# Trinity and reads "smaller than 25 base pairs" **URL:** \ **Category:** Resources\ **Tags:** assembly, troubleshooting, exceeds-memory-error, resources, tool-help, quality-control, trinity\ **Created:** [May 2, 2022, 12:38pm UTC](https://help.galaxyproject.org/t/trinity-and-reads-smaller-than-25-base-pairs/7967 "2022-05-02T12:38:39Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![balrajsharma](https://avatars.discourse-cdn.com/v4/letter/b/e47c2d/32.png) [@balrajsharma](https://help.galaxyproject.org/u/balrajsharma)\ **Post date:** [May 2, 2022, 12:38pm UTC](https://help.galaxyproject.org/t/trinity-and-reads-smaller-than-25-base-pairs/7967/1 "2022-05-02T12:38:40Z")
Trying to do RNA seq data analysis denovo based but trinity giving error. Please help. Galaxy Tool Error Report from [https://usegalaxy.org/](https://usegalaxy.org/) Error Localization Dataset 79869624 (bbd44e69cb8906b5cf64175ab8c7a2f7) History 5619023 (07bef24c7a90ef05) Failed Job 121: Trinity on data 56 and data 55: Gene to transcripts map (bbd44e69cb8906b57bc5840c89cd6fe5) User Provided Information The user _(admin redacted for privacy)_ provided the following information: None Detailed Job Information Job environment and execution information is available at the job info page. Job ID 42383847 (bbd44e69cb8906b58ccb29cce2790c64) Tool ID toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2 Tool Version 2.9.1+galaxy2 Job PID or DRM id 42383847 Job Tool Version Job Execution and Failure Information Command Line if [-z “$GALAXY\_MEMORY\_MB”] ; then GALAXY\_MEMORY\_GB=1 ; else GALAXY\_MEMORY\_GB=$((GALAXY\_MEMORY\_MB / 1024)) ; fi ; if [! -z “$TRINITY\_SCRATCH\_DIR”] ; then workdir=`pwd` ; scratchfolder=$(mktemp -d -p “$TRINITY\_SCRATCH\_DIR”); emptyfolder=$(mktemp -d -p “$TRINITY\_SCRATCH\_DIR”); cd “$scratchfolder” ; fi ; ln -s ‘/scratch1/03166/xcgalaxy/main/staging//42383847/inputs/dataset\_6d325f88-9577-4499-9b5a-bc6044005616.dat’ left\_input0.fastqsanger.gz && ln -s ‘/scratch1/03166/xcgalaxy/main/staging//42383847/inputs/dataset\_641bd050-dc3a-4114-8811-acf13a33f5de.dat’ right\_input0.fastqsanger.gz && Trinity --no\_version\_check --left ‘left\_input0.fastqsanger.gz’ --right ‘right\_input0.fastqsanger.gz’ --seqType fq --min\_contig\_length 200 --min\_kmer\_cov 1 --CPU ${GALAXY\_SLOTS:-4} --max\_memory ${GALAXY\_MEMORY\_GB:-1}G --bflyHeapSpaceMax ${GALAXY\_MEMORY\_GB:-1}G --bfly\_opts ‘-V 10 --stderr’ && if [! -z “$TRINITY\_SCRATCH\_DIR”] ; then mkdir -p “$workdir/trinity\_out\_dir”; cp -p trinity\_out\_dir/Trinity\* “$workdir/trinity\_out\_dir”; cd “$TRINITY\_SCRATCH\_DIR”; rsync -a --delete “$emptyfolder/” “$scratchfolder/”; rmdir “$emptyfolder” “$scratchfolder/”; cd “$workdir”; fi ; stderr stdout ``` __________ ________ __________ ____ | || \ | || \ | || || | | | || D ) | | | _ | | | | || | | |_| |_|| / | | | | | | | |_| |_|| ~ | | | | \ | | | | | | | | | |___, | | | | . \ | | | | | | | | | | | | __| |__ |\_|| ____||__ | __||____ | | __| |____ / Trinity-v2.9.1 ``` Left read files: $VAR1 = [ ‘left\_input0.fastqsanger.gz’ ]; Right read files: $VAR1 = [ ‘right\_input0.fastqsanger.gz’ ]; Monday, May 2, 2022: 02:41:37 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support\_scripts/ExitTester.jar 0 Picked up \_JAVA\_OPTIONS: -Xmx7g -Xms256m Monday, May 2, 2022: 02:41:38 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/opt/trinity-2.9.1/util/support\_scripts/ExitTester.jar 1 Picked up \_JAVA\_OPTIONS: -Xmx7g -Xms256m Monday, May 2, 2022: 02:41:38 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42383847/working/trinity\_out\_dir Monday, May 2, 2022: 02:41:38 CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42383847/working/trinity\_out\_dir/chrysalis * * * ## -------------- Trinity Phase 1: Clustering of RNA-Seq Reads --------------------- * * * ## ------------ In silico Read Normalization --------------------- – (Removing Excess Reads Beyond 200 Coverage – # running normalization on reads: $VAR1 = [ ``` [ '/scratch1/03166/xcgalaxy/main/staging/42383847/working/left_input0.fastqsanger.gz' ], [ '/scratch1/03166/xcgalaxy/main/staging/42383847/working/right_input0.fastqsanger.gz' ] ]; ``` ## Monday, May 2, 2022: 02:41:38 CMD: /usr/local/opt/trinity-2.9.1/util/insilico\_read\_normalization.pl --seqType fq --JM 190G --max\_cov 200 --min\_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42383847/working/trinity\_out\_dir/insilico\_read\_normalization --max\_CV 10000 --left /scratch1/03166/xcgalaxy/main/staging/42383847/working/left\_input0.fastqsanger.gz --right /scratch1/03166/xcgalaxy/main/staging/42383847/working/right\_input0.fastqsanger.gz --pairs\_together --PARALLEL\_STATS -prepping seqs Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A -R 1 \<(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42383847/working/left\_input0.fastqsanger.gz) \>\> left.fa CMD: seqtk-trinity seq -A -R 2 \<(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42383847/working/right\_input0.fastqsanger.gz) \>\> right.fa CMD finished (73 seconds) CMD finished (74 seconds) CMD: touch left.fa.ok CMD finished (0 seconds) CMD: touch right.fa.ok CMD finished (0 seconds) Done converting input files.CMD: cat left.fa right.fa \> both.fa CMD finished (11 seconds) CMD: touch both.fa.ok CMD finished (0 seconds) -kmer counting. ## ----------- Jellyfish -------------------- – (building a k-mer catalog from reads) – CMD: jellyfish count -t 56 -m 25 -s 27321675151 --canonical both.fa CMD finished (95 seconds) CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer\_counts.jf CMD finished (11 seconds) CMD: jellyfish dump -L 2 mer\_counts.jf \> jellyfish.K25.min2.kmers.fa CMD finished (31 seconds) CMD: touch jellyfish.K25.min2.kmers.fa.success CMD finished (0 seconds) -generating stats files CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer\_size 25 --num\_threads 28 --DS \> left.fa.K25.stats CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer\_size 25 --num\_threads 28 --DS \> right.fa.K25.stats -reading Kmer occurrences… -reading Kmer occurrences… done parsing 81736069 Kmers, 81736069 added, taking 87 seconds. Sequence: CCGTCTTGGACCAAACTAis smaller than 25 base pairs, skipping Sequence: TGATGATGTASequence: GGCAAAAis smaller than 25 base pairs, skippingis smaller than 25 base pairs, skipping Sequence: Sequence: Sequence: Sequence: CTAGTGCCACAGCACAGAGCCCACGGSequence: AGGTGCATCAGTis smaller than 25 base pairs, skipping is smaller than is smaller than 25 base pairs, skipping25CGTGTTCTTGCTGAAGis smaller than AGGAGCCTGSequence: CTCTAGCACis smaller than 25 base pairs, skipping base pairs, skippingSequence: CTTAGGis smaller than 25 base pairs, skipping Sequence: 25Sequence: TTTCAAAATCAGTAGGCAAAAis smaller than base pairs, skipping CGGCAAG25is smaller than is smaller than base pairs, skippingSequence: CGGGGATGGATCAACACAAGCCis smaller than 25 base pairs, skipping2525 base pairs, skipping base pairs, skipping Sequence: ATGATGACTGTCGAAAis smaller than 25 base pairs, skipping Sequence: GTCCis smaller than 25 base pairs, skippingSequence: TAAGAAGGGTAis smaller than 25 base pairs, skipping Sequence: TTCAAGGAAAGTGAGTCGis smaller than 25 base pairs, skippingSequence: Sequence: GGCCACATCSequence: GTTTCATGGCTCAAis smaller than Sequence: is smaller than 25is smaller than CATCCCis smaller than base pairs, skipping 2525 base pairs, skipping base pairs, skipping25 Sequence: Sequence: CCACTTAGis smaller than 25 base pairs, skipping base pairs, skipping Sequence: CTCCATTGCTCis smaller than 25 base pairs, skippingSequence: ACAAAis smaller than CTTGTTTCATGis smaller than 25 base pairs, skipping Sequence: CCTGACTis smaller than 25Sequence: Sequence: 25 base pairs, skippingCCCGCGTCTAGTCGATTCCTTCis smaller than 25 Sequence: CAGCAGis smaller than 25 base pairs, skipping base pairs, skipping Sequence: GTCCGAAGGGCAGTSequence: CTAGGACis smaller than 25 base pairs, skipping base pairs, skippingis smaller than 25 base pairs, skippingGGCATTGGCACTGTGCis smaller than 25 