Cutadapt using issue

Question

[woongjaej]

Hi, guys

I have an issue using trim_galore

I have two computers(linux) and installed trim_galore which uses cutadapt 1.15 version in both computers.

One, it works fine but the other one gives me error message below.

 No quality encoding type selected. Assuming that the data provided
 uses Sanger encoded Phred scores (default) Path to Cutadapt set as:
 '~/.local/bin/cutadapt' (default)
 1.15 Cutadapt seems to be working fine (tested command '~/.local/bin/cutadapt --version') AUTO-DETECTING ADAPTER TYPE
 =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>>
 ../raw_data/AdMSC_060P3_1.fastq.gz <<) Found perfect matches for the
 following adapter sequences: Adapter type    Count   Sequence       
 Sequences analysed      Percentage Illumina        329585 
 AGATCGGAAGAGC   1000000 32.96 smallRNA        1       TGGAATTCTCGG   
 1000000 0.00 Nextera 0       CTGTCTCTTATA    1000000 0.00 Using
 Illumina adapter for trimming (count: 329585). Second best hit was
 smallRNA (count: 1) Writing report to
 '../trimmed_data_galore/AdMSC_060P3_1.fastq.gz_trimming_report.txt'
 SUMMARISING RUN PARAMETERS
 ========================== Input filename: ../raw_data/AdMSC_060P3_1.fastq.gz Trimming mode: paired-end Trim
 Galore version: 0.4.4 Cutadapt version: 1.15 Quality Phred score
 cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence:
 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum
 trimming error rate: 0.1 (default) Minimum required adapter overlap
 (stringency): 1 bp Minimum required sequence length for both reads
 before a sequence pair gets removed: 20 bp Running FastQC on the data
 once trimming has completed Output file(s) will be GZIP compressed
 Writing final adapter and quality trimmed output to
 AdMSC_060P3_1_trimmed.fq.gz
 Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file
 ../raw_data/AdMSC_060P3_1.fastq.gz <<< Traceback (most recent call
 last):   File "/home/wjjung/.local/bin/cutadapt", line 600, in
<module>
    sys.exit(main())   File "/home/wjjung/.local/bin/cutadapt", line 547, in main
    reader = read_sequences(input_filename, quality_filename, colorspace=options.colorspace, fileformat=options.format)   File
"/home/wjjung/.local/bin/cutadapt", line 255, in read_sequences
    return seqio.SequenceReader(seqfilename, colorspace, fileformat) 
TypeError: __init__() takes exactly 2 arguments (4 given) Cutadapt
terminated with exit signal: '256'. Terminating Trim Galore run,
please check error message(s) to get an idea what went wrong...

Difference between two computers is just that one(works) has root permission and one(doesn't work) doesn't.

Does someone have had this kind of issue using it? Or if someone knows how to fix it, give me some help, please.

Thank you.

Woongjae

[chen]

You error message is not shown, you need to edit your post.

BTW, you can use fastp to trim adapters for Illumina sequencing data, without the need of knowing the adapter sequences.

Just download fastp and run:

fastp -i in.fq -o out.fq

And then everything is done, the adapters are trimmed in out.fq

For paired end data, the command is like:

fastp -i in1.fq -o out1.fq -I in2.fq -O out2.fq

Gzip is supported for both input and output.

[woongjaej]

Thank you Chen!

I'll take a look at fastp you recommended!

Sorry but now I must use trim_galore because of an order.

Thank you very much for your recommendation