moold
commented
1 year ago 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.
Open JolandadeB opened 1 year ago
moold
commented
1 year ago 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.
tim-oconnor
commented
1 year ago I have the same issue. The seq_split program is in the utils directory rather than bin. Not sure how to best resolve the issue, though!
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
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 sinceD' is the default (seeU') 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 ofrle_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 2Could you please help me out?