“nohup cat” — write the complete content to the log file rather to concatenate file
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I used the below command
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz > merge_R1.out.log 2>&1 &
but unfortunately, the output went to merge_R1.out.log
and not to merge_R1.fq.gz
.
What did I miss?
bash io-redirection cat nohup
|
show 1 more comment
I used the below command
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz > merge_R1.out.log 2>&1 &
but unfortunately, the output went to merge_R1.out.log
and not to merge_R1.fq.gz
.
What did I miss?
bash io-redirection cat nohup
What do you expect fromcat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress
– Romeo Ninov
Mar 15 at 11:21
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
showsa
.
– Weijun Zhou
Mar 15 at 12:50
@WeijunZhou Yes, because two concatenatedtar
archives don't make much sense. Trycat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same ascat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00
|
show 1 more comment
I used the below command
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz > merge_R1.out.log 2>&1 &
but unfortunately, the output went to merge_R1.out.log
and not to merge_R1.fq.gz
.
What did I miss?
bash io-redirection cat nohup
I used the below command
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz > merge_R1.out.log 2>&1 &
but unfortunately, the output went to merge_R1.out.log
and not to merge_R1.fq.gz
.
What did I miss?
bash io-redirection cat nohup
bash io-redirection cat nohup
edited Mar 15 at 12:17
Kusalananda♦
141k18263439
141k18263439
asked Mar 15 at 10:39
user977828user977828
3491617
3491617
What do you expect fromcat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress
– Romeo Ninov
Mar 15 at 11:21
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
showsa
.
– Weijun Zhou
Mar 15 at 12:50
@WeijunZhou Yes, because two concatenatedtar
archives don't make much sense. Trycat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same ascat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00
|
show 1 more comment
What do you expect fromcat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress
– Romeo Ninov
Mar 15 at 11:21
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
showsa
.
– Weijun Zhou
Mar 15 at 12:50
@WeijunZhou Yes, because two concatenatedtar
archives don't make much sense. Trycat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same ascat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00
What do you expect from
cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress– Romeo Ninov
Mar 15 at 11:21
What do you expect from
cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress– Romeo Ninov
Mar 15 at 11:21
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
shows a
.– Weijun Zhou
Mar 15 at 12:50
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
shows a
.– Weijun Zhou
Mar 15 at 12:50
@WeijunZhou Yes, because two concatenated
tar
archives don't make much sense. Try cat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same as cat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou Yes, because two concatenated
tar
archives don't make much sense. Try cat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same as cat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00
|
show 1 more comment
1 Answer
1
active
oldest
votes
Redirections are processed in a left-to-right fashion.
When executing a command like
somecommand >f1 >f2 >f3
the shell will first create or truncate (empty) the file f1
, then f2
and lastly f3
. Then it starts somecommand
with its standard output connected to f3
.
To save the output of a command to multiple files, you would have to duplicate the data for each output file. This is easiest done with tee
:
somecommand | tee f1 f2 >f3
This sends the output of somecommand
to tee
which duplicates it into the two files f1
and f2
. The tee
utility also produces the same data on its own standard output, and in the command above we simply redirect this into f3
.
In your case, you would use
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz 2>&1 |
tee fastp-filtered-merged4racon/merge_R1.fq.gz >merge_R1.out.log &
The 2>&1
makes the error stream from cat
be sent to tee
as well (this may not be wanted as any errors would corrupt the resulting archive).
tee
truncates its output files, just like >
would do. Use tee
with its -a
option to append data to an output file.
It's unlikely that you actually meant for all output from cat
to be written to two files though, so assuming that you want to save the errors to the log file and the concatenated archives to the output file, you would instead do
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz
>fastp-filtered-merged4racon/merge_R1.fq.gz
2>merge_R1.out.log &
without the need for using tee
at all.
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
Redirections are processed in a left-to-right fashion.
When executing a command like
somecommand >f1 >f2 >f3
the shell will first create or truncate (empty) the file f1
, then f2
and lastly f3
. Then it starts somecommand
with its standard output connected to f3
.
To save the output of a command to multiple files, you would have to duplicate the data for each output file. This is easiest done with tee
:
somecommand | tee f1 f2 >f3
This sends the output of somecommand
to tee
which duplicates it into the two files f1
and f2
. The tee
utility also produces the same data on its own standard output, and in the command above we simply redirect this into f3
.
In your case, you would use
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz 2>&1 |
tee fastp-filtered-merged4racon/merge_R1.fq.gz >merge_R1.out.log &
The 2>&1
makes the error stream from cat
be sent to tee
as well (this may not be wanted as any errors would corrupt the resulting archive).
tee
truncates its output files, just like >
would do. Use tee
with its -a
option to append data to an output file.
It's unlikely that you actually meant for all output from cat
to be written to two files though, so assuming that you want to save the errors to the log file and the concatenated archives to the output file, you would instead do
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz
>fastp-filtered-merged4racon/merge_R1.fq.gz
2>merge_R1.out.log &
without the need for using tee
at all.
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
add a comment |
Redirections are processed in a left-to-right fashion.
When executing a command like
somecommand >f1 >f2 >f3
the shell will first create or truncate (empty) the file f1
, then f2
and lastly f3
. Then it starts somecommand
with its standard output connected to f3
.
