Control: severity -1 normal
Control: retitle -1 fastqc: FAIL strings in output - what does this mean?
Hi,
while I have uploaded a fixed autopkgtest which is now passing
I have not closed this bug. The log in testing[1] says:
...
+ gunzip example.fastq.gz
+ /usr/bin/fastqc example.fastq
Started analysis of example.fastq
Analysis complete for example.fastq
+ unzip example_fastqc.zip
Archive: example_fastqc.zip
creating: example_fastqc/
creating: example_fastqc/Icons/
creating: example_fastqc/Images/
inflating: example_fastqc/Icons/fastqc_icon.png
inflating: example_fastqc/Icons/warning.png
inflating: example_fastqc/Icons/error.png
inflating: example_fastqc/Icons/tick.png
inflating: example_fastqc/summary.txt
inflating: example_fastqc/Images/per_base_quality.png
inflating: example_fastqc/Images/per_tile_quality.png
inflating: example_fastqc/Images/per_sequence_quality.png
inflating: example_fastqc/Images/per_base_sequence_content.png
inflating: example_fastqc/Images/per_sequence_gc_content.png
inflating: example_fastqc/Images/per_base_n_content.png
inflating: example_fastqc/Images/sequence_length_distribution.png
inflating: example_fastqc/Images/duplication_levels.png
inflating: example_fastqc/Images/adapter_content.png
inflating: example_fastqc/fastqc_report.html
inflating: example_fastqc/fastqc_data.txt
inflating: example_fastqc/fastqc.fo
+ cat example_fastqc/summary.txt
PASS Basic Statistics example.fastq
WARN Per base sequence quality example.fastq
PASS Per tile sequence quality example.fastq
PASS Per sequence quality scores example.fastq
WARN Per base sequence content example.fastq
WARN Per sequence GC content example.fastq
PASS Per base N content example.fastq
PASS Sequence Length Distribution example.fastq
PASS Sequence Duplication Levels example.fastq
WARN Overrepresented sequences example.fastq
PASS Adapter Content example.fastq
+ rm -rf example_fastqc example_fastqc.html example_fastqc.zip
+ /usr/bin/fastqc toy.sam
Started analysis of toy.sam
Analysis complete for toy.sam
+ unzip toy_fastqc.zip
Archive: toy_fastqc.zip
creating: toy_fastqc/
creating: toy_fastqc/Icons/
creating: toy_fastqc/Images/
inflating: toy_fastqc/Icons/fastqc_icon.png
inflating: toy_fastqc/Icons/warning.png
inflating: toy_fastqc/Icons/error.png
inflating: toy_fastqc/Icons/tick.png
inflating: toy_fastqc/summary.txt
inflating: toy_fastqc/Images/per_base_quality.png
inflating: toy_fastqc/Images/per_sequence_quality.png
inflating: toy_fastqc/Images/per_base_sequence_content.png
inflating: toy_fastqc/Images/per_sequence_gc_content.png
inflating: toy_fastqc/Images/per_base_n_content.png
inflating: toy_fastqc/Images/sequence_length_distribution.png
inflating: toy_fastqc/Images/duplication_levels.png
inflating: toy_fastqc/Images/adapter_content.png
inflating: toy_fastqc/fastqc_report.html
inflating: toy_fastqc/fastqc_data.txt
inflating: toy_fastqc/fastqc.fo
+ cat toy_fastqc/summary.txt
PASS Basic Statistics toy.sam
PASS Per base sequence quality toy.sam
FAIL Per sequence quality scores toy.sam
FAIL Per base sequence content toy.sam
FAIL Per sequence GC content toy.sam
PASS Per base N content toy.sam
WARN Sequence Length Distribution toy.sam
PASS Sequence Duplication Levels toy.sam
FAIL Overrepresented sequences toy.sam
PASS Adapter Content toy.sam
+ rm -rf toy_fastqc toy_fastqc.html toy_fastqc.zip
+ /usr/bin/fastqc toy.bam
Started analysis of toy.bam
Analysis complete for toy.bam
+ unzip toy_fastqc.zip
Archive: toy_fastqc.zip
creating: toy_fastqc/
creating: toy_fastqc/Icons/
creating: toy_fastqc/Images/
inflating: toy_fastqc/Icons/fastqc_icon.png
inflating: toy_fastqc/Icons/warning.png
inflating: toy_fastqc/Icons/error.png
inflating: toy_fastqc/Icons/tick.png
inflating: toy_fastqc/summary.txt
inflating: toy_fastqc/Images/per_base_quality.png
inflating: toy_fastqc/Images/per_sequence_quality.png
inflating: toy_fastqc/Images/per_base_sequence_content.png
inflating: toy_fastqc/Images/per_sequence_gc_content.png
inflating: toy_fastqc/Images/per_base_n_content.png
inflating: toy_fastqc/Images/sequence_length_distribution.png
inflating: toy_fastqc/Images/duplication_levels.png
inflating: toy_fastqc/Images/adapter_content.png
inflating: toy_fastqc/fastqc_report.html
inflating: toy_fastqc/fastqc_data.txt
inflating: toy_fastqc/fastqc.fo
+ cat toy_fastqc/summary.txt
PASS Basic Statistics toy.bam
PASS Per base sequence quality toy.bam
FAIL Per sequence quality scores toy.bam
FAIL Per base sequence content toy.bam
FAIL Per sequence GC content toy.bam
PASS Per base N content toy.bam
WARN Sequence Length Distribution toy.bam
PASS Sequence Duplication Levels toy.bam
FAIL Overrepresented sequences toy.bam
PASS Adapter Content toy.bam
+ rm -rf toy_fastqc toy_fastqc.html toy_fastqc.zip
+ echo PASS
PASS
But this "PASS" in the end does not reflect the fact that the
summary.txt files contain a lot of "FAIL" strings! I have no
idea what this actually means. The current test has the same
failures (???) which I can not tell whether these are really
failures or expected output. In any case I adapted the
autopkgtest to make those "FAIL" more visible. The new output
is now:
...
Started analysis of example.fastq
Analysis complete for example.fastq
All passing in: fastqc example.fastq
Started analysis of toy.sam
Analysis complete for toy.sam
There were some failures logged in summary of
fastqc "toy.sam"
Please investigate!
FAIL Per sequence quality scores toy.sam
FAIL Per base sequence content toy.sam
FAIL Per sequence GC content toy.sam
FAIL Overrepresented sequences toy.sam
Started analysis of toy.bam
Analysis complete for toy.bam
There were some failures logged in summary of
fastqc "toy.bam"
Please investigate!
FAIL Per sequence quality scores toy.bam
FAIL Per base sequence content toy.bam
FAIL Per sequence GC content toy.bam
FAIL Overrepresented sequences toy.bam
PASS
I'd love if some users of fastqc could comment on the outcome of these
tests.
Kind regards
Andreas.
[1] https://ci.debian.net/data/autopkgtest/testing/amd64/f/fastqc/4103489/log.gz
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