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trinityrnaseq / trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly
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Not able to install trinityrnaseq-v2.10.0 ? #808

Closed sunnyEV closed 4 years ago

sunnyEV commented 4 years ago

make last few lines of error sift_bam_max_cov.cpp:212:22: error: ‘it’ does not name a type auto it = current_cigar_counts.find(tmp_cigar); ^ sift_bam_max_cov.cpp:213:21: error: ‘it’ was not declared in this scope if (it != current_cigar_counts.end()) { // found ^ sift_bam_max_cov.cpp:222:42: error: ‘class std::map<std::vector, int>’ has no member named ‘emplace’ current_cigar_counts.emplace(std::move(tmp_cigar), 1); ^ sift_bam_max_cov.cpp:222:50: error: ‘move’ is not a member of ‘std’ current_cigar_counts.emplace(std::move(tmp_cigar), 1); ^ sift_bam_max_cov.cpp:249:47: error: request for member ‘insert’ in ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::mtid]’, which is of non-class type ‘int’ mates_to_keep[aln->core.mtid].insert(bam_get_qname(aln)); ^ make[2]: ** [sift_bam_max_cov] Error 1 make[2]: Leaving directory `/DATA//softwares/trinityrnaseq-v2.10.0/trinity-plugins/bamsifter' make[1]: [bamsifter_target] Error 2 make[1]: Leaving directory `/DATA/softwares/trinityrnaseq-v2.10.0/trinity-plugins' make: *** [trinity_essentials] Error 2

brianjohnhaas commented 4 years ago

Hi,

Try replacing the bamsifter makefile with this: https://github.com/trinityrnaseq/bamsifter/blob/master/Makefile

or include the -std=c++11 flag and let's see if that helps.

On Sat, Mar 28, 2020 at 3:03 PM sunnykevin19 notifications@github.com wrote:

make last few lines of error sift_bam_max_cov.cpp:212:22: error: ‘it’ does not name a type auto it = current_cigar_counts.find(tmp_cigar); ^ sift_bam_max_cov.cpp:213:21: error: ‘it’ was not declared in this scope if (it != current_cigar_counts.end()) { // found ^ sift_bam_max_cov.cpp:222:42: error: ‘class std::map<std::vector, int>’ has no member named ‘emplace’ current_cigar_counts.emplace(std::move(tmp_cigar), 1); ^ sift_bam_max_cov.cpp:222:50: error: ‘move’ is not a member of ‘std’ current_cigar_counts.emplace(std::move(tmp_cigar), 1); ^ sift_bam_max_cov.cpp:249:47: error: request for member ‘insert’ in ‘mates_to_keep[aln->bam1_t::core.bam1_core_t::mtid]’, which is of non-class type ‘int’ mates_to_keep[aln->core.mtid].insert(bam_get_qname(aln)); ^ make[2]: ** [sift_bam_max_cov] Error 1 make[2]: Leaving directory /DATA//softwares/trinityrnaseq-v2.10.0/trinity-plugins/bamsifter' make[1]: [bamsifter_target] Error 2 make[1]: Leaving directory /DATA/softwares/trinityrnaseq-v2.10.0/trinity-plugins' make: *** [trinity_essentials] Error 2

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sunnyEV commented 4 years ago

HI, Tried by replacing the makefile, shows error CMD

./Trinity --seqType fq --max_memory 50G --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq --CPU 6

Tuesday, March 31, 2020: 09:43:45 CMD: /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 6 --output /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq -prepping seqs CMD: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq >> single.fa Error encountered at sequence entry[331] ... corrupt file?Error, cmd: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq >> single.fa died with ret 1024 at /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/insilico_read_normalization.pl line 793. Error, cmd: /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 6 --output /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq died with ret 512 at ./Trinity line 2805. main::process_cmd("/DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/ut"...) called at ./Trinity line 3355 main::normalize("/DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/tr"..., 200, ARRAY(0x7f1c69b5eea8)) called at ./Trinity line 3298 main::run_normalization(200, ARRAY(0x7f1c69b5eea8)) called at ./Trinity line 1366

brianjohnhaas commented 4 years ago

Hi,

It looks like this command is having trouble: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq >> single.fa Error encountered at sequence entry[331] ... corrupt file?

If you run fastqc on your fastq file, does it identify any problems?

