Comments (8)
Thanks for your email. It looks that the code staff_bwa failed. Could you send me a few lines of the texts from align.dat? 10 or two line should be fine. I just want to check if the data format is in line with the pipeline.
Best regards,
Zemin
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Sorry 10 or 20 lines from align.dat.
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It is also possible that BWA didn't get finished and the number of column in the last line is not equal the one in other lines. If this is the case, you can repeat another run.
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Thanks. The file align.dat seems to be fine. How much RAM do you have in your computer? The code of staff_bwa does not use much RAM at this stage, maybe 5-6 GB.
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I have the same question when I ran to scaff_bwa. My RAM is 3TB and my genome is 500Mb. I think it can't be the RAM problem.
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Hi all,
is there a solution in the end?
I am encountering the same problem.
I also have 400 GB memory, so no memory issue.
the align.dat lines:
head align.dat
A00685:102:HWLNMDRXX:1:2101:1217:1000 99 tarseq_73 587650 56
A00685:102:HWLNMDRXX:1:2101:1235:1000 99 tarseq_37 491377 60
A00685:102:HWLNMDRXX:1:2101:1307:1000 83 tarseq_16 526825 60
A00685:102:HWLNMDRXX:1:2101:1976:1000 83 tarseq_44 103907 60
A00685:102:HWLNMDRXX:1:2101:2211:1000 99 tarseq_31 2014651 60
A00685:102:HWLNMDRXX:1:2101:2230:1000 83 tarseq_12 1873831 60
A00685:102:HWLNMDRXX:1:2101:3296:1000 99 tarseq_43 628817 9
A00685:102:HWLNMDRXX:1:2101:3351:1000 83 tarseq_56 766484 60
A00685:102:HWLNMDRXX:1:2101:3477:1000 83 tarseq_76 662403 60
A00685:102:HWLNMDRXX:1:2101:3586:1000 99 tarseq_90 226154 60
tail align.dat
A00685:102:HWLNMDRXX:2:2278:30752:37059 99 tarseq_16 1050079 60
A00685:102:HWLNMDRXX:2:2278:30843:37059 83 tarseq_14 2815439 34
A00685:102:HWLNMDRXX:2:2278:31186:37059 83 tarseq_14 1183768 60
A00685:102:HWLNMDRXX:2:2278:31222:37059 81 tarseq_7 4039605 0
A00685:102:HWLNMDRXX:2:2278:31656:37059 99 tarseq_113 391255 60
A00685:102:HWLNMDRXX:2:2278:31982:37059 83 tarseq_29 451249 60
A00685:102:HWLNMDRXX:2:2278:32072:37059 83 tarseq_93 58721 40
A00685:102:HWLNMDRXX:2:2278:32145:37059 99 tarseq_7 3602339 60
A00685:102:HWLNMDRXX:2:2278:32452:37059 99 tarseq_41 197280 60
A00685:102:HWLNMDRXX:2:2278:32633:37059 65 tarseq_9 2755947 21
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I encountered the same segfault issue mentioned here and in #18 when using the raw R1 and R2 linked reads as inputs (in this case, TELL-seq reads with barcodes converted to be 10X compatible) for Scaff10X v4.2.
Running scaff_reads to generate debarcoded *.fastq.gz R1 and R2 files, and using these as inputs for scaff10x v4.2 seemed to fix it, as alluded to here.
Note that there may be a path issue with scaff_reads as previously raised (#5) - quick fix here.
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Related Issues (20)
- No scaffolding being done on the Scaff10xV4 HOT 4
- Segmentation fault HOT 24
- cannot find input.dat HOT 2
- can you update the docs to reflect the actual usage
- segfault HOT 10
- run fails at scaff_matrix HOT 8
- another seg fault issue HOT 6
- Floating point exception in break10x HOT 11
- scaff_reads: Segmentation fault HOT 3
- scaff_bwa segmentation fault HOT 3
- pre n50 = scaff10x n50 HOT 1
- scaff_screeN not found HOT 4
- how does scaff_reads works
- "Numbers of contigs are difference," error in "scaff_bwa-barcode"
- add gnuplot and inkscape to install.sh
- segmentation fault scaff_bwa.c
- scaff10x still running after 22 days
- Pigz installation
- Scaffolding with parental reads
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