base pairs, skippingSequence: Sequence: CCCCGATCCAGTTCTCGCATCTGTis smaller than GCACT25is smaller than base pairs, skipping25 base pairs, skippingSequence: CTGTCis smaller than 25 base pairs, skippingSequence: TTCAAATCTCAAAis smaller than 25 base pairs, skipping Sequence: GCCCTCACAACCAis smaller than 25 base pairs, skipping Sequence: CCGCTis smaller than 25 base pairs, skippingSequence: Sequence: ATTGAAAGGAAATACAAATCTGATis smaller than 25is smaller than Sequence: CTGTTCG base pairs, skipping Sequence: is smaller than 25 base pairs, skipping Sequence: AGACCACCGTCTCCGAis smaller than 25 base pairs, skipping Sequence: AACAGAAACAAGTAAACis smaller than 25 base pairs, skippingSequence: ACGGGGAAGAATAis smaller than 25 base pairs, skipping 25 base pairs, skipping CAGGTGACATGGTTis smaller than Sequence: 25Sequence: GTGGCGC base pairs, skippingCAAGCATCCGAGGACis smaller than is smaller than 2525 base pairs, skipping base pairs, skipping Sequence: Sequence: CTGATCACCACGCTGTACTCGTACis smaller than 25Sequence: CTCAACTis smaller than 25 base pairs, skipping Sequence: CGTATis smaller than 25 base pairs, skippingSequence: ATAAACTTTACCCTGCis smaller than 25 base pairs, skipping is smaller than Sequence: ATGAGATGTis smaller than 25 base pairs, skipping Sequence: AAGGAATACGAATCTCAis smaller than 25 base pairs, skipping Sequence: CGCGGTGis smaller than 25Sequence: CCTTAACATTACTTAATACCis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skipping25 base pairs, skipping Sequence: Sequence: Sequence: Sequence: TGTAATTGCTTTCACCAACAACAACGTAis smaller than 25is smaller than TGAAGGCTCTTGis smaller than base pairs, skipping25 base pairs, skipping Sequence: is smaller than 25GGCTGTCGAAGAGTCGTT25Sequence: base pairs, skipping base pairs, skippingGGCCAAis smaller than Sequence: CTCCCCCTGAATGAGis smaller than 25 base pairs, skippingis smaller than 25 base pairs, skipping 25Sequence: base pairs, skippingSequence: CGTTACACATGTis smaller than 25GGCGSequence: CCGGACGis smaller than base pairs, skipping Sequence: 25is smaller than Sequence: CCAASequence: CACCis smaller than 25 base pairs, skipping base pairs, skipping CCTCAACACTTGCAGCis smaller than 25 base pairs, skippingis smaller than 25Sequence: CGGCGCGGGCAGAGGis smaller than 25 base pairs, skippingSequence: GCTACis smaller than 25 base pairs, skipping 25 base pairs, skipping Sequence: ACCGAis smaller than 25 Sequence: AGGGC base pairs, skipping is smaller than base pairs, skipping25 base pairs, skippingSequence: Sequence: CAGGCAGTGGTAGAGAAis smaller than 25 base pairs, skipping Sequence: Sequence: Sequence: CGAGAGGGAGACAAis smaller than 25 base pairs, skipping CTACCTAATCAAis smaller than Sequence: TGTTGAGis smaller than 2525 base pairs, skipping GCCCGTTAGCCCTCTCTGCAA base pairs, skipping Sequence: is smaller than 25 base pairs, skippingSequence: CCGACAAATCCATis smaller than 25 base pairs, skippingCCGGGTGTTTGACis smaller than 25 CGCSequence: base pairs, skippingis smaller than CCTGCCATCATASequence: TGGAGACGGCAACGAGGTGG25 base pairs, skipping is smaller than Sequence: is smaller than 25 base pairs, skipping25GGGGAAGTAACGCTGGTis smaller than Sequence: base pairs, skipping 25Sequence: CCCCis smaller than base pairs, skippingCTCGGGTGGCGCACTTCTTGGGis smaller than 25 25 base pairs, skipping Sequence: Sequence: Sequence: GGCTGCCGCAAGGACCATCG base pairs, skippingAATCACTTGAGis smaller than 25 is smaller than 25CACGTCSequence: base pairs, skippingSequence: GCCGGTGCGGCCGATGCis smaller than 25 base pairs, skippingSequence: CGTTCCTTCACGTAis smaller than 25 base pairs, skipping base pairs, skippingCCCCTCCTC Sequence: GCTACCCTTCTTCTTCis smaller than 25 base pairs, skipping is smaller than 25 base pairs, skipping Sequence: CCCGCCGTCis smaller than 25 base pairs, skipping Sequence: CTCTGCCGCAGTAGGTCTGACis smaller than 25 base pairs, skipping Sequence: CCCACACGAACCACACCCTis smaller than 25 base pairs, skipping Sequence: Sequence: CGCCAGATCACCGCCGAGGASequence: CGCCAAGAis smaller than 25Sequence: CCTGGATGTis