Luigi Faino comments

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Luigi Faino

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

Hi @cgjosephlee , in the past few days I made few changes and few (about 50) new images. I see that that the image that you are using is a...

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

is this the output after that you re-downloaded the image?

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

I saw an old error (on my side) in your images: the image is not anymore docker://lfaino/lorean:noiIPRS but docker://lfaino/lorean:noIPRS. if you notice, there is not anymore the i before IPRS....

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

The easiest way is to provide a file with the adapter sequence. Are you using PacBio or Nanopore data?

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

do you mind to share your test data? I will test and see if i can find the error and fix it

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

@cgjosephlee ok. do you have /data/LoReAn_Example/Crispa/LoReAn_annotation/run/Trinity/trinity_out_dir/Trinity-GG.fasta file? is it empty or full? can you tell me about the system that you are using (amount of Memory and CPU)?

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

@zcrself; do you mind to share your test data? I will test and see if i can find the error and fix it

raise ValueError("No lines parsed -- was an empty file provided?") ValueError: No lines parsed -- was an empty file provided?

@cgjosephlee: Dir_STAR_shortreadsAligned.out.bam.sorted.bam.minC1.gff/seq1/4/nity.reads.out.Trinity.fasta; this is strange... the file is truncated (4/nity.reads.out.Trinity.fasta).... no idea why

Unable to pull docker image lfaino/lorean:latest. Image is far too big

Dear @eburgueno, why do you need to build the image? the image is already build. This image was so big because in included interproscan and few databases that are required....

Unable to pull docker image lfaino/lorean:latest. Image is far too big

@eburgueno, I will be happy to try to fix this issues. please open a new issue and I will try to fix ASAP