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Title:
No report when --report=minimal Β· Issue #381 Β· marcelm/cutadapt
Description:
Cutadapt removes adapter sequences from sequencing reads - marcelm/cutadapt
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marcelm, report, cutadapt, sign, reportminimal, issue, adefelicibus, commented, navigation, pull, requests, actions, security, closed, version, resultstmpcutadapttrimmedslrfastqgz, resultstmpcutadaptuntrimmedslrfastqgz, resultstmpfastqslrfastqgz, minimal, option, status, wadapters, qualtrimbp, outbp, owner, react, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open, source, enterprise, pricing, search, jump, public, notifications, fork, star, code, issues, insights,
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gz --untrimmed-paired-output results/tmp/cutadapt/untrimmed/180503651071-1-1-1_s29_l001_r2 gz --untrimmed-output results/tmp/cutadapt/untrimmed/180503651071-1-1-1_s29_l001_r1 results/tmp/cutadapt/trimmed/180503651071-1-1-1_s29_l001_r2 results/tmp/cutadapt/trimmed/180503651071-1-1-1_s29_l001_r1 gz results/tmp/fastq/180503651071-1-1-1_s29_l001_r2 gz results/tmp/fastq/180503651071-1-1-1_s29_l001_r1 working --report=minimal option command-line parameteters comment metadata assignees marcelm closed ggactachvgggtwtctaat --report=minimal desired minimal report option --report=full cutadapt version 2 cutadapt --trim cutadapt version 1 cutadapt documentation cutadapt release output minimal report full report gz gz 7 Β΅s/read assigned labels labels projects projects milestone milestone relationships personal information reads/minute github report fastq skip jump sign installed conda cctacgggrsgcagcag received changed traveling moment return patience ve reproduce problem fix π react
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DiscussionForumPosting:
context:https://schema.org
headline:No report when --report=minimal
articleBody:<!--
When reporting an issue, please include this information:
- Cutadapt and Python version
- How you installed the tool (conda or pip, for example)
- Which command-line parameters you used
If you report unexpected trimming behavior, this would also be helpful:
- An example input read (or read pair)
- The output that cutadapt produces
- The output that you would have expected
Feel free to delete this text before submitting your issue.
-->
Hi, I'm using Cutadapt version 2.3 that I installed with conda with the command-line parameteters:
```sh
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:
```sh
[ 8<---------] 00:00:03 30,000 reads @ 145.7 Β΅s/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:
```sh
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.
author:
url:https://github.com/adefelicibus
type:Person
name:adefelicibus
datePublished:2019-05-06T16:16:37.000Z
interactionStatistic:
type:InteractionCounter
interactionType:https://schema.org/CommentAction
userInteractionCount:3
url:https://github.com/381/cutadapt/issues/381
context:https://schema.org
headline:No report when --report=minimal
articleBody:<!--
When reporting an issue, please include this information:
- Cutadapt and Python version
- How you installed the tool (conda or pip, for example)
- Which command-line parameters you used
If you report unexpected trimming behavior, this would also be helpful:
- An example input read (or read pair)
- The output that cutadapt produces
- The output that you would have expected
Feel free to delete this text before submitting your issue.
-->
Hi, I'm using Cutadapt version 2.3 that I installed with conda with the command-line parameteters:
```sh
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:
```sh
[ 8<---------] 00:00:03 30,000 reads @ 145.7 Β΅s/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:
```sh
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.
author:
url:https://github.com/adefelicibus
type:Person
name:adefelicibus
datePublished:2019-05-06T16:16:37.000Z
interactionStatistic:
type:InteractionCounter
interactionType:https://schema.org/CommentAction
userInteractionCount:3
url:https://github.com/381/cutadapt/issues/381
Person:
url:https://github.com/adefelicibus
name:adefelicibus
url:https://github.com/adefelicibus
name:adefelicibus
InteractionCounter:
interactionType:https://schema.org/CommentAction
userInteractionCount:3
interactionType:https://schema.org/CommentAction
userInteractionCount:3
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