smaller than 25 base pairs, skipping GCCis smaller than Sequence: GGACTATis smaller than 25 base pairs, skipping Sequence: CGAis smaller than 25 base pairs, skipping is smaller than 25 base pairs, skipping Sequence: Sequence: ATCAATAAACATGTGis smaller than is smaller than 25 base pairs, skipping 25CTCCAGCCGis smaller than 25Sequence: GATCTCis smaller than 25Sequence: CTCGGAis smaller than 25 base pairs, skipping base pairs, skipping25 base pairs, skipping base pairs, skipping base pairs, skipping base pairs, skipping Sequence: CCTGCGis smaller than 25Sequence: CGTGGTGGTGCTCGCCATCCTTCTis smaller than Sequence: Sequence: CGACAATATCGACAC25AGACCTTAGATTTTCATCCGis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skippingis smaller than Sequence: 25Sequence: AGAAGATAAGCGAis smaller than TCGTCCCCTTTis smaller than base pairs, skipping25 base pairs, skipping25 base pairs, skippingSequence: GAAGTCGAAGGCCis smaller than 25 base pairs, skipping Sequence: ATTTTCTCis smaller than 25Sequence: base pairs, skippingCTTCCTTGAGCTG Sequence: is smaller than 25CACCTGCGCAGCCCTT base pairs, skippingSequence: is smaller than 25 base pairs, skippingCCGATTCTCGTTGCTCAAGGGTSequence: CCCGTAATACis smaller than 25 Sequence: base pairs, skipping Sequence: CTACTGis smaller than Sequence: TGGCCTTATTGCTGCAis smaller than 25CAACis smaller than 25 base pairs, skipping 25 base pairs, skippingSequence: CGGGGAGTAAGCCGGAis smaller than is smaller than base pairs, skipping 25 base pairs, skipping 25 base pairs, skipping Sequence: Sequence: CTGis smaller than Sequence: GGGCGGGCAGACGCC25Sequence: GGAGis smaller than Sequence: CGTGGATGTGTCis smaller than 25 base pairs, skipping Sequence: CTGTTGGTTCTGCTis smaller than 25 base pairs, skipping is smaller than 25 base pairs, skipping base pairs, skipping Sequence: Sequence: ATCCCATCCAATGAGAAATCAis smaller than CAAGSequence: AGATAAGAGTGGCGATGGCTis smaller than 25 base pairs, skipping CCTGC25 base pairs, skipping is smaller than is smaller than 25Sequence: TGTis smaller than 2525 base pairs, skipping base pairs, skipping base pairs, skipping 25 base pairs, skippingSequence: Sequence: CTGCAGGTTCTTCTCGACAAis smaller than Sequence: CCTTis smaller than 25AAGAGGGCGTCCAAGASequence: CGACCATATCCGTC base pairs, skippingis smaller than 25is smaller than 25 base pairs, skipping Sequence: 25 base pairs, skippingSequence: GCCSequence: AAGGCATAACCCCTTis smaller than 25is smaller than 25 CACCG base pairs, skipping base pairs, skippingis smaller than base pairs, skipping Sequence: TTCGTGTCGG25 base pairs, skipping is smaller than Sequence: Sequence: CCATTGis smaller than 25ATTTTis smaller than 25 base pairs, skipping 25Sequence: CCTCSequence: CTTGCis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skippingis smaller than Sequence: 25 base pairs, skipping Sequence: Sequence: AGCGGAGCTTGTTis smaller than 25Sequence: GCCTGGGTSequence: CATTAATCCCTTAAAGis smaller than 25 base pairs, skipping CCAAGAAGis smaller than 25 base pairs, skipping Sequence: Sequence: ATAAAACGCGGATCis smaller than base pairs, skipping ACCG25 base pairs, skipping Sequence: CGACis smaller than 25 base pairs, skipping is smaller than 25 base pairs, skipping is smaller than GTCACGATAACATACTGGAATCTis smaller than 25 base pairs, skipping Sequence: CGACTGGAGATCis smaller than 25 base pairs, skipping Sequence: Sequence: AAGGCATAACCCCTTATGACis smaller than 25 base pairs, skipping GGT25Sequence: CTCCGGAGis smaller than Sequence: CTTGCGGCAGCCT base pairs, skipping Sequence: ACTGAis smaller than 25Sequence: TATTGCTCTis smaller than 25 base pairs, skipping is smaller than is smaller than 25 base pairs, skipping 2525Sequence: base pairs, skipping GTTCATCCTCC base pairs, skipping base pairs, skippingis smaller than Sequence: 25CAGACCG base pairs, skippingSequence: ACAAGATCACACAGCTCACGGATAis smaller than is smaller than 2525Sequence: TCGGTAGGCTCTCGCTGC base pairs, skipping base pairs, skippingSequence: ATAGAACCGis smaller than is smaller than 25Sequence: 25 base