Error running Diamond

¡Hi Dear !

I got this error (attached at the end), when I was running diamond
(diamond blastx --db /vault2/bioinfDBs/diamondDB/nr.dmnd --out reads_shotgun_filtradas.daa --outfmt 100 --query shotgun_concat.fastq.gz),

I have 72 files named “SAMPLE_host_removed_r1_TxPx_Tx.fastq” representing my 36 paired-samples,
I concatenated them in one file named “shotgun_concat.fastq.gz” using this command (cat *.fastq > shotgun_concat.fastq.gz)

According to the error, I understand that it was no possible to open the file. Also, I noticed that in another post

In this case, how I can procedure? Do I need to process every paired file individually (all 36) using daa2rma? Is there another way to join all files?
Please if you have any idea to solve this error, please, tell me.

Many thanks in advance.

This is the first part of the error

Error: Invalid parameter count for option ‘–out’
diamond v0.9.29.130 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 32
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database… [0.935993s]
#Target sequences to report alignments for: 25
Opening the input file… No such file or directory
[0.133652s]
Error: Error opening file /vault2/homehpc/voteroj/SEQ_SHOTG/shotgun_concat.fastq.gz
diamond v0.9.29.130 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 32
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database… [0.668361s]
#Target sequences to report alignments for: 25

According to the error, I understand that it was no possible to open the file.
In this case, how I can procedure? Do I need to process every paired file individually (all 36)? Is there another way to join all files?
Please if you have any idea to solve this error, please, tell me.
Many thanks in advance.

This is the first part of the error

Error: Invalid parameter count for option ‘–out’
diamond v0.9.29.130 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 32
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database… [0.935993s]
#Target sequences to report alignments for: 25
Opening the input file… No such file or directory
[0.133652s]
Error: Error opening file /vault2/homehpc/voteroj/SEQ_SHOTG/shotgun_concat.fastq.gz
diamond v0.9.29.130 | by Benjamin Buchfink buchfink@gmail.com
Licensed under the GNU GPL https://www.gnu.org/licenses/gpl.txt
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 32
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Opening the database… [0.668361s]
#Target sequences to report alignments for: 25I have 72 files named “SAMPLE_host_removed_r1_TxPx_Tx.fastq” representing my 36 paired-samples,
I joined all files in one file named “shotgun_concat.fastq.gz” using this command (cat *.fastq > shotgun_concat.fastq.gz)
Then, I got an error when I was running diamond (error attached at the end).
According to the error, I understand that it was no possible to open the file.
The command used was:
(diamond blastx --db /vault2/bioinfDBs/diamondDB/nr.dmnd --out reads_shotgun_filtradas.daa --outfmt 100 --query shotgun_concat.fastq.gz),

So I have some questions:

  1. I noticed that in a response of a past post from Ally nov’19, that it is not possible do an analysis using paired-reads,
    it means that my file was wrong? it was a big crazy?
  2. How I can procedure? Do I need to process every file individually (all 36) using daa2rma instead of diamond?

Thank you very much in advance.
Vanessa

This is incorrect:

cat *.fastq > shotgun_concat.fastq.gz

Should be either:

cat *.fastq > shotgun_concat.fastq

or

cat *.fastq | gzip > shotgun_concat.fastq.gz

¡Thank you very much Daniel!

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