IndexError: list index out of range

[BeyondMyPast228]

你好，新年快乐，我再运行CeleScope这个R包管道的Cutadapt步骤时，出现了以下报错，不知道是怎么回事？ Analysis complete for SC003BM1_2.fq.gz 2021-02-09 14:07:46,090 - celescope.tools.barcode.barcode - INFO - fastqc done! 2021-02-09 14:07:46,090 - celescope.tools.report - INFO - generate report: rna barcode 2021-02-09 14:07:46,121 - celescope.tools.report - INFO - generate report done! 2021-02-09 14:07:46,146 - celescope.tools.barcode.barcode - INFO - done. time used: 1:09:22.840118 2021-02-09 14:07:46,146 - celescope.tools.cutadapt.cutadapt - INFO - start... 2021-02-09 14:07:46,152 - celescope.tools.cutadapt.cutadapt - INFO - cutadapt -a polyT=A{18} -a p5=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n 2 -j 16 -m 20 --nextseq-trim=20 --overlap 10 -l 150 -o SC003BM1/02.cutadapt//SC003BM1_clean_2.fq.gz SC003BM1/01.barcode/SC003BM1_2.fq.gz /data/singlecell/sc/COVID_19/BM1_3/SC003BM1_R1.fq.gz /data/singlecell/sc/COVID_19/BM1_3/SC003BM1_R1.fq.gz Traceback (most recent call last): File "/home/zfzf/.local/bin/celescope", line 8, in sys.exit(main()) File "/home/zfzf/.local/lib/python3.6/site-packages/celescope/celescope.py", line 566, in main args.func(args) File "/home/zfzf/.local/lib/python3.6/site-packages/celescope/rna/run.py", line 32, in run cutadapt(args) File "/home/zfzf/.local/lib/python3.6/site-packages/celescope/tools/utils.py", line 45, in wrapper result = func(*args, kwargs) File "/home/zfzf/.local/lib/python3.6/site-packages/celescope/tools/cutadapt.py", line 75, in cutadapt format_stat(args.outdir + '/cutadapt.log', args.sample) File "/home/zfzf/.local/lib/python3.6/site-packages/celescope/tools/cutadapt.py", line 30, in format_stat p_list.append({"item": attr[0], "value": attr[1]}) IndexError: list index out of range** 我该如何解决这个错误呢？感谢您的帮助

[zhouyiqi91]

新年快乐！ 这个问题可能是安装的cutadapt的版本!=1.1.7。 麻烦将02.cutadapt/cutadapt.log 的内容贴上

[BeyondMyPast228]

Hi@zhouyiqi91, The error is: This is cutadapt 1.17 with Python 3.6.9 Command line parameters: -a polyT=A{18} -a p5=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n 2 -j 16 -m 20 --nextseq-trim=20 --overlap 10 -l 150 -o SC003BM1/02.cutadapt//SC003BM1_clean_2.fq.gz SC003BM1/01.barcode/SC003BM1_2.fq.gz Running on 16 cores Trimming 2 adapters with at most 10.0% errors in single-end mode ... ERROR: Traceback (most recent call last): File "/home/zfzf/.local/lib/python3.6/site-packages/cutadapt/pipeline.py", line 461, in run (n, bp1, bp2) = self._pipeline.process_reads() File "/home/zfzf/.local/lib/python3.6/site-packages/cutadapt/pipeline.py", line 220, in process_reads for read in self._reader: File "src/cutadapt/_seqio.pyx", line 181, in iter File "src/cutadapt/_seqio.pyx", line 82, in cutadapt._seqio.Sequence.init cutadapt.seqio.FormatError: In read named 'CACCTTACAACCGAGAACAAGCTA_TCGCAGTG_None_190542844': length of quality sequence (103) and length of read (150) do not match

cutadapt: error: In read named 'CACCTTACAACCGAGAACAAGCTA_TCGCAGTG_None_190542844': length of quality sequence (103) and length of read (150) do not match

[zhouyiqi91]

报的错是fastq文件SC003BM1/01.barcode/SC003BM1_2.fq.gz中read名称为CACCTTACAACCGAGAACAAGCTA_TCGCAGTG_None_190542844 的read 质量值的长度（103）和 read长度（150) 不对应。 有可能是原始的R1 reads的fastq不完整导致的。 使用下面的命令检查一下原始的R1 reads fastq文件中第190542844个reads： less {R1 read fastq.gz} | sed -n 762171372,762171375p

[zhouyiqi91]

报的错是fastq文件SC003BM1/01.barcode/SC003BM1_2.fq.gz中read名称为CACCTTACAACCGAGAACAAGCTA_TCGCAGTG_None_190542844 的read 质量值的长度（103）和 read长度（150) 不对应。 有可能是原始的R1 reads的fastq不完整导致的。 使用下面的命令检查一下原始的R1 reads fastq文件中第190542844个reads： less {R1 read fastq.gz} | sed -n 762171372,762171375p

如果这个样本包含多个fastq，上面这个命令可能不适用。 MD5 check一下原始的fastq文件。

[zhouyiqi91]

有另外的用户遇到了同样的问题，经检查是fastq文件不完整导致的。

[BeyondMyPast228]

谢谢您的帮助！

	井锐

@. | 签名由网易邮箱大师定制 On 3/3/2021 09:41，Tony @.> wrote：

有另外的用户遇到了同样的问题，经检查是fastq文件不完整导致的。

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