output is overriden when multiple fastq files are provided.

[guilhermesena1]

If multiple inputs are given and the -o flag sets a directory name, only the results for the last file shows up. This is due to each file overriding the previous because they are all called output_dir/fastqc_data.txt.

Fastqc zips each report. We should create subdirectories within the output directory, one for each file name, but only if more than one file is provided.

[guilhermesena1]

e662544 should fix this.

[kevin-wamae]

Hi @guilhermesena1, the bug seems to have persisted with v1.2.1 installed from conda.

I analysed two fastq files and redirected the output to a directory.

falco writes to the same files and fails to add prefixes.

falco fastq/* --outdir falco_out
[Tue Nov 29 09:11:02 2022] creating directory for output: falco_out
[limits] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/limits.txt
[adapters] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/adapter_list.txt
[contaminants] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/contaminant_list.txt
[Tue Nov 29 09:11:02 2022] Started reading file fastq/pfs-1_R1.fastq.gz
[Tue Nov 29 09:11:02 2022] reading file as gzipped FASTQ format
[running falco|===================================================|100%]
[Tue Nov 29 09:11:02 2022] Finished reading file
[Tue Nov 29 09:11:02 2022] Writing summary to falco_out/_summary.txt
[Tue Nov 29 09:11:02 2022] Writing text report to falco_out/_fastqc_data.txt
[Tue Nov 29 09:11:02 2022] Writing HTML report to falco_out/_fastqc_report.html
Elapsed time for file fastq/pfs-1_R1.fastq.gz: 0s
[limits] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/limits.txt
[adapters] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/adapter_list.txt
[contaminants] using file /home/user/miniconda3/envs/genomics/opt/falco/Configuration/contaminant_list.txt
[Tue Nov 29 09:11:02 2022] Started reading file fastq/pfs-1_R2.fastq.gz
[Tue Nov 29 09:11:02 2022] reading file as gzipped FASTQ format
[running falco|===================================================|100%]
[Tue Nov 29 09:11:02 2022] Finished reading file
[Tue Nov 29 09:11:02 2022] Writing summary to falco_out/_summary.txt
[Tue Nov 29 09:11:02 2022] Writing text report to falco_out/_fastqc_data.txt
[Tue Nov 29 09:11:02 2022] Writing HTML report to falco_out/_fastqc_report.html
Elapsed time for file fastq/pfs-1_R2.fastq.gz: 0s

[guilhermesena1]

Hello,

Thank you for reporting the issue. Thar's really strange.

From the empty names before the underscore I think this may be an issue with how filenames are escaped.

Would you be able to just answer one question and run two quick tests?

(1) question: which operating system and shell are you using (bash? zsh?)

(2) does the program behave as expected if you change the command to

falco $(ls -1 fastq | tr '\n' ' ') --outdir falco_out

(3) does the program behave as expected if you switch the order of the arguments and put the filenames at the end? (that's how the program should be run) i.e.

falco --outdir falco_out fastq/*

Either way I'll try to reproduce as soon as I have access to my computer again.

Thank you!

[guilhermesena1]

I pushed a fixed at the most recent commit ( a97182e ). Unfortunately this fix is only available for now by cloning and compiling the repo. I'll leave this open until we create a new release and conda update to fix this problem. Thanks for reporting again!

[kevin-wamae]

Thanks @guilhermesena1 and sorry for the late response.

I cloned the directory, run make all and got this error:

I'm using Ubuntu Version="20.04.5 LTS"

make[1]: Entering directory '/home/kwamae/software/falco/src'
g++ -Wall -std=c++11 -O3 -c -o FalcoConfig.o FalcoConfig.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o FastqStats.o FastqStats.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o HtmlMaker.o HtmlMaker.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o Module.o Module.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o OptionParser.o OptionParser.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o smithlab_utils.o smithlab_utils.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
g++ -Wall -std=c++11 -O3 -c -o StreamReader.o StreamReader.cpp -DPROGRAM_PATH="/home/kwamae/software/falco"
In file included from StreamReader.cpp:16:
StreamReader.hpp:23:10: fatal error: zlib.h: No such file or directory
23 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make[1]: *** [Makefile:43: StreamReader.o] Error 1
make[1]: Leaving directory '/home/kwamae/software/falco/src'
make: *** [Makefile:20: all] Error 2

[andrewdavidsmith]

Quick look suggests you're missing zlib. See the README.md file for installation instructions of dependencies. Should be straightforward but let us know.

[kevin-wamae]

Thanks, @andrewdavidsmith. 🤦‍♂️

@guilhermesena1, thanks for the fix. It works fine now.