Empty bin directory after installation?

Question

Empty bin directory after installation?

JolandadeB opened this issue a year ago · comments

Describe the bug

**I've been trying to run the test data but I run into an 127 exit error. **

Error message
[6577 INFO] 2023-05-08 11:50:23 NextPolish start...
[6577 INFO] 2023-05-08 11:50:23 version:v1.4.1 logfile:pid6577.log.info
[6577 WARNING] 2023-05-08 11:50:23 Re-write workdir
[6577 WARNING] 2023-05-08 11:50:23 Delete task: 6 due to missing hifi_fofn.
[6577 INFO] 2023-05-08 11:50:23 scheduled tasks:
[5, 1, 2]
[6577 INFO] 2023-05-08 11:50:23 options:
[6577 INFO] 2023-05-08 11:50:23
rerun: 3
rewrite: 1
kill: None
cleantmp: 0
use_drmaa: 0
deltmp: True
submit: None
job_type: local
task: [5, 1, 2]
sgs_unpaired: 0
sgs_rm_nread: 1
parallel_jobs: 2
align_threads: 3
check_alive: None
job_id_regex: None
sgs_max_depth: 100
lgs_max_depth: 100
lgs_read_type: ont
multithread_jobs: 3
genome_size: 111129
lgs_max_read_len: 0
hifi_max_depth: 100
polish_options: -p 3
lgs_min_read_len: 5k
hifi_max_read_len: 0
hifi_block_size: 500M
hifi_min_read_len: 1k
job_prefix: nextPolish
sgs_block_size: 5556450.0
lgs_block_size: 5556450.0
sgs_use_duplicate_reads: 0
hifi_minimap2_options: -x map-pb
sgs_align_options: bwa mem -p -t 3
lgs_minimap2_options: -x map-ont -t 3
workdir: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir
sgs_fofn: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./sgs.fofn
lgs_fofn: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./lgs.fofn
genome: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./raw.genome.fasta
snp_phase: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.snp_phase
snp_valid: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.snp_valid
lgs_polish: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.lgs_polish
kmer_count: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.kmer_count
hifi_polish: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.hifi_polish
score_chain: /home/jolanda/NextPolish_tryout/NextPolish/test_data/./01_rundir/%02d.score_chain
[6577 INFO] 2023-05-08 11:50:23 step 0 and task 5 start:
[6577 INFO] 2023-05-08 11:50:28 Total jobs: 3
[6577 INFO] 2023-05-08 11:50:28 Submitted jobID:[6579] jobCmd:[/home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh] in the local_cycle.
[6579 CRITICAL] 2023-05-08 11:50:28 Command '/bin/bash /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh > /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.o 2> /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e' returned non-zero exit status 127, error info: .
[6577 INFO] 2023-05-08 11:50:29 Submitted jobID:[6585] jobCmd:[/home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split2/nextPolish.sh] in the local_cycle.
[6585 CRITICAL] 2023-05-08 11:50:29 Command '/bin/bash /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split2/nextPolish.sh > /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split2/nextPolish.sh.o 2> /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split2/nextPolish.sh.e' returned non-zero exit status 127, error info: .
[6577 INFO] 2023-05-08 11:50:29 Submitted jobID:[6591] jobCmd:[/home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split3/nextPolish.sh] in the local_cycle.
[6591 CRITICAL] 2023-05-08 11:50:29 Command '/bin/bash /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split3/nextPolish.sh > /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split3/nextPolish.sh.o 2> /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split3/nextPolish.sh.e' returned non-zero exit status 127, error info: .
[6577 ERROR] 2023-05-08 11:50:35 db_split failed: please check the following logs:
[6577 ERROR] 2023-05-08 11:50:35 /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e
[6577 ERROR] 2023-05-08 11:50:35 /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split2/nextPolish.sh.e
[6577 ERROR] 2023-05-08 11:50:35 /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split3/nextPolish.sh.e

Operating system

Ubuntu 22.04.2

GCC

gcc version 11.3.0

Python

Python 3.10.8

NextPolish

nextPolish v1.4.1

To Reproduce (Optional)

I just ran the test command and this produces the error

Additional context (Optional)

