Can't push to github

[cskalley]

I'm trying to push to github but I keep getting an error that some files exceed the size limit. I used git reset --mixed HEAD~1 and updated my gitignore with large files listed but I keep getting errors at every push/pull step. My branch is ahead of origin/main by 5 commits which I have tried to resolve by pulling and committing, but nothing seems to work. Something is going on here and I have't been able to figure out. Any ideas?

[sr320]

Run

git reset --mixed HEAD~1

A few more times until you reset commit with large files

This command does one commit at a time

On Fri, May 19, 2023 at 8:07 AM Courtney Skalley @.***> wrote:

I'm trying to push to github but I keep getting an error that some files exceed the size limit. I used git reset --mixed HEAD~1 and updated my gitignore with large files listed but I keep getting errors at every push/pull step. My branch is ahead of origin/main by 5 commits which I have tried to resolve by pulling and committing, but nothing seems to work. Something is going on here and I have't been able to figure out. Any ideas?

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[cskalley]

Ah okay, thanks. Now that that is resolved, I get "permission denied" when I try to unzip this fastq.gz file: /home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz

You can find it here starting on line 47.

[sr320]

No need to unzip the file

On Fri, May 19, 2023 at 8:20 AM Courtney Skalley @.***> wrote:

Ah okay, thanks. Now that that is resolved, I get "permission denied" when I try to unzip this fastq.gz file: /home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz

You can find it here https://urldefense.com/v3/__https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/6eea0a2f5433c82f83472e524ad43c81b61b429a/code/02-blast.Rmd__;!!K-Hz7m0Vt54!jdfPfzZOZlKfWKc8C2xNekue7Oan8TApj-q2wSDXEYJ8ugL4fN1RAmjVkdGMlxZBv7KWDvpwrQeEvNBdxyyc5CI$ starting on line 47.

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[cskalley]

But when I run the chunk starting on line 53, head doesn't seem to work. When I run blast (the next chunk on line 71), there's a warning message saying "Near line 1, there's a line that doesn't look like plausible data." The uniprot_blastx table appears in output as it should, but as an empty file. Do I need to change the sequence in some way?

[sr320]

You do not blast fastq files - explain what you are trying to do and why

On Fri, May 19, 2023 at 8:31 AM Courtney Skalley @.***> wrote:

But when I run the chunk starting on line 53, head doesn't seem to work. When I run blast (the next chunk on line 71), there's a warning message saying "Near line 1, there's a line that doesn't look like plausible data." The uniprot_blastx table appears in output as it should, but as an empty file. Do I need to change the sequence in some way?

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[cskalley]

I'm trying to blast one of the crab sequences but they are in fastq format. I didn't realize that blast required fasta, so now I need to figure out how to convert fastq to fasta. I tried running this code gunzip -c /home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > 5010_10_S10_L003_R1_001.fasta but it didn't make a fasta file.

I also tried this input_file="/home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz" output_file="/home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fasta" zcat "$input_file" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$output_file" but I got another permission denied message.

[sr320]

There no reason to blast seq reads (fastq) - and you cannot do it. Big picture- what are you trying to do?

On Fri, May 19, 2023 at 9:25 AM Courtney Skalley @.***> wrote:

I'm trying to blast one of the crab sequences but they are in fastq format. I didn't realize that blast required fasta, so now I need to figure out how to convert fastq to fasta. I tried running this code gunzip -c /home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}'

5010_10_S10_L003_R1_001.fasta but it didn't make a fasta file.

I also tried this input_file="/home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fastq.gz" output_file="/home/shared/8TB_HDD_01/snow_crab/5010/5010_10_S10_L003_R1_001.fasta" zcat "$input_file" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$output_file" but I got another permission denied message.

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[cskalley]

I'm trying to annotate the snow crab sequences. When we did the assignment in week 2, our query was b_4denovo_CLC6_a.fa, which I thought was a type of fasta file. That's why I'm trying to convert the fastq files into fasta.

[sr320]

You mean the snow crab fasta files I got you and posted in issue?

On Fri, May 19, 2023 at 9:37 AM Courtney Skalley @.***> wrote:

I'm trying to annotate the snow crab sequences. When we did the assignment in week 2, our query was b_4denovo_CLC6_a.fa, which I thought was a type of fasta file. That's why I'm trying to convert the fastq files into fasta.

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[cskalley]

No, I was trying to annotate the sequences that Laura gave me. I assumed that I could use those in blast if I got them in a fasta format, but I guess that wouldn't work because they haven't been aligned yet. I have a lot of questions about this whole process that would probably be best to go over during office hours.

Big picture: annotate a snow crab transcriptome so that I know what genes are being over/under expressed.

I also tried running blast (line 77) using the transcriptome you provided and am getting a new error. Feel free to take a look or we can go over it on Tuesday in office hours.

[sr320]

Only thing to do with reads Laura provide is align (kallisto) to reference sequence (fasta). And you annotate transcriptome. Note line 77 (https://github.com/course-fish546-2023/courtney_RNAseq_crabs/blob/6eea0a2f5433c82f83472e524ad43c81b61b429a/code/02-blast.Rmd#L77) does not appear to be blast