pairs, skippingCTCCATTCTCAGTCCCGGCAA base pairs, skipping is smaller than Sequence: CCTTGAis smaller than 25 base pairs, skipping 25Sequence: GGAA base pairs, skipping is smaller than Sequence: CGCCATSequence: CAAAGCGCTACCis smaller than 25 base pairs, skipping 25 base pairs, skippingis smaller than 25 base pairs, skipping Sequence: CGCTGGACTGGTis smaller than Sequence: CGTAGCTCCC25is smaller than 25 base pairs, skippingSequence: base pairs, skipping CCGAAACCCTAACCSequence: TCTCTTCTC is smaller than 25is smaller than 25 base pairs, skipping Sequence: CTAGGGCAGATTCTis smaller than 25 base pairs, skipping Sequence: CTCCAis smaller than 25Sequence: GTTCGis smaller than 25 base pairs, skipping Sequence: CCTCGCCCACTTis smaller than 25 base pairs, skipping Sequence: CTGTTGis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skipping Sequence: CTCCCCACGGAGACTTTCTTGis smaller than 25 base pairs, skipping Sequence: TGCTCTTCCCAAGTTCCGCAAGCTis smaller than 25 base pairs, skipping Sequence: TGGCACGGis smaller than Sequence: 25CGACCGSequence: base pairs, skippingSequence: CGATCCTCGAis smaller than 25 base pairs, skipping is smaller than ACSequence: CTTCGAGCTTCTCATCCCGCAis smaller than 25 base pairs, skipping 25 base pairs, skipping is smaller than Sequence: 25CTCAis smaller than 25 base pairs, skipping base pairs, skipping Sequence: GTCAACGis smaller than Sequence: 25Sequence: AAGGATCTCACCAGCATG base pairs, skippingTAGAis smaller than Sequence: is smaller than 25ATGTCTACAATCTATGATGAis smaller than 25 base pairs, skipping base pairs, skipping Sequence: 25 base pairs, skipping ATGAAGCTG Sequence: is smaller than GTTACGGT25is smaller than base pairs, skipping25 Sequence: base pairs, skippingGTAGGAGTT is smaller than 25 base pairs, skippingSequence: Sequence: Sequence: CTGGTCAAACTATACTGAACTCCGATTTATCCTTAis smaller than 25is smaller than is smaller than base pairs, skipping25 base pairs, skipping 25 Sequence: base pairs, skippingCCCAGCTGAAACTAACAAACis smaller than 25 base pairs, skipping Sequence: TTGTCATCAGCTTTCAGTGATAGis smaller than 25 base pairs, skipping Sequence: Sequence: AGACAGGCCGTTGGATTGCCCSequence: is smaller than is smaller than Sequence: CTCGATGGATCAAAGAAAGCCATTis .. than 25 base pairs, skipping Sequence: is smaller than 25GCTGGGTGSequence: base pairs, skippingSequence: ATACGGTGTis smaller than 25 base pairs, skipping GTGGA is smaller than Sequence: Sequence: GGAAGATGG25 base pairs, skipping is smaller than 25 base pairs, skippingis smaller than 25 base pairs, skipping Sequence: Sequence: GTTGATGTTGCTGAAGCCAAis smaller than 25CAAAGSequence: GGAAGACACis smaller than 25TGATG base pairs, skipping base pairs, skippingis smaller than 25 base pairs, skipping is smaller than Sequence: 25 base pairs, skippingGGCCCAAACAT is smaller than 25 base pairs, skipping Sequence: TGGAAGAGAASequence: is smaller than Sequence: TCCTTis smaller than ATCTAACCCA2525is smaller than base pairs, skipping base pairs, skipping25 base pairs, skippingSequence: CTTCGAAACGGATCAis smaller than Sequence: 25Sequence: CGGAAis smaller than 25 base pairs, skipping Sequence: Sequence: GTTCATACAis smaller than GACACGAATATGTACGGAACCTis smaller than 25 base pairs, skipping base pairs, skipping 25CAGGAAASequence: Sequence: CTTGCCCCTTis smaller than ATCGCC base pairs, skipping 25 base pairs, skipping Sequence: Sequence: is smaller than 25is smaller than 25 base pairs, skipping Sequence: GTTTis smaller than 25 base pairs, skipping TTCCTis smaller than 25 base pairs, skipping base pairs, skipping Sequence: CACCACSequence: CCCAGis smaller than 25 base pairs, skipping CTAAACTTCAATCTis smaller than Sequence: Sequence: is smaller than 25CTATAAATGATTTGGCTis smaller than 25 base pairs, skipping 25Sequence: base pairs, skippingSequence: CGCCGis smaller than 25 base pairs, skipping CCACCATCAACAGCAATTGTCis smaller than base pairs, skipping GAAGAGGG25 is smaller than base pairs, skipping 25Sequence: CAAAGGTATGAGAAGAGGis smaller than base pairs, skipping25 base