记录一次用SPAdes组装公司返回的 cleandata 时的报错。
报错信息如下：
SPADES assembly failed, unequal amount of reads.
== Error == system call for: "['/home/huanjing/miniconda3/envs/spades/bin/spades-hammer', '/home/huanjing/test/spades/test/corrected/config s/config.info']" finished abnormally, OS return value: 21
可以看到SPAdes读取的reads是不成对的。
image.png
解决办法
- 使用 Trimmomatic 过滤测序Raw Fastq文件
- 使用BBMap 的 repair.sh 修复程序
- 使用fastq_pair进行修复
在这里使用 Trimmomatic 重新过滤后，能用SPAdes组装成功，没有出现上诉报错。
trimmomatic PE test.R1.fastq.gz test.R2.fastq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36
TrimmomaticPE: Started with arguments:
test.R1.fastq.gz test.R2.fastq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36
java.io.FileNotFoundException: /home/huanjing/test/spades/TruSeq3-PE.fa
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:220)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:158)
at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Quality encoding detected as phred33
Input Read Pairs: 3768530 Both Surviving: 3768530 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
#再调用SPAdes进行组装
spades.py --isolate -1 output_forward_paired.fq.gz -2 output_reverse_paired.fq.gz -o test
参考资料
Github：Trimmomatic
https://github.com/rrwick/Unicycler/issues/152