I did a bit of research on this error by running the first bash script NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh. This resulted in the following output:

hostname

hostname
jolanda-VirtualBox
cd /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1
cd /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1
( time /home/jolanda/NextPolish_tryout/NextPolish/bin/seq_split -d /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir -m 5556450.0 -n 2 -t 3 -i 1 -s 11112900 -p input.sgspart /home/jolanda/NextPolish_tryout/NextPolish/test_data/sgs.fofn )
/home/jolanda/NextPolish_tryout/NextPolish/bin/seq_split -d /home/jolanda/NextPolish_tryout/NextPolish/test_data/01_rundir -m 5556450.0 -n 2 -t 3 -i 1 -s 11112900 -p input.sgspart /home/jolanda/NextPolish_tryout/NextPolish/test_data/sgs.fofn
test_data/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh: line 5: /home/jolanda/NextPolish_tryout/NextPolish/bin/seq_split: No such file or directory

It seems that the bin directory is empty. Is this supposed to? During the installation, this is part of the output:

mkdir /home/jolanda/NextPolish_tryout/NextPolish/bin
make -C util;
make[1]: Entering directory '/home/jolanda/NextPolish_tryout/NextPolish/util'
gcc -Wall -O3 -s -pthread -o seq_split seq_split.c thpool.c -lz
seq_split.c: In function ‘get_fp_index’:
seq_split.c:76:13: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘count = 4294967295’ to ‘-1’ [-Woverflow]
76 | k = count = -1;
| ^~~~~
seq_split.c: In function ‘init_opt’:
seq_split.c:120:9: warning: ignoring return value of ‘getcwd’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
120 | getcwd(opt->outdir, sizeof(opt->outdir));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seq_split.c: In function ‘main’:
seq_split.c:406:32: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
406 | sprintf(opt.out, "%s/%s", opt.outdir, opt.outpre);
| ^
In file included from /usr/include/stdio.h:894,
from seq_split.c:1:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 2 or more bytes (assuming 1025) into a destination of size 1024
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
seq_split.c:162:33: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
162 | sprintf(fn, "%s.%03d.%s", opt->out, i, suffix);
| ^~~~
seq_split.c:162:29: note: directive argument in the range [0, 2147483647]
162 | sprintf(fn, "%s.%03d.%s", opt->out, i, suffix);
| ^~~~~~~~~~~~
In file included from /usr/include/stdio.h:894,
from seq_split.c:1:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 14 and 1044 bytes into a destination of size 1024
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | _va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
gcc -Wall -O3 -s -std=c99 -o seq_count seq_count.c -lz
make[2]: Entering directory '/home/jolanda/NextPolish_tryout/NextPolish/util/bwa'
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
879 | bgint_t oldInverseSa0RelativeRank = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
953 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o
rope.c: In function ‘rope_restore_node’:
rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
282 | fread(&is_bottom, 1, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
283 | fread(&n, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~~
rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
291 | fread(p[i].c, 8, 6, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
292 | fread(q, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~
rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
293 | fread(q + 1, 1, *q, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c: In function ‘rope_restore’:
rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
312 | fread(&r->max_nodes, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
313 | fread(&r->block_len, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
ar: u' modifier ignored since D' is the default (see U') gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o bwashm.c: In function ‘bwa_shm_stage’: bwashm.c:29:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:66:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt /usr/bin/ld: ./libbwa.a(rope.o):/home/jolanda/NextPolish_tryout/NextPolish/util/bwa/rle.h:33: multiple definition of rle_auxtab'; ./libbwa.a(bwtindex.o):/home/jolanda/NextPolish_tryout/NextPolish/util/bwa/rle.h:33: first defined here
/usr/bin/ld: ./libbwa.a(rle.o):/home/jolanda/NextPolish_tryout/NextPolish/util/bwa/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/home/jolanda/NextPolish_tryout/NextPolish/util/bwa/rle.h:33: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:30: bwa] Error 1
make[2]: Leaving directory '/home/jolanda/NextPolish_tryout/NextPolish/util/bwa'
make[1]: *** [Makefile:19: bwa] Error 2
make[1]: Leaving directory '/home/jolanda/NextPolish_tryout/NextPolish/util'
make: *** [Makefile:18: all] Error 2

Could you please help me out?

Hu Jiang · Answer 1 · Tue May 09 2023 09:58:56 GMT+0800 (China Standard Time)

Hi, if your system has already installed bwa and samtools, You can also use your own alignment pipeline see here, to avoid these installation problems.