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TrinityFusion software
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TrinityFusion fails while running GMAP-Fusion #2

Closed think-o closed 11 months ago

think-o commented 2 years ago

Hello! I get the following error while running TrinityFusion, when the GMAP-Fusion script is being run. I get empty files starting from "gmap.map.gff3.chims_described" to "gmap.map.gff3.chims_described.revised.w_read_support" and the run fails at this point. Is it because the datasets I have taken are not detected with chimeric reads? Please help me to sort this error out.

Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir  --left_fq /homeresults/reads/SRR13626503_1_trim.fastq  --right_fq /homeresults/reads/SRR13626503_2_trim.fastq  --CPU 55  -L 30  --min_J 1  --min_sumJS 2  --min_novel_junction_support 3  --split_breakpoint_extend_length 25  --max_fuzzy_overlap 12  -o trinity_fusion-UC_gmap

Error encountered::  <!----
CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir  --left_fq /homeresults/reads/SRR13626503_1_trim.fastq  --right_fq /homeresults/reads/SRR13626503_2_trim.fastq  --CPU 55  -L 30  --min_J 1  --min_sumJS 2  --min_novel_junction_support 3  --split_breakpoint_extend_length 25  --max_fuzzy_overlap 12  -o trinity_fusion-UC_gmap 2>tmp.6324.1632830593.stderr

Errmsg:
* Running CMD: gmap -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /homeresults/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta -f 3 -n 0 -x 30 -t 55  > /homeresults/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3
GMAP version 2017-11-15 called with args: gmap.avx2 -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /homeresults/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta -f 3 -n 0 -x 30 -t 55
Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1
Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends
Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 __builtin_ctz=0 _mm_popcnt_u32=17 __builtin_popcount=17
Finished checking compiler assumptions
Pre-loading compressed genome (oligos)......done (44,875,416 bytes, 10956 pages, 0.05 sec)
Pre-loading compressed genome (bits)......done (44,875,440 bytes, 10956 pages, 0.10 sec)
Looking for index files in directory /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap
  Pointers file is ref_genome.fa.gmap.ref133offsets64meta
  Offsets file is ref_genome.fa.gmap.ref133offsets64strm
  Positions file is ref_genome.fa.gmap.ref133positions
Offsets compression type: bitpack64
Allocating memory for ref offset pointers, kmer 13, interval 3...Attached new memory for /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap/ref_genome.fa.gmap.ref133offsets64meta...done (8,388,624 bytes, 0.11 sec)
Allocating memory for ref offsets, kmer 13, interval 3...Attached new memory for /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap/ref_genome.fa.gmap.ref133offsets64strm...done (29,407,552 bytes, 0.07 sec)
Pre-loading ref positions, kmer 13, interval 3......done (159,305,108 bytes, 0.32 sec)
Starting alignment
Processed 19 queries in 0.77 seconds (24.68 queries/sec)
Removed existing memory for shmid 688167
Removed existing memory for shmid 688166

* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/gmap_genome_gff3_to_chim_summary.pl --gmap_gff3 /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3 --annot_gtf /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_annot.gtf > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described
-parsing /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_annot.gtf
-building interval tree for fast searching of gene overlaps
-loading alignment data
-mapping candidate fusion transcripts to gene annotations.
* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/retrieve_fusion_transcript_candidates.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta
* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/split_fusion_gmap_parts.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta 25 /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir
* Running CMD: gmap -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa -f 3 -n 1 -t 4 --min-identity 0.98 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa.gmap.gff3
* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/compare_fusion_align_to_best_nonfusion_align.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa.gmap.gff3 25 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split_align_stats
-loading alignment data
* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/revise_chim_candidate_list_via_split_align_reassessment.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split_align_stats 12 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised
* Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised /home/results/reads/SRR13626503_1_trim.fastq /home/results/reads/SRR13626503_2_trim.fastq > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised.w_read_support
Error, cannot locate file /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl line 33.
Error, cmd: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised /home/results/reads/SRR13626503_1_trim.fastq /home/results/reads/SRR13626503_2_trim.fastq > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised.w_read_support died with ret 65280 No such file or directory at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/PerlLib/Pipeliner.pm line 181.
        Pipeliner::run('Pipeliner=HASH(0x743a68)') called at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion line 259

