TRUST4 fails with error 139 at ./run-trust4 line 54

Question

TRUST4 fails with error 139 at ./run-trust4 line 54

seunghun23 opened this issue a year ago · comments

Hi,
I tried to run TRUST4 on paired end Bulk RNA-Seq Fastq files, but it failed with "139 at ./run-trust4 line 54" as shown in the screenshot below. Could you tell me what this error message means and a way to fix this?

Thanks!

Li Song · Answer 1 · Thu Sep 14 2023 03:17:47 GMT+0800 (China Standard Time)

Could you please use zcat to check whether the fastq files are in the right path and the format is correct?

Seunghun Han · Answer 2 · Thu Sep 14 2023 04:24:20 GMT+0800 (China Standard Time)

Hi,

I tried zcat using the same path I used for the fastq files and they are in the right path with right format.
I used the same fastq files to run MixCR without any problem

Li Song · Answer 3 · Thu Sep 14 2023 04:39:26 GMT+0800 (China Standard Time)

Do you have the write permission to the folder /mnt/TCR/TRUST4?

Seunghun Han · Answer 4 · Thu Sep 14 2023 04:40:05 GMT+0800 (China Standard Time)

I do have the write permission.

Li Song · Answer 5 · Thu Sep 14 2023 04:40:57 GMT+0800 (China Standard Time)

Could you please run the example files provided in TRUST4 package, just to make sure the installation is fine? Thank you.

Jia Ben · Answer 6 · Fri Sep 15 2023 10:51:03 GMT+0800 (China Standard Time)

Could you please run the example files provided in TRUST4 package, just to make sure the installation is fine? Thank you.

Hi, I have the same error info when I run the example files.

Li Song · Answer 7 · Fri Sep 15 2023 11:24:56 GMT+0800 (China Standard Time)

@jiqingxiaoxi @seunghun23 Thank you for letting me know about this issue. I think this is a bug from the latest git push. I'll fix it in the next a few hours or tomorrow. In the meantime, you can use the v1.0.12 package on the github release page. Thank you!

Li Song · Answer 8 · Fri Sep 15 2023 11:33:02 GMT+0800 (China Standard Time)

Sorry for writing too many messages. I think I've fixed the issue, and pushed the new code to the github repo. Could you please pull the new repo, recompile TRUST4, and give it a try? Thank you.

Seunghun Han · Answer 9 · Mon Sep 18 2023 23:03:10 GMT+0800 (China Standard Time)

@mourisl Thank you for the quick fix. Looks like fastq-extractor is now working correctly without the above mentioned error. I will let you know if I encounter any other problem with this version.

YB0101 · Answer 10 · Tue Jan 09 2024 14:23:20 GMT+0800 (China Standard Time)

Hi @mourisl
I downloaded TRUST4 today and tried to run the example fastq file. It did not work and I got similar error message. The error messagge is as follows: failed: -1 at ./run-trust4 line 54.
I really appreciate it, if you can help me fixing this bug.
Thank you so much.

Li Song · Answer 11 · Tue Jan 09 2024 14:29:14 GMT+0800 (China Standard Time)

Could you please show me the full output on the screen by TRUST4?

YB0101 · Answer 12 · Tue Jan 09 2024 14:33:25 GMT+0800 (China Standard Time)

The following is the command that I typed and the error message:
$ ./run-trust4 -f human_IMGT+C.fa --ref human_IMGT+C.fa -1 example/example_1.fq -2 eample/example_2.fq -o TRUST_example
[Tue Jan 9 15:15:51 2024] TRUST4 begins.
[Tue Jan 9 15:15:51 2024] SYSTEM CALL: /c/Users/YB/Desktop/TRUST4/astq-extractor -t 1 -f human_IMGT+C.fa -o TRUST_example_toassemble -1 example/exampe_1.fq -2 example/example_2.fq
Can't exec "/c/Users/YB": No such file or directory at ./run-trust4 line 54.
system /c/Users/YB/Desktop/TRUST4/fastq-extractor -t 1 -f human_IMG+C.fa -o TRUST_example_toassemble -1 example/example_1.fq -2 example/example_2.fq filed: -1 at ./run-trust4 line 54.

