:N:0:NTCACG CNACGATGTTCCGGATGACGAACTTCTTGATGGCCTTGTCCTTGGGGACGCAGCGGGCGCAGTTGGTGCAGCGGATGGGCTGGACGTGCCCGCGGCCCTTCTTAGCGCGCCCGTTGAGATCGGAAGAGCACACGTCCGAACTCCAGTCAC + A#AFFJJJFFJJJJJFF<FAJJJJ<FJF<AJF<FJJJFFJJ7<FAAAJJFFFAAFJFJJJJJ--7----FA<--A-7A7<7<<FJ<<-77FFJF-A-A7FAJ7JFJ<FAF-AAAF7<JJFAJ<J-7--7FFFJF-A)7AAF-AFF<-AJF @K00315:112:HTGNJBBXX:6:1101:1418:1595 1:N:0:NTCACG CNACACGGATCTCACTCCCAGTGAAACGGCAGGGTGGGAGGATGGGCACCGCATCCTCCTTGTATTTAAAGGGAATTCCACTCATGTGCTGCCTGGCAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATG + A#AFFJJJJJJJJJJJJJJJJAJJJJJJFJJJJJ7<JJJJJJJFJJJJFA<J<7FJ-A<--<-7-7<AFJ<A<JJFJFAJJA-A-A<-AFF7JFA<FJJJJ-A7FAF<AFAFJJJA7F<A7<<FF7<AJFFJAFFFAJJJA-77-<<<-A

Thank you for your assistance.

Sincerely,

Jonathan

Jonathan Stoltzfus, Ph.D. Assistant Professor of Biology Millersville University of Pennsylvania

From: Li Song [notifications@github.com] Sent: Monday, June 11, 2018 1:12 PM To: mourisl/Rcorrector Cc: Jonathan Stoltzfus; Author Subject: Re: [mourisl/Rcorrector] Fails at stage 3 (#9)

Do you have the write access to the /1RNAseq/ folder? Since there is no "." in front of it, it points to the root directory which we usually don't have access right. If this is not the case, can you show me a few lines of the fastq file?

Thanks

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/mourisl/Rcorrector/issues/9#issuecomment-396316736, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmUItWecxcrRdlQjRfDVwjZWFhCQ1vJJks5t7qUBgaJpZM4Ui6gd.

mourisl commented 6 years ago

Can you show me the first lines of tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump? And how many lines in that file?

StoltzfusJ commented 6 years ago

Hi,

The first 10 lines of tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump are: p

1830207 AAAAAAAAAAAAAAAAAAAAAAA 3 ACACATCCAGTGTGGTAGATCTA 5 ACTTGTGCTGGGACACCAAGCGC 2 GTAGGTTGTGGTGGTATCTCGGA 3 GCCCCATGTTGCCAACTCCAGAA

The number of lines in the file is 462359212: T3500:/1RNAseq/Programs/Rcorrector-1.0.2$ wc -l tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump 462359212 tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump

Thank you,

Jonathan

From: Li Song [notifications@github.com] Sent: Monday, June 11, 2018 5:06 PM To: mourisl/Rcorrector Cc: Jonathan Stoltzfus; Author Subject: Re: [mourisl/Rcorrector] Fails at stage 3 (#9)

Can you show me the first lines of tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump? And how many lines in that file?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/mourisl/Rcorrector/issues/9#issuecomment-396387360, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmUItbQ_hmKEZ2vYlNdJ9rgcRY4HJ0Jzks5t7tvTgaJpZM4Ui6gd.

mourisl commented 6 years ago

Can you directly run "/1RNAseq/Programs/Rcorrector-1.0.2/rcorrector -od /1RNAseq/rCorrector_out/ -t 2 -verbose -p /1RNAseq/read_1.fastq.gz /1RNAseq/read_2.fastq.gz -c tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump" to see whether there is any error message? Sorry for the troubles.

StoltzfusJ commented 6 years ago

Hi Li,

I think I figured out the problem. When I ran “make”, there was an error that I didn’t catch (one of the libraries in the version of Ubuntu that I am running wasn’t updated, resulting in the error). After updating the library, and re-configuring, I now have rCorrector running.

My apologies for not realizing this earlier. Thank you for your assistance and your work in making this tool.

Sincerely,

Jonathan

Jonathan Stoltzfus, Ph.D. Assistant Professor of Biology

MILLERSVILLE UNIVERSITY P.O. Box 1002, Millersville, PA 17551-0302 Phone: 717-871-4098 https://www.millersville.edu/biology/faculty/j-stoltzfus.php

From: Li Song [mailto:notifications@github.com] Sent: Tuesday, June 12, 2018 1:32 PM To: mourisl/Rcorrector Rcorrector@noreply.github.com Cc: Jonathan Stoltzfus Jonathan.Stoltzfus@millersville.edu; Author author@noreply.github.com Subject: Re: [mourisl/Rcorrector] Fails at stage 3 (#9)

Can you directly run "/1RNAseq/Programs/Rcorrector-1.0.2/rcorrector -od /1RNAseq/rCorrector_out/ -t 2 -verbose -p /1RNAseq/read_1.fastq.gz /1RNAseq/read_2.fastq.gz -c tmp_d8b9e7e64de6664e34a42a1e89d74e8e.jf_dump" to see whether there is any error message? Sorry for the troubles.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/mourisl/Rcorrector/issues/9#issuecomment-396671494, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AmUIteeSsnfTJNPXVW-xHNS1orMOKa4mks5t7_sVgaJpZM4Ui6gd.

mourisl commented 6 years ago

You are welcome :). I have just updated the wrapper to make sure the rcorrector binary file is there.