--->

Error, cmd: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir  --left_fq /home/results/reads/SRR13626503_1_trim.fastq  --right_fq /home/results/reads/SRR13626503_2_trim.fastq  --CPU 55  -L 30  --min_J 1  --min_sumJS 2  --min_novel_junction_support 3  --split_breakpoint_extend_length 25  --max_fuzzy_overlap 12  -o trinity_fusion-UC_gmap 2>tmp.6324.1632830593.stderr died with ret 512  at /home/software/TrinityFusion-v0.3.5/PerlLib/Pipeliner.pm line 186.
        Pipeliner::run('Pipeliner=HASH(0x1fcda00)') called at /home/software/TrinityFusion-v0.3.5/TrinityFusion line 276

Trinity-Fusion run failed for SRR13626503 at line 112
brianjohnhaas commented 2 years ago

hi,

Does this file exist?

/home/results/TrinityFusion_out/trinity_fusion-UC_gmap/ gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised

On Wed, Sep 29, 2021 at 1:25 AM think-o @.***> wrote:

Hello! I get the following error while running TrinityFusion, when the GMAP-Fusion script is being run. I get empty files starting from "gmap.map.gff3.chims_described" to "gmap.map.gff3.chims_described.revised.w_read_support" and the run fails at this point. Is it because the datasets I have taken are not detected with chimeric reads? Please help me to sort this error out.

Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir --left_fq /homeresults/reads/SRR13626503_1_trim.fastq --right_fq /homeresults/reads/SRR13626503_2_trim.fastq --CPU 55 -L 30 --min_J 1 --min_sumJS 2 --min_novel_junction_support 3 --split_breakpoint_extend_length 25 --max_fuzzy_overlap 12 -o trinity_fusion-UC_gmap

Error encountered:: <!---- CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir --left_fq /homeresults/reads/SRR13626503_1_trim.fastq --right_fq /homeresults/reads/SRR13626503_2_trim.fastq --CPU 55 -L 30 --min_J 1 --min_sumJS 2 --min_novel_junction_support 3 --split_breakpoint_extend_length 25 --max_fuzzy_overlap 12 -o trinity_fusion-UC_gmap 2>tmp.6324.1632830593.stderr

Errmsg:

  • Running CMD: gmap -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /homeresults/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta -f 3 -n 0 -x 30 -t 55 > /homeresults/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3 GMAP version 2017-11-15 called with args: gmap.avx2 -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /homeresults/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta -f 3 -n 0 -x 30 -t 55 Checking compiler assumptions for SSE2: 6B8B4567 327B23C6 xor=59F066A1 Checking compiler assumptions for SSE4.1: -103 -58 max=198 => compiler zero extends Checking compiler options for SSE4.2: 6B8B4567 __builtin_clz=1 builtin_ctz=0 _mm_popcnt_u32=17 builtin_popcount=17 Finished checking compiler assumptions Pre-loading compressed genome (oligos)......done (44,875,416 bytes, 10956 pages, 0.05 sec) Pre-loading compressed genome (bits)......done (44,875,440 bytes, 10956 pages, 0.10 sec) Looking for index files in directory /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap Pointers file is ref_genome.fa.gmap.ref133offsets64meta Offsets file is ref_genome.fa.gmap.ref133offsets64strm Positions file is ref_genome.fa.gmap.ref133positions Offsets compression type: bitpack64 Allocating memory for ref offset pointers, kmer 13, interval 3...Attached new memory for /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap/ref_genome.fa.gmap.ref133offsets64meta...done (8,388,624 bytes, 0.11 sec) Allocating memory for ref offsets, kmer 13, interval 3...Attached new memory for /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_genome.fa.gmap/ref_genome.fa.gmap.ref133offsets64strm...done (29,407,552 bytes, 0.07 sec) Pre-loading ref positions, kmer 13, interval 3......done (159,305,108 bytes, 0.32 sec) Starting alignment Processed 19 queries in 0.77 seconds (24.68 queries/sec) Removed existing memory for shmid 688167 Removed existing memory for shmid 688166

