Entering edit mode
6.1 years ago
waqaskhokhar999
▴
160
RNA-seq data is single ended and distributed among different lanes. I am trying to assembel the transcriptome using this command:
trinity/trinityrnaseq-Trinity-v2.8.3/Trinity --seqType fq --max_memory 10G --single SRR3460466.fastq,SRR3460467.fastq,SRR3460468.fastq,SRR3460469.fastq,SRR3460470.fastq,SRR3460471.fastq,SRR3460472.fastq,SRR3460473.fastq,SRR3460474.fastq,SRR3460475.fastq,SRR3460476.fastq,SRR3460477.fastq
But I am getting this error
Error, not recognizing read name formatting: [SRR3460466.1]
Command line summary:
waqas@waqas-Hybris:/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq$ trinity/trinityrnaseq-Trinity-v2.8.3/Trinity --seqType fq --max_memory 10G --single SRR3460466.fastq,SRR3460467.fastq,SRR3460468.fastq,SRR3460469.fastq,SRR3460470.fastq,SRR3460471.fastq,SRR3460472.fastq,SRR3460473.fastq,SRR3460474.fastq,SRR3460475.fastq,SRR3460476.fastq,SRR3460477.fastq
______ ____ ____ ____ ____ ______ __ __
| || \ | || \ | || || | |
| || D ) | | | _ | | | | || | |
|_| |_|| / | | | | | | | |_| |_|| ~ |
| | | \ | | | | | | | | | |___, |
| | | . \ | | | | | | | | | | |
|__| |__|\_||____||__|__||____| |__| |____/
Trinity-v2.8.3
Single read files: $VAR1 = [
'SRR3460466.fastq',
'SRR3460467.fastq',
'SRR3460468.fastq',
'SRR3460469.fastq',
'SRR3460470.fastq',
'SRR3460471.fastq',
'SRR3460472.fastq',
'SRR3460473.fastq',
'SRR3460474.fastq',
'SRR3460475.fastq',
'SRR3460476.fastq',
'SRR3460477.fastq'
];
Trinity version: Trinity-v2.8.3
** NOTE: Latest version of Trinity is Trinity-v2.8.4, and can be obtained at:
https://github.com/trinityrnaseq/trinityrnaseq/releases
Wednesday, November 7, 2018: 16:00:20 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity/trinityrnaseq-Trinity-v2.8.3/util/support_scripts/ExitTester.jar 0
Wednesday, November 7, 2018: 16:00:20 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity/trinityrnaseq-Trinity-v2.8.3/util/support_scripts/ExitTester.jar 1
----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------
---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 200 Coverage --
---------------------------------------------------------------
# running normalization on reads: $VAR1 = [
[
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460466.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460467.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460468.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460469.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460470.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460471.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460472.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460473.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460474.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460475.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460476.fastq',
'/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460477.fastq'
]
];
Wednesday, November 7, 2018: 16:00:20 CMD: /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity/trinityrnaseq-Trinity-v2.8.3/util/insilico_read_normalization.pl --seqType fq --JM 10G --max_cov 200 --min_cov 1 --CPU 2 --output /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity_out_dir/insilico_read_normalization --max_pct_stdev 10000 --single /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460466.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460467.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460468.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460469.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460470.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460471.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460472.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460473.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460474.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460475.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460476.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460477.fastq
CMD: seqtk-trinity seq -A /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460466.fastq >> single.fa
Error, not recognizing read name formatting: [SRR3460466.1]
If your data come from SRA, be sure to dump the fastq file like so:
SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra
Error, cmd: seqtk-trinity seq -A /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460466.fastq >> single.fa died with ret 512 at /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity/trinityrnaseq-Trinity-v2.8.3/util/insilico_read_normalization.pl line 762.
Error, cmd: /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity/trinityrnaseq-Trinity-v2.8.3/util/insilico_read_normalization.pl --seqType fq --JM 10G --max_cov 200 --min_cov 1 --CPU 2 --output /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity_out_dir/insilico_read_normalization --max_pct_stdev 10000 --single /media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460466.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460467.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460468.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460469.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460470.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460471.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460472.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460473.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460474.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460475.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460476.fastq,/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/SRR3460477.fastq died with ret 512 at trinity/trinityrnaseq-Trinity-v2.8.3/Trinity line 2684.
main::process_cmd("/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity"...) called at trinity/trinityrnaseq-Trinity-v2.8.3/Trinity line 3230
main::normalize("/media/waqas/waqas_data/19_Accessions_w/new/BUR/fastq/trinity"..., 200, ARRAY(0x56443710b4b0)) called at trinity/trinityrnaseq-Trinity-v2.8.3/Trinity line 3177
main::run_normalization(200, ARRAY(0x56443710b4b0)) called at trinity/trinityrnaseq-Trinity-v2.8.3/Trinity line 1319
I have used SRA_TOOLKIT/fastq-dump to dump the fastq files, since my data is single ended, do i still need to use --split-files as this option is used for paired ended data