The file is truncated. The last line is actually "@HWI-ST" without a new line character at the end of it so it is getting merged with "gauravs@calculus:~/gaurav/assembly/217$". You will need to regenerate the file.
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com]
Sent: Tuesday, March 06, 2012 11:38 AM
To: Ka Ming Nip
Cc: abyss...@googlegroups.com; Tony Raymond
Subject: Re: Assembling single end reads in abyss
Hi Ming,
I got this :
--------------------------------------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217.fastq | cat -e
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG$
+$
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-ST261:3:42:1600:139196#TGACCA/1$
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC$
+$
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------------------
Thanks,
Gaurav
Ka Ming
On Tue, Mar 6, 2012 at 6:32 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi Gaurav,
Yes, let's give that a shot. After that, please try `tail -n 8 217removed.fastq` and see if you are getting 8 lines now.
Ka Ming
On Tuesday, March 6, 2012 10:24:14 AM UTC-8, Gaurav wrote:
Hi Ming,
I removed the empty line using sed '/^$/d' 217.fastq > 217removed.fastq. Is it OK or I should use any other method.
Best,
Gaurav
Cheers,
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com]
Sent: Tuesday, March 06, 2012 12:02 PM
To: Tony Raymond
Cc: Ka Ming Nip; abyss...@googlegroups.com
Subject: Re: Assembling single end reads in abyss
Hi Tony,
I tried again
--------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217removed2.fastq
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG
+
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:3:42:1600:139196#TGACCA/1
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC
+
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 7:46 PM, Tony Raymond <tray...@bcgsc.ca<mailto:tray...@bcgsc.ca>> wrote:
Hi Gaurav,
The file is truncated. The last line is actually "@HWI-ST" without a new line character at the end of it so it is getting merged with "gauravs@calculus:~/gaurav/assembly/217$". You will need to regenerate the file.
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com<mailto:sab...@gmail.com>]
Sent: Tuesday, March 06, 2012 11:38 AM
To: Ka Ming Nip
Cc: abyss...@googlegroups.com<mailto:abyss...@googlegroups.com>; Tony Raymond
Subject: Re: Assembling single end reads in abyss
Hi Ming,
I got this :
--------------------------------------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217.fastq | cat -e
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG$
+$
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-ST261:3:42:1600:139196#TGACCA/1$
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC$
+$
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------------------
Thanks,
Gaurav
Ka Ming
On Tue, Mar 6, 2012 at 6:32 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>> wrote:
Hi Gaurav,
Yes, let's give that a shot. After that, please try `tail -n 8 217removed.fastq` and see if you are getting 8 lines now.
Ka Ming
On Tuesday, March 6, 2012 10:24:14 AM UTC-8, Gaurav wrote:
Hi Ming,
I removed the empty line using sed '/^$/d' 217.fastq > 217removed.fastq. Is it OK or I should use any other method.
Best,
Gaurav
On Tue, Mar 6, 2012 at 6:16 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>> wrote:
Ok, I get it now.
1. Your error message was:
Reading `217.fastq'...
217.fastq:86206077: error: expected `+' and saw end-of-file
2. The tail -n 8 command returned 7 non-empty lines instead 8 lines.
3. wc -l return 86206076 lines
Please remove the extra empty line at the end of the FASTQ file.
Ka Ming
On Tuesday, March 6, 2012 10:10:05 AM UTC-8, Gaurav wrote:
Hi Ming,
--------------------
root@calculus:~/gaurav/assembly/217$ wc -l 217.fastq
86206076 217.fastq
-----------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 6:06 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi Gaurav,
Can you tell me how many lines are there in 217.fastq?
wc -l 217.fastq
Ka Ming
On Tuesday, March 6, 2012 9:45:18 AM UTC-8, Gaurav wrote:
Hi Ming,
I am getting this problem again. How to solve this problem.
Best regards,
Gaurav
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com]
Sent: Tuesday, March 06, 2012 12:52 PM
To: Tony Raymond
Cc: Ka Ming Nip; abyss...@googlegroups.com
Subject: Re: Assembling single end reads in abyss
So, how to regenerate the file without deleting any reads. Any suggestion?. I was thinking of deleting the empyt line using perl
perl -00 -pe ' ' 217.fastq or using awk.
What you suggest.