pairs, skipping Sequence: Sequence: GTGTASequence: CGGCis smaller than 25GCCAAATCGAATCGAGGAGACTTTis smaller than 25 base pairs, skippingSequence: CAAGGTTGis smaller than 25 base pairs, skipping Sequence: GTTCAAACTTGATAAis smaller than base pairs, skipping Sequence: CTAGAAis smaller than 25 is smaller than 25 base pairs, skipping25 base pairs, skipping base pairs, skipping Sequence: CGTGCAGTAGCTGTGis smaller than 25 base pairs, skipping Sequence: GGAGGAis smaller than Sequence: 25 base pairs, skipping Sequence: Sequence: Sequence: CCCACAAACTAATAAis smaller than 25 base pairs, skipping CTGAAGATGGTCTCGGTCAGAGTATis smaller than is smaller than 25 base pairs, skipping25CAAGGCGGTSequence: CGCAGGTGTCCTAAGATis smaller than 25is smaller than 25 base pairs, skipping Sequence: base pairs, skipping CTCCTTTCACGCCTTGTCTTTTAT base pairs, skippingSequence: is smaller than 25 base pairs, skipping CCGTGCATATACTACTGCCTCTSequence: is smaller than GGCGAGGGTTCAis smaller than 2525 base pairs, skipping Sequence: GCAACGTCis smaller than base pairs, skippingSequence: ACGACTAGCTGCis smaller than Sequence: AACTC25Sequence: Sequence: CCAATCAis smaller than 25 base pairs, skipping base pairs, skipping is smaller than GCTCis smaller than 2525 base pairs, skipping base pairs, skipping Sequence: AATCTCACAAACACATTATTCis smaller than 25 base pairs, skipping 25Sequence: Sequence: CTCCACATGCTGATGAAACCSequence: GGCGGCCCGCAAis smaller than 25is smaller than 25 base pairs, skipping Sequence: ATGCAAATGCis smaller than 25 base pairs, skipping base pairs, skippingSequence: CTAGTGTCGTCGTTCCTCCTCGis smaller than 25 CGGCATAGTGGis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skippingSequence: CCTGTGGAAGCCCCTCCSequence: TGAAGis smaller than 25 base pairs, skipping Sequence: GGCCGTTGGAGis smaller than is smaller than 2525 base pairs, skippingSequence: base pairs, skipping TTGTAAGTGGCTCGTAC is smaller than 25 base pairs, skippingSequence: CCGCAAGCACCAis smaller than Sequence: GTTTGGAis smaller than 25 base pairs, skipping 25Sequence: Sequence: CCCAAATTGAGTACTCGGGAAC base pairs, skipping Sequence: GTCTCCGGTAACGCTCTCAAis smaller than 25 base pairs, skippingis smaller than AGTTAAGACT25 base pairs, skipping Sequence: CTCGGAis smaller than 25 base pairs, skipping Sequence: Sequence: is smaller than 25GACCGis smaller than 25 base pairs, skipping base pairs, skipping CTGATATCCGis smaller than 25 base pairs, skipping Sequence: CGTAAT Sequence: is smaller than Sequence: GGACis smaller than 25 base pairs, skipping 25TGTTT base pairs, skippingis smaller than 25Sequence: CGCCCTTGACCis smaller than Sequence: CTGTGATGAGTGTGGTATCis smaller than 25Sequence: ATCTCis smaller than 25 base pairs, skipping Sequence: CTTCGCCGCCATCTCGCTCTGGis smaller than 25Sequence: GTACAAGCTGCTATACT base pairs, skipping base pairs, skipping25 base pairs, skipping base pairs, skipping is smaller than Sequence: 25TCTACATTATAGTAA base pairs, skipping is smaller than 25 base pairs, skipping Sequence: Sequence: Sequence: GTTGTACGAAATACGis smaller than is smaller than is smaller than 252525 base pairs, skipping base pairs, skipping base pairs, skipping Sequence: Sequence: CCACGSequence: CAGGCGAAGGTGCCis smaller than TAAAAACTTCAis smaller than 25 base pairs, skipping Sequence: Sequence: CTCCTCAGCACCCTCCTTTis smaller than 25 base pairs, skipping Sequence: Sequence: 25 base pairs, skipping Sequence: CCTAis smaller than 25CTAGTTTACAACTis smaller than 25 base pairs, skipping Sequence: CCGCTis smaller than 25 base pairs, skipping CGCTis smaller than 25 base pairs, skippingis smaller than base pairs, skipping 25Sequence: GTACCGCGTTCACTGTGis smaller than 25CAAGAATGTTGCTGTCAAGGAis smaller than base pairs, skipping 25 base pairs, skipping base pairs, skipping Sequence: CGAGCGATCACCGis smaller than 25 base pairs, skipping Sequence: CTCCTTCATTCTCCTTGGCTTCCis smaller than 25 base pairs, skippingSequence: CCTCGTis smaller than Sequence: CCAACAATTAis smaller than 25 base pairs, skipping 25Sequence: base