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No report when --report=minimal #381

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adefelicibus opened this issue May 6, 2019 · 3 comments

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@adefelicibus
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commented May 6, 2019

Hi, I'm using Cutadapt version 2.3 that I installed with conda with the command-line parameteters:

cutadapt --trim-n -m 100 -g CCTACGGGRSGCAGCAG -G GGACTACHVGGGTWTCTAAT --report=minimal -o results/tmp/cutadapt/trimmed/180503651071-1-1-1_S29_L001_R1.fastq.gz -p results/tmp/cutadapt/trimmed/180503651071-1-1-1_S29_L001_R2.fastq.gz --untrimmed-output results/tmp/cutadapt/untrimmed/180503651071-1-1-1_S29_L001_R1.fastq.gz --untrimmed-paired-output results/tmp/cutadapt/untrimmed/180503651071-1-1-1_S29_L001_R2.fastq.gz results/tmp/fastq/180503651071-1-1-1_S29_L001_R1.fastq.gz results/tmp/fastq/180503651071-1-1-1_S29_L001_R2.fastq.gz

I received the output like this:

[ 8<---------] 00:00:03        30,000 reads  @    145.7 µs/read;   0.41 M reads/minute

and no minimal report.

But, if I use the option --report=full, I get the full report.

Using Cutadapt version 1.18 I get the desired minimal report:

status  in_reads        in_bp   too_short       too_long        too_many_n      out_reads       w/adapters      qualtrim_bp     out_bp  w/adapters2     qualtrim2_bp    out2_bp
OK      140663  71738130        0       0       0       131208  135612  0       37789941        135005  0       24283833

According to the Cutadapt documentation, nothing has changed about the report.

Best.

@marcelm

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commented May 7, 2019

Hi and thanks for the report. I’m traveling at the moment and will look into this after I return.

@marcelm marcelm closed this in a408005 Jun 10, 2019

@marcelm

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commented Jun 10, 2019

Thanks for your patience. I’ve been able to reproduce the problem and was able to fix it. The next Cutadapt release will again have a working --report=minimal option.

@adefelicibus

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commented Jun 10, 2019

Thanks @marcelm!

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