To save the output of a command to multiple files, you would have to duplicate the data for each output file. This is easiest done with tee
:
somecommand | tee f1 f2 >f3
This sends the output of somecommand
to tee
which duplicates it into the two files f1
and f2
. The tee
utility also produces the same data on its own standard output, and in the command above we simply redirect this into f3
.
In your case, you would use
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz 2>&1 |
tee fastp-filtered-merged4racon/merge_R1.fq.gz >merge_R1.out.log &
The 2>&1
makes the error stream from cat
be sent to tee
as well (this may not be wanted as any errors would corrupt the resulting archive).
tee
truncates its output files, just like >
would do. Use tee
with its -a
option to append data to an output file.
It's unlikely that you actually meant for all output from cat
to be written to two files though, so assuming that you want to save the errors to the log file and the concatenated archives to the output file, you would instead do
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz
>fastp-filtered-merged4racon/merge_R1.fq.gz
2>merge_R1.out.log &
without the need for using tee
at all.
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
add a comment |
Redirections are processed in a left-to-right fashion.
When executing a command like
somecommand >f1 >f2 >f3
the shell will first create or truncate (empty) the file f1
, then f2
and lastly f3
. Then it starts somecommand
with its standard output connected to f3
.
To save the output of a command to multiple files, you would have to duplicate the data for each output file. This is easiest done with tee
:
somecommand | tee f1 f2 >f3
This sends the output of somecommand
to tee
which duplicates it into the two files f1
and f2
. The tee
utility also produces the same data on its own standard output, and in the command above we simply redirect this into f3
.
In your case, you would use
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz 2>&1 |
tee fastp-filtered-merged4racon/merge_R1.fq.gz >merge_R1.out.log &
The 2>&1
makes the error stream from cat
be sent to tee
as well (this may not be wanted as any errors would corrupt the resulting archive).
tee
truncates its output files, just like >
would do. Use tee
with its -a
option to append data to an output file.
It's unlikely that you actually meant for all output from cat
to be written to two files though, so assuming that you want to save the errors to the log file and the concatenated archives to the output file, you would instead do
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz
>fastp-filtered-merged4racon/merge_R1.fq.gz
2>merge_R1.out.log &
without the need for using tee
at all.
Redirections are processed in a left-to-right fashion.
When executing a command like
somecommand >f1 >f2 >f3
the shell will first create or truncate (empty) the file f1
, then f2
and lastly f3
. Then it starts somecommand
with its standard output connected to f3
.
To save the output of a command to multiple files, you would have to duplicate the data for each output file. This is easiest done with tee
:
somecommand | tee f1 f2 >f3
This sends the output of somecommand
to tee
which duplicates it into the two files f1
and f2
. The tee
utility also produces the same data on its own standard output, and in the command above we simply redirect this into f3
.
In your case, you would use
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz 2>&1 |
tee fastp-filtered-merged4racon/merge_R1.fq.gz >merge_R1.out.log &
The 2>&1
makes the error stream from cat
be sent to tee
as well (this may not be wanted as any errors would corrupt the resulting archive).
tee
truncates its output files, just like >
would do. Use tee
with its -a
option to append data to an output file.
It's unlikely that you actually meant for all output from cat
to be written to two files though, so assuming that you want to save the errors to the log file and the concatenated archives to the output file, you would instead do
nohup cat fastp-filtered/OZBenth*_R1.fastp.fq.gz
>fastp-filtered-merged4racon/merge_R1.fq.gz
2>merge_R1.out.log &
without the need for using tee
at all.
edited Mar 15 at 12:40
answered Mar 15 at 12:33
Kusalananda♦Kusalananda
141k18263439
141k18263439
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
add a comment |
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
Conceptually correct, but I don't think this is what the OP is asking for.
– Weijun Zhou
Mar 15 at 12:37
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
@WeijunZhou I just realized this. It's unclear what they want to write into the log file.
– Kusalananda♦
Mar 15 at 12:38
add a comment |
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What do you expect from
cat fastp-filtered/OZBenth*_R1.fastp.fq.gz > fastp-filtered-merged4racon/merge_R1.fq.gz
This will be mess from compressed files and with high probability will not be able to decompress– Romeo Ninov
Mar 15 at 11:21
@RomeoNinov No it wouldn't. The concatenated file, when uncompressed, would be concatenation of the uncompressed files. This is likely what is intended and it will work.
– Kusalananda♦
Mar 15 at 12:43
cat <(tar zcf - a) <(tar zcf - b) | tar -ztf -
showsa
.– Weijun Zhou
Mar 15 at 12:50
@WeijunZhou Yes, because two concatenated
tar
archives don't make much sense. Trycat <( gzip -cf <<<"HELLO" ) <( gzip -cf <<<"WORLD" ) | gzip -dc
instead. The result would be the same ascat <( echo HELLO ) <( echo WORLD )
– Kusalananda♦
Mar 15 at 12:58
@WeijunZhou What the user is dealing with here is a collection compressed text files containing genomic "fastq" sequence data. They are merging the compressed files together and will later used the merged file for something. There will be no issues with this.
– Kusalananda♦
Mar 15 at 13:00