SPAdes组装细菌基因组Error: unequal amount of reads

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.(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