Comments (6)
haowenz
commented on August 24, 2024
I see the issue. It should work with low memory mode turned off. In this case, the temp mapping files won't be generated. Otherwise, it will generate temp mapping file in the same directory, which caused the issue. We should have a fix for this. When the output is /dev/stdout, we just use the current directory as the temp directory.
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lvyunyunSCI
commented on August 24, 2024
Thank you for your prompt reply, how should I fix this bug now or fix it when the next version is updated (but I see you have updated a version in recent days).
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主题: Re: [haowenz/chromap] [BUG] output to /dev/stdout (Issue #150)
I see the issue. It should work with low memory mode turned off. In this case, the temp mapping files won't be generated. Otherwise, it will generate temp mapping file in the same directory, which caused the issue. We should have a fix for this. When the output is /dev/stdout, we just use the current directory as the temp directory.
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mourisl
commented on August 24, 2024
Thank you for bringing up this issue. We move the temporary files to the local directory when outputting to stdout. The updated code is in the li_dev5 branch. Could you please checkout this branch and give it a try? If it works on your system, we will merge it to the master branch. Thank you.
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mourisl
commented on August 24, 2024
Hi @lvyunyunSCI have you got a chance to test the code in the li_dev5 branch?
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Related Issues (20)
- An unknown error HOT 32
- [BUG] summary and log are confusing. HOT 6
- "Number of mapped reads" from log file HOT 3
- [Feature Request] report number of duplicated fragments in bulk HOT 4
- Different ValidPairs rate between chromap and bowtie2 in HiC data HOT 9
- how to keep multi-mapped paires for HiC data. HOT 1
- Understanding the multi-mapping reads and whether they are part of the bed file HOT 2
- ATAC-seq single end? HOT 3
- Coordinate system of the output fragment file? HOT 1
- multi-mapped reads HOT 3
- [BUG] Manpage is down HOT 1
- [BUG] Support for combinatorial barcode indexing(like SHARE) not present HOT 3
- [BUG] chromap map Hi-C short reads Parameters: error threshold HOT 2
- [BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM HOT 4
- Repetitive or low-quality barcode sequences in scATAC data HOT 1
- [BUG] possibly improper MD tag generation whej running atac data. HOT 3
- Mapping paired-end single-cell ATAC-Seq reads HOT 2
- why so slow? HOT 2
- Failure to load cellular barcodes containing Ns HOT 3
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