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/gmap_genome_gff3_to_chim_summary.pl --gmap_gff3 /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3 --annot_gtf /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_annot.gtf > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described -parsing /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir/ref_annot.gtf -building interval tree for fast searching of gene overlaps -loading alignment data -mapping candidate fusion transcripts to gene annotations.

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/retrieve_fusion_transcript_candidates.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/split_fusion_gmap_parts.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta 25 /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir

  • Running CMD: gmap -D /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir -d ref_genome.fa.gmap /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa -f 3 -n 1 -t 4 --min-identity 0.98 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa.gmap.gff3

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/compare_fusion_align_to_best_nonfusion_align.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split.fa.gmap.gff3 25 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split_align_stats -loading alignment data

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/revise_chim_candidate_list_via_split_align_reassessment.pl /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.fasta.split_align_stats 12 > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised

  • Running CMD: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised /home/results/reads/SRR13626503_1_trim.fastq /home/results/reads/SRR13626503_2_trim.fastq > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised.w_read_support Error, cannot locate file /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl line 33. Error, cmd: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/util/estimate_fusion_read_support.pl /home/results/TrinityFusion_out/trinity_discasm/discasm.Trinity.fasta /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised /home/results/reads/SRR13626503_1_trim.fastq /home/results/reads/SRR13626503_2_trim.fastq > /home/results/TrinityFusion_out/trinity_fusion-UC_gmap/gmap_fusion_intermediates_dir/gmap.map.gff3.chims_described.revised.w_read_support died with ret 65280 No such file or directory at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/PerlLib/Pipeliner.pm line 181. Pipeliner::run('Pipeliner=HASH(0x743a68)') called at /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion line 259

--->

Error, cmd: /home/software/TrinityFusion-v0.3.5/GMAP-fusion/GMAP-fusion -T trinity_discasm/discasm.Trinity.fasta --genome_lib_dir /home/genome_files/CTAT_Library/ctat_genome_lib_build_dir --left_fq /home/results/reads/SRR13626503_1_trim.fastq --right_fq /home/results/reads/SRR13626503_2_trim.fastq --CPU 55 -L 30 --min_J 1 --min_sumJS 2 --min_novel_junction_support 3 --split_breakpoint_extend_length 25 --max_fuzzy_overlap 12 -o trinity_fusion-UC_gmap 2>tmp.6324.1632830593.stderr died with ret 512 at /home/software/TrinityFusion-v0.3.5/PerlLib/Pipeliner.pm line 186. Pipeliner::run('Pipeliner=HASH(0x1fcda00)') called at /home/software/TrinityFusion-v0.3.5/TrinityFusion line 276

Trinity-Fusion run failed for SRR13626503 at line 112

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/TrinityFusion/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX2GDSZ36GQOTRS3C6DUEKPMVANCNFSM5E67IZLA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

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think-o commented 2 years ago

Thank you for the response.

Yes the file exists, but is an empty file

brianjohnhaas commented 2 years ago

I see.

Can you tar up the directory: gmap_fusion_intermediates_dir

and send it to me? I'll take a look. You can send to @.***

thanks,

~brian

On Thu, Sep 30, 2021 at 2:33 AM think-o @.***> wrote:

Thank you for the response.

Yes the file exists, but is an empty file

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/TrinityFusion/issues/2#issuecomment-930846655, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXYKRCZK4R5UEBPDSCDUEQAELANCNFSM5E67IZLA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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think-o commented 2 years ago

Sure! Thank you. I have sent it to the email ID listed on your profile. Have sent you the compressed version of the whole of my output directory by mistake. Hope that would not be a problem.

brianjohnhaas commented 11 months ago

gmap-fusion now replaced with ctat-LR-fusion module