I have a local backup of all the mm9 Fasta files from an earlier successful bowtie2 build, and I decided to use the same files to build the indices for bowtie1. I copied the Fasta files into the mm9.ebwt directory and ran the included .sh file. This is the result:
end-lazar-010:ATACseq_0845 kaestnerlab$ sh mm9.ebwt/make_mm9.sh
/Users/kaestnerlab/Tuxedo/bowtie-1.1.0/bowtie-build
Running /Users/kaestnerlab/Tuxedo/bowtie-1.1.0/bowtie-build chr1.fa,chr2.fa,chr3.fa,chr4.fa,chr5.fa,chr6.fa,chr7.fa,chr8.fa,chr9.fa,chr10.fa,chr11.fa,chr12.fa,chr13.fa,chr14.fa,chr15.fa,chr16.fa,chr17.fa,chr18.fa,chr19.fa,chrX.fa,chrY.fa,chrM.fa mm9
mm9.ebwt/make_mm9.sh: line 104: 16365 Segmentation fault $CMD
Index building failed; see error message
Concurrent with this output, OS X returns a dialog box exclaiming that Python has crashed. What could be the cause of this?
Running OS X 10.6.8
EDIT: Same thing happens with a fresh download. Here's the text dump from the Python crash notice:
Date/Time: 2014-08-11 14:51:12.401 -0400
OS Version: Mac OS X 10.6.8 (10K549)
Report Version: 6
Interval Since Last Report: 1634610 sec
Crashes Since Last Report: 25
Per-App Crashes Since Last Report: 3
Anonymous UUID: D36853D8-EE6C-4941-A5F8-017ED3F42306
Model: MacPro4,1, BootROM MP41.0081.B08, 8 processors, Quad-Core Intel Xeon, 2.66 GHz, 16 GB, SMC 1.39f5
Graphics: NVIDIA GeForce GT 120, NVIDIA GeForce GT 120, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8E), Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en2
PCI Card: NVIDIA GeForce GT 120, sppci_displaycontroller, Slot-1
Serial ATA Device: HL-DT-ST DVD-RW GH41N
Serial ATA Device: HL-DT-ST DVD-RW GH41N
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
USB Device: Hub, 0x05ac (Apple Inc.), 0x9136, 0xfd300000 / 2
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1006, 0xfd320000 / 7
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x0220, 0xfd322000 / 8
USB Device: Hub, 0x05ac (Apple Inc.), 0x9137, 0xfd340000 / 3
USB Device: Apple LED Cinema Display, 0x05ac (Apple Inc.), 0x9236, 0xfd343000 / 6
USB Device: Display Audio, 0x05ac (Apple Inc.), 0x2912, 0xfd341000 / 5
USB Device: Display iSight, 0x05ac (Apple Inc.), 0x8508, 0xfd342000 / 4
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x5a100000 / 2
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8215, 0x5a110000 / 4
FireWire Device: built-in_hub, Up to 800 Mb/sec
EDIT2: I'm beginning to suspect that this is a memory-related error based on feedback from a Linux-based HPC building the same genome. Developer might want to look into that.
EDIT3: Running bowtie locally to align a .FASTQ file to mm9, also raises a similar exception.
Last edit: PikalaxALT 2014-08-11
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I have a local backup of all the mm9 Fasta files from an earlier successful bowtie2 build, and I decided to use the same files to build the indices for bowtie1. I copied the Fasta files into the mm9.ebwt directory and ran the included .sh file. This is the result:
Concurrent with this output, OS X returns a dialog box exclaiming that Python has crashed. What could be the cause of this?
Running OS X 10.6.8
EDIT: Same thing happens with a fresh download. Here's the text dump from the Python crash notice:
Process: Python [16767]
Path: /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: sh [16414]
Date/Time: 2014-08-11 14:51:12.401 -0400
OS Version: Mac OS X 10.6.8 (10K549)
Report Version: 6
Interval Since Last Report: 1634610 sec
Crashes Since Last Report: 25
Per-App Crashes Since Last Report: 3
Anonymous UUID: D36853D8-EE6C-4941-A5F8-017ED3F42306
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0xfffffffffffffff8
Crashed Thread: Unknown
Backtrace not available
Unknown thread crashed with X86 Thread State (64-bit):
rax: 0x0000000000000055 rbx: 0x0000000000000000 rcx: 0x0000000000000000 rdx: 0x0000000000000000
rdi: 0x0000000000000000 rsi: 0x0000000000000000 rbp: 0x0000000000000000 rsp: 0x0000000000000000
r8: 0x0000000000000000 r9: 0x0000000000000000 r10: 0x0000000000000000 r11: 0x0000000000000000
r12: 0x0000000000000000 r13: 0x0000000000000000 r14: 0x0000000000000000 r15: 0x0000000000000000
rip: 0x00007fff5fc01028 rfl: 0x0000000000010203 cr2: 0xfffffffffffffff8
Binary images description not available
Model: MacPro4,1, BootROM MP41.0081.B08, 8 processors, Quad-Core Intel Xeon, 2.66 GHz, 16 GB, SMC 1.39f5
Graphics: NVIDIA GeForce GT 120, NVIDIA GeForce GT 120, PCIe, 512 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8E), Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en2
PCI Card: NVIDIA GeForce GT 120, sppci_displaycontroller, Slot-1
Serial ATA Device: HL-DT-ST DVD-RW GH41N
Serial ATA Device: HL-DT-ST DVD-RW GH41N
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
Serial ATA Device: Hitachi HDE721010SLA330, 931.51 GB
USB Device: Hub, 0x05ac (Apple Inc.), 0x9136, 0xfd300000 / 2
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1006, 0xfd320000 / 7
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x0220, 0xfd322000 / 8
USB Device: Hub, 0x05ac (Apple Inc.), 0x9137, 0xfd340000 / 3
USB Device: Apple LED Cinema Display, 0x05ac (Apple Inc.), 0x9236, 0xfd343000 / 6
USB Device: Display Audio, 0x05ac (Apple Inc.), 0x2912, 0xfd341000 / 5
USB Device: Display iSight, 0x05ac (Apple Inc.), 0x8508, 0xfd342000 / 4
USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x5a100000 / 2
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8215, 0x5a110000 / 4
FireWire Device: built-in_hub, Up to 800 Mb/sec
EDIT2: I'm beginning to suspect that this is a memory-related error based on feedback from a Linux-based HPC building the same genome. Developer might want to look into that.
EDIT3: Running bowtie locally to align a .FASTQ file to mm9, also raises a similar exception.
Last edit: PikalaxALT 2014-08-11
I have the same crash with bowtie 1.1.1. Have you solved it?
I have solved it building bowtie from source code
Hi all,
I confirm Allison solution is the way to go (build bowtie from the source code). The current binaries are built for Mavericks.
Val