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

[seunghun23]

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!

[mourisl]

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

[seunghun23]

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

[mourisl]

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

[seunghun23]

I do have the write permission.

[mourisl]

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

[jiqingxiaoxi]

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.

[mourisl]

@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!

[mourisl]

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.

[seunghun23]

@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-cli]

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.

[mourisl]

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

[YB0101-cli]

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.

[mourisl]

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-cli]

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-cli]

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.

1. 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 tocompressBound' 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 tocompressBound' collect2.exe: error: ld returned 1 exit status

2. 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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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 toimp_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

include

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.

[mourisl]

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?