On Tue, Mar 31, 2020 at 3:53 AM sunnykevin19 notifications@github.com wrote:

HI, Tried by replacing the makefile, shows error CMD

./Trinity --seqType fq --max_memory 50G --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq --CPU 6

Tuesday, March 31, 2020: 09:43:45 CMD: /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/ insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 6 --output /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq -prepping seqs CMD: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq >> single.fa Error encountered at sequence entry[331] ... corrupt file?Error, cmd: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq >> single.fa died with ret 1024 at /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/ insilico_read_normalization.pl line 793. Error, cmd: /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/util/ insilico_read_normalization.pl --seqType fq --JM 50G --max_cov 200 --min_cov 1 --CPU 6 --output /DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/trinity_out_dir/insilico_read_normalization --max_CV 10000 --single /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq died with ret 512 at ./Trinity line 2805. main::process_cmd("/DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/ut"...) called at ./Trinity line 3355 main::normalize("/DATA/MarineEcology/softwares/trinityrnaseq-v2.10.0/tr"..., 200, ARRAY(0x7f1c69b5eea8)) called at ./Trinity line 3298 main::run_normalization(200, ARRAY(0x7f1c69b5eea8)) called at ./Trinity line 1366

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sunnyEV commented 4 years ago

Not at all. I tried with other pipelines, it going smoothly. Problem with Trinity, how do i fix this ?

brianjohnhaas commented 4 years ago

If you run this directly: seqtk-trinity seq -A -R 1 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq

single.fa

does it crash reproducibly?

if so, can you share with me the top records in the file so I can debug it directly?

ie. head -n10000 /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq

forbrian.fastq

On Tue, Mar 31, 2020 at 9:38 AM sunnykevin19 notifications@github.com wrote:

Not at all. I tried with other pipelines, it going smoothly. Problem with Trinity, how do i fix this ?

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sunnyEV commented 4 years ago

Using seqtk

seqtk seq -A -R -l /home/data/brain_samples/fastqgz/1_S4_R1_001_trim.fastq > single1.fa says "seq: invalid option -- 'R'" . generated a empy file.

head -n10000 1_S4_R1_001_trim.fastq | head @A00943:16:HHMNGDRXX:1:2101:4173:1016 1:N:0:TGGCCGGT+NAGAGCGC NGAGAGGACAGAGGAGAGAGGACAGAGGAGAGTGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAAAGAGGAAAGAGGAGAGAGG +

,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFF,FFFFFF,FFFFF:FFFFF:F:FFFFFF,FFF:,FFFFFFFF:FFFFFF,FFF,F

@A00943:16:HHMNGDRXX:1:2101:4481:1016 1:N:0:TGGCCGGT+NAGAGCGC NTAAGAAGTTGGACGCCGACCACACGGGGCCGCGTAACTAGTTAGCATGCCGGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTA +

FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFF,F,FFF,FFFFFFF:FFFFFFFFFFFFF,

@A00943:16:HHMNGDRXX:1:2101:4878:1016 1:N:0:TGGCCGGT+NAGAGCGC NCTGGTTGAAAGCTCTCAGTGGAGGGAACGCTTCCTGTTGGCTTGAGGGATTCTGCCTCCGTTGGTACAATAGATTCTTGTCCTTTGCATGTGCCAATTGC

brianjohnhaas commented 4 years ago

it's in the trinity-plugins/BIN directory.

Try running head -n10000 on it and send it to me (bhaas@broadinstitute.org)

On Tue, Mar 31, 2020 at 10:07 AM sunnykevin19 notifications@github.com wrote:

I'm unable to find seqtk-trinity script were do i find it ?

head -n10000 1_S4_R1_001_trim.fastq | head @A00943:16:HHMNGDRXX:1:2101:4173:1016 1:N:0:TGGCCGGT+NAGAGCGC

NGAGAGGACAGAGGAGAGAGGACAGAGGAGAGTGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAGAGAGGAAAGAGGAAAGAGGAGAGAGG +

,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,FF:FFF,FFFFFF,FFFFF:FFFFF:F:FFFFFF,FFF:,FFFFFFFF:FFFFFF,FFF,F

@A00943:16:HHMNGDRXX:1:2101:4481:1016 1:N:0:TGGCCGGT+NAGAGCGC

NTAAGAAGTTGGACGCCGACCACACGGGGCCGCGTAACTAGTTAGCATGCCGGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTA +

FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFF,F,FFF,FFFFFFF:FFFFFFFFFFFFF,

@A00943:16:HHMNGDRXX:1:2101:4878:1016 1:N:0:TGGCCGGT+NAGAGCGC

NCTGGTTGAAAGCTCTCAGTGGAGGGAACGCTTCCTGTTGGCTTGAGGGATTCTGCCTCCGTTGGTACAATAGATTCTTGTCCTTTGCATGTGCCAATTGC

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sunnyEV commented 4 years ago

I sent.

brianjohnhaas commented 4 years ago

hi,

the files you shared with me are fasta and not fastq. Could that be the issue?

On Tue, Mar 31, 2020 at 11:52 AM sunnykevin19 notifications@github.com wrote:

I sent.

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sunnyEV commented 4 years ago

Sorry, the files what i sent you all of them fastq files, i name wrongly (fasta).

brianjohnhaas commented 4 years ago

I see.

OK, it's interesting - the read @A00943:16:HHMNGDRXX:1:2101:14950:1172

has no sequence or quality values. It's an empty entry. I've not come across this before...

