About run data preprocess

[WeiZhaoLuck]

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?

[WeiZhaoLuck]

But there are already partial results

[monoplasty]

I think you may need to run samtools index possorted_genome_bam.bam to generate the possorted_genome_bam.bam.bai index file

[WeiZhaoLuck]

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

[zuoyichen]

I had the same problem and had run samtools index

[zuoyichen]

Can you give me some advice?

[zuoyichen]

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

[swvanderlaan]

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?