重复序列分析，去除含有基因序列的库文件时候报错，你们示例数据也有这样的问题

基因组重复序列分析的时候，在运行【汇总不同软件生成的repeat库，并用RepeatMasker进行重复序列注释】时候

for lib in ModelerAll.lib MITE_LTR.lib Homology.db; do
  blastx -query ${lib} -db ${SPROT} -evalue 1e-10 -num_descriptions 10 -num_threads ${threads} -out ${lib}_blast_results.txt
  perl $scriptsdir/ProtExcluder1.2/ProtExcluder.pl ${lib}_blast_results.txt ${lib}
  echo -e "${lib}\tbefore\t$(grep -c ">" ${lib})\tafter\t$(grep -c ">" ${lib}noProtFinal)"
done

会报错如下：

Can not open the seqfile ModelerAll.lib_blast_results.txt.fnolowm50seq
mergeunmatchedregion.pl seqfile
Illegal division by zero at /public-supool/home/thli/scripts/genome_annotation/ProtExcluder1.2/GCcontent.pl line 122.
Can not open the seqfile MITE_LTR.lib_blast_results.txt.fnolowm50seq
mergeunmatchedregion.pl seqfile
Illegal division by zero at /public-supool/home/thli/scripts/genome_annotation/ProtExcluder1.2/GCcontent.pl line 122.
Can not open the seqfile Homology.db_blast_results.txt.fnolowm50seq
mergeunmatchedregion.pl seqfile
Illegal division by zero at /public-supool/home/thli/scripts/genome_annotation/ProtExcluder1.2/GCcontent.pl line 122.
vsearch v2.18.0_linux_x86_64, 503.4GB RAM, 128 cores

我看了你们示例输出文件中的Homology.db_blast_results.txt.fnolowm50seqmGC，发现输出都是：

A C G T N totalnoN total
00000000 00000000 00000000 00000000 00000000 00000000 00000000
AT 00000000 GC 00000000

明显你们的示例数据也计算错误。是不是脚本有问题

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2 个回答

Ti Amo 2024-09-11 10:14

我们的示例数据输出文件里面该文件内容如下：

建议check一下你的*_blast_results.txt是否正常，如果为空检查 ${SPROT} 变量是否赋值

litianhuan 2024-09-11 13:05

*_blast_results.txt输出如下：

cmd>head -50 Homology.db_blast_results.txt
BLASTX 2.14.1+

Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.


Database: uniprot_sprot_clean.fasta
           565,168 sequences; 203,477,143 total letters


Query= IS1#ARTEFACT @root [S:10]
Length=768
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value
sp|P59843|INSB_HAEDU                                                  348     2e-122
sp|A0A385XJL4|INSB9_ECOLI                                             348     2e-122
sp|P0CF30|INSB8_ECOLI                                                 348     2e-122
sp|P0CF29|INSB6_ECOLI                                                 348     2e-122
sp|P0CF28|INSB5_ECOLI                                                 348     2e-122
sp|P0CF25|INSB1_ECOLI                                                 348     2e-122
sp|P0CF31|INSB_ECOLX                                                  346     2e-121
sp|P57998|INSB4_ECOLI                                                 338     3e-118
sp|P0CF27|INSB3_ECOLI                                                 335     3e-117
sp|P0CF26|INSB2_ECOLI                                                 335     3e-117

>sp|P59843|INSB_HAEDU
Length=167
 Score = 348 bits (893),  Expect = 2e-122, Method: Compositional matrix adjust.
 Identities = 167/167 (100%), Positives = 167/167 (100%), Gaps = 0/167 (0%)
 Frame = +1
Query  250  MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLF  429
            MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLF
Sbjct  1    MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLF  60
Query  430  YAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKR  609
            YAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKR
Sbjct  61   YAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKR  120
Query  610  YTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVIGHYLNIKHYQ  750
            YTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVIGHYLNIKHYQ

*_blast_results.txt输出正常，但是Homology.db_blast_results.txt.fnolowm50seqmGC，输出还是错误：

A C G T N totalnoN total
00000000 00000000 00000000 00000000 00000000 00000000 00000000
AT 00000000 GC 00000000

重复序列分析，去除含有基因序列的库文件时候报错，你们示例数据也有这样的问题

2 个回答

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