Try running trimmomatic or some other read cleaner to remove fastq entries that are too short or non-existent.

sunnyEV commented 4 years ago

I used, Cutadapt for trimming the adapters. After that I'm view the fastq files their was no adapter content. The RNA_seq data obtained from NovaSeq SE library.

brianjohnhaas commented 4 years ago

You can try running Trinity with the --no_seqtk flag, but I'm not sure that empty fastq records are valid entries and they should probably be removed from your file before running Trinity or other tools.

On Tue, Mar 31, 2020 at 12:34 PM sunnykevin19 notifications@github.com wrote:

I used, Cutadapt for trimming the adapters. After that I'm view the fastq files their was no adapter content. The RNA_seq data obtained from NovaSeq SE library.

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sunnyEV commented 4 years ago

K, I did quality trimming using sickle. I email the Fastq files, Please check them. Thanks!

brianjohnhaas commented 4 years ago

try including Trinity --trimmomatic with your run. I expect that should remove any remaining offending entries.

On Wed, Apr 1, 2020 at 8:09 AM sunnykevin19 notifications@github.com wrote:

K, I did quality trimming using sickle. I email the Fastq files, Please check them. Thanks!

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Kange2014 commented 4 years ago

hi, similar questions happen in my case. Do we have a solution now, to help fix the seqtk-trinity command issue? here, it cannot process single-end fastq file correctly with an error message "Segmentation fault (core dumped)" . But in singularity container, it can generate single.fa by using the same input fastq file normally. Below lists the first several sequences in the fastq file.

@V2BYL:00301:02064 GGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGATG + C@C?BBCCCCBCCD>CCB@CCCCBBCM@BBCCC?CBBBCD>@@?BB???@BD>BCAABB?ABAA@=>??@@AACCBBBBB<A=@>A9AAA5;;(666)8=><=>??<?AAADCBBBA8><AA>>>>?:>>>>>>>AAA;<<??BBBD8;7;<@@<??A;:>BBAAAAA7=???AA?<>=>><<888:AA>;>>>B:==@@;:7:@@AA=@@A<AA8@@AA=B@@@<>=>>@@@@@@@@@B??==B>>5>C7:99959919999884888/62... @V2BYL:00802:04082 GTTTTAAGCTCTTCAACGGTAATAGTTGTGTCCGTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCAC + 9999497BBCCC?CC@CB=BC@CCBB?CCC@?@??<ACCDBBAA>BBABBDDBBB?CCCBCC>C9:6;BC=CDD;ABBCCB??<>BBBCCCBAA>ABBBBCCCB@CCCCBCCCCCAABBBBBBB?B?B?BB?AAA?B@DBBBA@@@<>>@@=@@>>>@>>>@B@@@A?@@BA<@@@>>=A;;;??@F<@@6?BBA=AA=:>>@BC<@@@@A:;:AA@@

Thank you!

xiucz commented 4 years ago

Good, I have compiled the bamsifter with the new Makefile.

brianjohnhaas commented 4 years ago

Hi,

Try adding '-static' to the seqtk-trinity makefile, rebuild it and then copy the updated binary to trinity-plugins/BIN/

Then, rerun your original Trinity command. Let's see if that helps. I'll build as -static in the next release.

best,

~b

On Wed, Apr 15, 2020 at 3:58 AM Kange2014 notifications@github.com wrote:

hi, similar questions happen in my case. Do we have a solution now, to help fix the seqtk-trinity command issue? here, it cannot process single-end fastq file correctly with an error message "Segmentation fault (core dumped)" . But in singularity container, it can generate single.fa by using the same input fastq file normally. Below lists the first several sequences in the fastq file.

@V2BYL:00301:02064

GGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGATG + C@C?BBCCCCBCCD>CCB@CCCCBBCM@BBCCC?CBBBCD>@@?BB???@bd https://github.com/bd>BC<AABB?ABAA@ =>>??@@AACCBBBBB<A=@>A9AAA5;;(666)8=><=>??<?AAADCBBBA8>>>>?:>>>>>>>AAA;<<??BBBD8;7;<@@<??A;:>BBAAAAA7=???A<A?<>=>><<888:AA>;>>>B:==@@;:7:@ @aa https://github.com/aa=@@A https://github.com/A<AA8@@aa https://github.com/aa=B@@@<>>=>><@@@@@@@@@b https://github.com/b ??==>B>>5>C7:99959919999884888/62... @V2BYL:00802:04082

GTTTTAAGCTCTTCAACGGTAATAGTTGTGTCCGTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCAC + 9999497BBCCC?CC@CB=BC@CCBB?CCC@ ?<@??BBABBDDBBB?CCCBCC>C9:6;BC=CDD;ABBCCB??<>BBBCCCBAA>ABBBBCCCB@CCCCBCCCCCAABBBBBBB ?B?B?BB?AAA?B@DBBBA@@@>>>@@=@@>>@>>><@b https://github.com/b@@@A https://github.com/A?@@ba https://github.com/ba@@@>>=A;;;?<?@f https://github.com/f<@@6 https://github.com/6?BBA=AA>=:>>@bc https://github.com/bc<@@@@A https://github.com/A:;:AA@@

Thank you!

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