Li Song · Answer 13 · Tue Jan 09 2024 14:36:50 GMT+0800 (China Standard Time)

Some how your message is missing some character, for example, "fastq-extractor" is "astq-extractor" ,and "/c/Users/YB" seems incomplete too.

Have you run "make" to compile TRUST4 first, i.e. do you see executable files like fastq-extractor in the folder? I never tested TRUST4 on Windows, so I'm not sure how it will work out.

YB0101 · Answer 14 · Tue Jan 09 2024 15:30:03 GMT+0800 (China Standard Time)

I thought that i compiled TRUST4 just now, but apparently it was not complete. The command "make" could not compile TRUST4 completely. I am trying to figure out how to do this first.

YB0101 · Answer 15 · Tue Jan 09 2024 17:46:07 GMT+0800 (China Standard Time)

I am almost done with compiling TRUST4. I had to excute the commands one by one since "make" did not work for some reasons. I am almost done with the compilation, I believe. I just got stuck at 2 steps which involve: bgzf.c and knetfile.c.

the problem related to bgzf.c is the following:
when I typed: g++ -o bam-extractor -I./samtools-0.1.19 -L./samtools-0.1.19 -O3 -Wall -g BamExtractor.o -lpthread -lz -lbam -lws2_32,
I got the following error messages:
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ./samtools-0.1.19/libbam.a(bgzf.o): in function bgzf_open': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19/bgzf.c:142: undefined reference to compressBound'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ./samtools-0.1.19/libbam.a(bgzf.o): in function bgzf_dopen': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19/bgzf.c:160: undefined reference to compressBound'
collect2.exe: error: ld returned 1 exit status
the problem related to knetfile.c is the following:
when i inputted: gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
I got the following error messages:
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function socket_connect': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:163: undefined reference to __imp_socket'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:164: undefined reference to __imp_setsockopt' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:170: undefined reference to __imp_inet_addr'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:171: undefined reference to __imp_gethostbyaddr' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:177: undefined reference to __imp_htons'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:178: undefined reference to __imp_connect' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:167: undefined reference to __imp_gethostbyname'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:164: undefined reference to __imp_WSAGetLastError' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:163: undefined reference to __imp_WSAGetLastError'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:178: undefined reference to __imp_WSAGetLastError' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:173: undefined reference to __imp_WSAGetLastError'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function socket_wait': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:72: undefined reference to __imp_select'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:79: undefined reference to __imp_WSAGetLastError' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_get_response':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:215: undefined reference to __imp_recv' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function knet_win32_init':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:139: undefined reference to __imp_WSAStartup' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function knet_win32_destroy':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:143: undefined reference to __imp_WSACleanup' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_send_cmd':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_reconnect':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:284: undefined reference to __imp_closesocket' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_send_cmd':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_connect_file':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:325: undefined reference to __imp_closesocket' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_send_cmd':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:238: undefined reference to __imp_send' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_connect_file':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:359: undefined reference to __imp_closesocket' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function khttp_connect_file':
C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:411: undefined reference to __imp_closesocket' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:417: undefined reference to __imp_send'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:419: undefined reference to __imp_recv' C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:440: undefined reference to __imp_closesocket'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function my_netread': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:191: undefined reference to __imp_recv'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function kftp_reconnect': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:284: undefined reference to __imp_closesocket'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../knetfile.o: in function knet_close': C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:586: undefined reference to __imp_closesocket'
C:/Users/YB/Desktop/mingw64/x86_64-13.2.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/13.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\YB\Desktop\mingw64\TRUST4\samtools-0.1.19\bcftools/../knetfile.c:581: undefined reference to `__imp_closesocket'
collect2.exe: error: ld returned 1 exit status

I added:
#include <winsock2.h>
#include <ws2tcpip.h>
at the beginning of knetfile.c and also added -lws2_32 at the end of the g++ command, but the command still did not work. I am very grateful if you have any suggestions on how to excute these two commands properly so that I can finish the compilation.

Thank you.

Li Song · Answer 16 · Tue Jan 09 2024 23:12:22 GMT+0800 (China Standard Time)

If your input data is in fastq format, you can skip the compiling for the "bam-extractor", which is for bam input file. This may save you some efforts?