Open WeiZhaoLuck opened 11 months ago
But there are already partial results
I think you may need to run samtools index possorted_genome_bam.bam
to generate the possorted_genome_bam.bam.bai
index file
Thanks. I have run samtools index possorted_genome_bam.bam
, but it reports the error:ValueError: fetch called on a bam file without index. Some chromosomes have output results except for the sex chromosomes
I had the same problem and had run samtools index
Can you give me some advice?
When I run prepocess.py with a sorted bam file, the following error occurs after some time: ValueError: fetch called on a bam file without index. How do I fix it?
I've solved the problem, you need to go to the apps directory and give executable permissions to samtools,like chmod +x samtools
I have a related issue:
bash monopogen/runPreprocess.sh
Monopogen: Preprocessing BAM files
[2024-02-16 15:39:22,812] INFO Monopogen.py Performing data preprocess before variant calling...
[2024-02-16 15:39:22,813] INFO germline.py Parameters in effect:
[2024-02-16 15:39:22,813] INFO germline.py --subcommand = [preProcess]
[2024-02-16 15:39:22,813] INFO germline.py --bamFile = [monopogen/bam.lst]
[2024-02-16 15:39:22,813] INFO germline.py --out = [monopogen]
[2024-02-16 15:39:22,813] INFO germline.py --app_path = [/Users/USER_NAME/git/Monopogen/apps]
[2024-02-16 15:39:22,813] INFO germline.py --max_mismatch = [3]
[2024-02-16 15:39:22,813] INFO germline.py --nthreads = [8]
[2024-02-16 15:39:22,899] DEBUG Monopogen.py PreProcessing sample CorArtHealthID1
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: Permission denied
This was solved using chmod -Rv a+rwx /Users/USER_NAME/git/Monopogen/apps/
.
But now I get this:
[2024-02-16 15:43:56,695] INFO Monopogen.py Performing data preprocess before variant calling...
[2024-02-16 15:43:56,696] INFO germline.py Parameters in effect:
[2024-02-16 15:43:56,696] INFO germline.py --subcommand = [preProcess]
[2024-02-16 15:43:56,696] INFO germline.py --bamFile = [monopogen/bam.lst]
[2024-02-16 15:43:56,696] INFO germline.py --out = [monopogen]
[2024-02-16 15:43:56,696] INFO germline.py --app_path = [/Users/USER_NAME/git/Monopogen/apps]
[2024-02-16 15:43:56,696] INFO germline.py --max_mismatch = [3]
[2024-02-16 15:43:56,696] INFO germline.py --nthreads = [8]
[2024-02-16 15:43:56,734] DEBUG Monopogen.py PreProcessing sample CorArtHealthID1
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file
[2024-02-16 15:51:23,069] INFO Monopogen.py Success! See instructions above.
How should I fix this? Presumably Monopogen
did not run properly with this [USER_NAME](sh: /Users/USER_NAME/git/Monopogen/apps/samtools: cannot execute binary file)
message.
And do the number of these messages (22) imply that there is data for 22 chromosomes?
FYI: am running this on macOS. Could this be the issue?
When I run prepocess.py with a sorted bam file, the following error occurs after some time: ValueError: fetch called on a bam file without index. How do I fix it?