Could not retrieve index file for 'A.merged.srtn.bam'

[jiangshan529]

Is MAPS only for cutting enzyme MboI?

[armenabnousi]

the text in the title is a warning that has appeared after switching to samtools1.10. It does not affect the operation as far as I've seen.

[jiangshan529]

But I cannot get the final .bedpe file.

[jiangshan529]

the text in the title is a warning that has appeared after switching to samtools1.10. It does not affect the operation as far as I've seen.

But I cannot get the final .bedpe file

[armenabnousi]

can you share the log file here?

[jiangshan529]

can you share the log file here?

I have a question, for bwa index----path to bwa indexed reference genome, I give the path, and also the genome name, such is "/media/ibm_disk/work/database/1.human/GRCh37.p13_cleangeome_index/GRCh37.p13.genome.clean.fa", is that correct? The feather output log is attached here, the map_out folder only has the file "maps_H3K27ac-AAA-shNC-1_val.maps" H3K27ac-AAA-shNC-1_val.feather.log

[armenabnousi]

I have a question, for bwa index----path to bwa indexed reference genome, I give the path, and also the genome name

That depends on how you have created the index file. Bwa index accepts a prefix argument, what goes in this line should include that prefix as well (I believe the default for the prefix in the bwa index is the genome name, in which case your input will be correct). If you check the name of the files in the /media/ibm_disk/work/database/1.human/GRCh37.p13_cleangeome_index/ directory, if all file names (maybe with one or two exceptions) start with GRCh37.p13.genome.clean.fa then I think you should be fine.

Your log file doesn't show any errors but your operation has exited before it was complete. The last message on your log file is "calling samtools flagstat...", after that it should do sorting and splitting the file by chromosome, and then loop calling. My suspicion is that "samtools flagstat" has failed. Try running this command and see whether it gives any errors:

samtools flagstat H3K27ac-AAA-shNC-1_val.paired.rmdup.bam > H3K27ac-AAA-shNC-1_val.paired.rmdup.flagstat

(make sure the file H3K27ac-AAA-shNC-1_val.paired.rmdup.bam exists in your feather_output/H3K27ac-AAA-shNC-1_val_20210515_095838 directory)

Also, try running the example set that comes with MAPS. It's a small set and shouldn't take longer than 10 minutes running. It will help make sure that packages and softwares are installed and are accessible.

[jiangshan529]

I have a question, for bwa index----path to bwa indexed reference genome, I give the path, and also the genome name

That depends on how you have created the index file. Bwa index accepts a prefix argument, what goes in this line should include that prefix as well (I believe the default for the prefix in the bwa index is the genome name, in which case your input will be correct). If you check the name of the files in the /media/ibm_disk/work/database/1.human/GRCh37.p13_cleangeome_index/ directory, if all file names (maybe with one or two exceptions) start with GRCh37.p13.genome.clean.fa then I think you should be fine.

Your log file doesn't show any errors but your operation has exited before it was complete. The last message on your log file is "calling samtools flagstat...", after that it should do sorting and splitting the file by chromosome, and then loop calling. My suspicion is that "samtools flagstat" has failed. Try running this command and see whether it gives any errors:

samtools flagstat H3K27ac-AAA-shNC-1_val.paired.rmdup.bam > H3K27ac-AAA-shNC-1_val.paired.rmdup.flagstat

(make sure the file H3K27ac-AAA-shNC-1_val.paired.rmdup.bam exists in your feather_output/H3K27ac-AAA-shNC-1_val_20210515_095838 directory)

Also, try running the example set that comes with MAPS. It's a small set and shouldn't take longer than 10 minutes running. It will help make sure that packages and softwares are installed and are accessible.

Thanks for your reply. I run MAPS for the test dataset. The log output is attached here, it seems there's something wrong with samtools. nohup.txt

[xumai-du]

Hello, jiangshan529: I am trying to analyze HICHIP data using MAPS and got the same index error messenger as you mentioned above. Similarly, I didn't get the .bedpe file as well. I wonder if you solved this problem eventually and would appreciate very much for any help here. Thanks!

[Xieeeee]

The samtools markdup -m option seems to be the legacy of older version samtools. Using later version like samtools 1.9 I think it is necessary to change the samtools markdup option (I think it is in feather_filter_chr.py)?