pairs, skippingSequence: AGCAGTTGCTTCAis smaller than GGACA Sequence: Sequence: AAGAAAGGis smaller than 25 base pairs, skipping 25CTGAis smaller than base pairs, skippingis smaller than 25 base pairs, skipping25 Sequence: base pairs, skipping Sequence: AAAGGCTAis smaller than 25CTCAGTGCACGCCGCCAis smaller than 25 base pairs, skipping Sequence: Sequence: GCAAAGCTCGATTTGGGSequence: base pairs, skipping is smaller than Sequence: Sequence: TCCAGATACAAATTACTTATTTAis smaller than 25 base pairs, skipping Sequence: CAGGGis smaller than 25 base pairs, skipping CAGTTCTCCGTGTTTCTGCAAis smaller than 25 base pairs, skipping CCTAGG25 base pairs, skippingCTGCTGis smaller than 25Sequence: CTGCis smaller than 25 base pairs, skipping Sequence: is smaller than 25 base pairs, skipping CTCGAGGTTAGGGTSequence: base pairs, skippingSequence: GCCTCTTCCCCCis smaller than 25 base pairs, skipping CGACCAGAGGAis smaller than 25 base pairs, skipping is smaller than 25 Sequence: base pairs, skippingCGCGGACTGAATCTSequence: AACCGACTGTGis smaller than 25 base pairs, skipping is smaller than Sequence: 25Sequence: base pairs, skipping CCCCGAACGCCAATCCCAGTGATTCTCTGGis smaller than is smaller than 25 base pairs, skipping25 base pairs, skipping Sequence: Sequence: GTGGSequence: GGCTTGGAis smaller than 25is smaller than GCAGGTTTCCGTTTTTTCis smaller than 25Sequence: base pairs, skipping base pairs, skippingACACCis smaller than 25Sequence: 25 base pairs, skippingCAGAAACATGCCTGACis smaller than 25 base pairs, skipping base pairs, skippingSequence: GTTASequence: is smaller than CTCTis smaller than 25 base pairs, skipping 25 base pairs, skipping Sequence: TGAGis smaller than 25 base pairs, skipping Sequence: CGAAGCCAAAGACTGTTCCCAAis smaller than 25 base pairs, skipping Sequence: CTGAATCTis smaller than 25Sequence: base pairs, skippingCTTTGGA is smaller than 25 base pairs, skipping Sequence: CTCATGGAACATTTACCis smaller than 25 base pairs, skipping Sequence: CAGTACCis smaller than 25 base pairs, skippingSequence: Sequence: CGGAGAGGGCGGGGGGGAAAGSequence: CTGAGis smaller than Sequence: CCCTGATGGTTACCTGTTTGAGis smaller than 25 base pairs, skippingis smaller than 25is smaller than 2525 base pairs, skipping base pairs, skippingSequence: base pairs, skipping TGTGATATATATGTCCCTTGATCASequence: is smaller than GCCCCTTATCTCGCTCTTTCTG25is smaller than base pairs, skipping25Sequence: base pairs, skipping Sequence: CATGAATACTAGTACis smaller than 25Sequence: CCAA base pairs, skippingTGGGACTCCAACGCis smaller than Sequence: is smaller than 25GGC25 base pairs, skippingis smaller than base pairs, skipping 25Sequence: base pairs, skippingGGATGATCAGTAC is smaller than 25 base pairs, skipping Sequence: GTCGACGCCGAAis smaller than Sequence: 25Sequence: ATCACATTCTCCAAis smaller than Sequence: CGAAGAGTGTATTTGAAGTGCis smaller than 25 base pairs, skipping base pairs, skippingSequence: GCTATACTGCCCCAGTGTCCGACGTCTCCTGCC 25Sequence: CTCGGAAis smaller than base pairs, skipping is smaller than is smaller than 25 base pairs, skippingSequence: 25 base pairs, skipping CAACTTT25Sequence: CACAACATis smaller than base pairs, skippingis smaller than Sequence: GGGAAATis smaller than 25 base pairs, skipping Sequence: 25Sequence: 25ATTGCCTGGCGCCis smaller than 25 base pairs, skippingSequence: CACCTCis smaller than base pairs, skipping base pairs, skippingGGATATTGGAATGGTis smaller than 25 base pairs, skipping Sequence: GGAAGis smaller than 25 base pairs, skipping 25 Sequence: Sequence: base pairs, skippingATCCCis smaller than 25Sequence: GGAGGCTis smaller than base pairs, skipping AACGA 25Sequence: GTTGCis smaller than is smaller than base pairs, skipping25 base pairs, skipping 25 Sequence: CCGTAGCGGTGCCTACATTGSequence: CGAACACTTCis smaller than 25is smaller than 25 base pairs, skippingSequence: CTGAACCTTATAis smaller than 25 base pairs, skipping base pairs, skipping base pairs, skipping Sequence: Sequence: Sequence: CGCCCTTGACCCGGTATis smaller than is smaller than 25 base pairs, skipping25GAAGAATSequence: