Bowtie2/Fastq-dump problem

Question

[rafailadam46]

I have been working with sequencing data for some months now on my external hard drive , on MacBook air m1 2020 and things have been running smoothly for the past 4 months . However ever since last month i kept getting an error either when trying to align with bowtie 2 in the external hard drive or when trying to convert sam files to bam in the external hard drive (incomplete aux field or expecting different kinds of characters). The drive itself is fine since other files can be properly read/written and the files are processed properly in the internal hard drive, meaning they are not corrupted. I need help resolving this issue so that i can continue my work since I don't have enough space in my internal hard drive.

[ATpoint]

Impossible to comment without code and error messages.

[Darked89]

on the command line:

• check that you got the space on the drives: df -h

• verify that at least at the gzip level your input fastq are decompressing OK: zcat some_r1_or_r2.fastq.gz > /dev/null

• check that files you expect to be compressed or not-compressed are what you think they are: file some.gz and file foobar.sam

[ATpoint]

Use gzip -cd as zcat (on macOS for example) behaves differently.

[rafailadam46]

Hello and thanks for the reply, my fastq files arent compressed and the alignment command looks like this : "bowtie2 -p 6 --local --reorder -x {genome_index_path} -U {fin} -S {outsam}" where fin is the input fastq file and outsam the output sam file. It is worth noting that while --reorder is set which was said to not function well with multithreading in some versions of bowtie2, the same problem occurs without it or by setting -p 1 as well, while this command works perfectly in my internal hard drive for the same files that i tried analysing on the external hard drive. I apologise for the formatting of my question as i am relatively new to programming and forums such as this. ps: The error i am talking about is an invalid line where either aux field is missing and so the sam to bam conversion fails or the alignment itself fails due to invalid characters on the fastq file. Also there is more than enough space on both drives.

[bk11]

Where did you get your fastq file from? Is it from SRA? Probably your file is corrupted. You could do quality control (fastQC) it before running bowtie2 on it.

fastqc file.fastq.gz

If fastqc runs fine, most probably your fastq files are ok and there could be something off with your parameter or system.

[rafailadam46]

I am converting sra files to fastq , yes. However there should be nothing wrong with the files since this also happens to files i have already processed and gotten results from before. When i try to redo the pipeline with them in the external hard drive instead of the laptop's internal hard drive the alignment/ sam to bam conversion step won't work regardless of the quality of the input file .