AGCCGTTCGGGGTT base pairs, skippingis smaller than 25is smaller than 25 base pairs, skipping base pairs, skippingSequence: CCGCAGATATCACAAGis smaller than Sequence: CGAGGTCAGTGCAGTis smaller than 25 base pairs, skipping Sequence: GCCTAATACGGCCGACACis smaller than 25 base pairs, skipping 25Sequence: CGGGGis smaller than 25 base pairs, skipping Sequence: GGCGCACACATCGATAAAACCCA base pairs, skippingis smaller than 25Sequence: CCGAAis smaller than base pairs, skipping Sequence: Sequence: GCTGTGGGTCTGCCTGCTATGis smaller than 25 base pairs, skipping is smaller than Sequence: AGCTCGGGAAis smaller than 25Sequence: 25 base pairs, skipping CATTCCTGAis smaller than base pairs, skippingSequence: 25 base pairs, skipping Sequence: GAAGAAGis smaller than 25CTACATGCTCGGCAGCCis smaller than 25 base pairs, skipping25 base pairs, skipping base pairs, skipping Sequence: GTGGTCTis smaller than Sequence: Sequence: 25CAGGGTCGGAGACAAATCCAATGTis smaller than is smaller than 25Sequence: CTCAGTCTTGACCTGCGis smaller than 25Sequence: CCACATATis smaller than base pairs, skipping base pairs, skipping base pairs, skipping25 25 base pairs, skipping base pairs, skipping Sequence: Sequence: Sequence: GTTCGACCAAAAAAGCCTGAGCCCGGCGACGAGAGCCGGCTGTTACGACGGCis smaller than is smaller than is smaller than 2525 base pairs, skipping 25 base pairs, skipping Sequence: CATTAAGAis smaller than Sequence: base pairs, skipping25CCACCTTAAATCCTCAAATTis smaller than Sequence: base pairs, skipping 25GCATCTATTGCTGATTCATis smaller than 25 base pairs, skipping base pairs, skippingSequence: CCCTGTCATCTAGTGTCGGTTGATSequence: TGGGis smaller than 25is smaller than 25 base pairs, skipping base pairs, skippingSequence: CCAATAis smaller than Sequence: CCGGCCAAGCAAGTis smaller than Sequence: 25 base pairs, skipping CCGATATCTCAATTACAGCTTCCTSequence: 25is smaller than 25 base pairs, skippingGAGG base pairs, skipping is smaller than 25Sequence: base pairs, skippingCGGGATTCCTCA Sequence: is smaller than TGAATGCTTACT25is smaller than Sequence: CCTCCCCCATCGAGTTATCAACis smaller than base pairs, skipping25 25 base pairs, skippingSequence: TGTAAATCTTCCGACTGSequence: ATTCis smaller than base pairs, skippingis smaller than 25 base pairs, skipping 25 base pairs, skippingSequence: ACGCCCCCGGCGCAGCCGCis smaller than 25 base pairs, skipping Sequence: CTGCCTGCAAGTGTGGCAGTGis smaller than Sequence: Sequence: Sequence: 25 base pairs, skippingGTCCTCGCTCTGTCCGCCGCCATTTis smaller than 25 base pairs, skippingSequence: ATCTCis smaller than 25 GCCis smaller than 25 base pairs, skippingSequence: CCACAACCCACCGTGCCCCACTCis smaller than 25 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 3, 2022, 3:25am UTC](https://help.galaxyproject.org/t/trinity-and-reads-smaller-than-25-base-pairs/7967/2 "2022-05-03T03:25:52Z")
Hi @balrajsharma This message repeating means that you have many reads that are too short to assemble. > [@balrajsharma](#): > > Sequence: ACGCCCCCGGCGCAGCCGCis smaller than 25 base pairs, skipping Try filtering out reads that are too short to be used, then rerun. The job is seems to be running out of resources when attempting to sorting out usable read pairs from those that are not. Pre-filtering by length will address that. Use a QA tool that will remove/separate both ends of a pair if one of the paired reads fails the filter. `Trinity` expects intact pairs as an input. If it seems like that length filter eliminates too many reads: - prior QA steps may have been too strict - you need to still run QA - the reads were originally too short - the read quality is actually low, and the QA steps are correct The last two would be the most concerning re is this data even usable? Tutorials: [Search Tutorials](https://training.galaxyproject.org/training-material/search?query=quality) Thanks! ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [December 20, 2023, 9:48pm UTC](https://help.galaxyproject.org/t/trinity-and-reads-smaller-than-25-base-pairs/7967/3 "2023-12-20T21:48:42Z")