Best regards,
Gaurav
On Tue, Mar 6, 2012 at 9:07 PM, Tony Raymond <tray...@bcgsc.ca<mailto:tray...@bcgsc.ca>> wrote:
Ah, it appears that the last line of your file 217.fastq is truncated. That is the file which needs to be regenerated. You can also remove the last line and the assembly should work, but you will be missing any reads that should follow the last line of the 217.fastq file.
Cheers,
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com<mailto:sab...@gmail.com>]
Sent: Tuesday, March 06, 2012 12:02 PM
To: Tony Raymond
Cc: Ka Ming Nip; abyss...@googlegroups.com<mailto:abyss...@googlegroups.com>
Subject: Re: Assembling single end reads in abyss
Hi Tony,
I tried again
--------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217removed2.fastq
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG
+
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:3:42:1600:139196#TGACCA/1
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC
+
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 7:46 PM, Tony Raymond <tray...@bcgsc.ca<mailto:tray...@bcgsc.ca><mailto:tray...@bcgsc.ca<mailto:tray...@bcgsc.ca>>> wrote:
Hi Gaurav,
The file is truncated. The last line is actually "@HWI-ST" without a new line character at the end of it so it is getting merged with "gauravs@calculus:~/gaurav/assembly/217$". You will need to regenerate the file.
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com<mailto:sab...@gmail.com><mailto:sab...@gmail.com<mailto:sab...@gmail.com>>]
Sent: Tuesday, March 06, 2012 11:38 AM
To: Ka Ming Nip
Cc: abyss...@googlegroups.com<mailto:abyss...@googlegroups.com><mailto:abyss...@googlegroups.com<mailto:abyss...@googlegroups.com>>; Tony Raymond
Subject: Re: Assembling single end reads in abyss
Hi Ming,
I got this :
--------------------------------------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217.fastq | cat -e
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG$
+$
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-ST261:3:42:1600:139196#TGACCA/1$
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC$
+$
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------------------
Thanks,
Gaurav
Ka Ming
On Tue, Mar 6, 2012 at 6:32 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>>> wrote:
Hi Gaurav,
Yes, let's give that a shot. After that, please try `tail -n 8 217removed.fastq` and see if you are getting 8 lines now.
Ka Ming
On Tuesday, March 6, 2012 10:24:14 AM UTC-8, Gaurav wrote:
Hi Ming,
I removed the empty line using sed '/^$/d' 217.fastq > 217removed.fastq. Is it OK or I should use any other method.
Best,
Gaurav
On Tue, Mar 6, 2012 at 6:16 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>>> wrote:
Ok, I get it now.
1. Your error message was:
Reading `217.fastq'...
217.fastq:86206077: error: expected `+' and saw end-of-file
2. The tail -n 8 command returned 7 non-empty lines instead 8 lines.
3. wc -l return 86206076 lines
Please remove the extra empty line at the end of the FASTQ file.
Ka Ming
On Tuesday, March 6, 2012 10:10:05 AM UTC-8, Gaurav wrote:
Hi Ming,
--------------------
root@calculus:~/gaurav/assembly/217$ wc -l 217.fastq
86206076 217.fastq
-----------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 6:06 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>> wrote:
Hi Gaurav,
Can you tell me how many lines are there in 217.fastq?
wc -l 217.fastq
Ka Ming
On Tuesday, March 6, 2012 9:45:18 AM UTC-8, Gaurav wrote:
Hi Ming,
I am getting this problem again. How to solve this problem.
Best regards,
Gaurav
`head -n -1 217.fastq >217removed3.fastq` will remove the last line and let you continue with the assembly. How was the 217.fastq file generated in the first place?Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com]
Sent: Tuesday, March 06, 2012 12:52 PM
To: Tony Raymond
Cc: Ka Ming Nip; abyss...@googlegroups.com
Subject: Re: Assembling single end reads in abyssSo, how to regenerate the file without deleting any reads. Any suggestion?. I was thinking of deleting the empyt line using perl
perl -00 -pe ' ' 217.fastq or using awk.What you suggest.
Best regards,
Gaurav
On Tue, Mar 6, 2012 at 9:07 PM, Tony Raymond <tray...@bcgsc.ca<mailto:traymo...@bcgsc.ca>> wrote:
Ah, it appears that the last line of your file 217.fastq is truncated. That is the file which needs to be regenerated. You can also remove the last line and the assembly should work, but you will be missing any reads that should follow the last line of the 217.fastq file.
Cheers,
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com<mailto:sablo...@gmail.com>]
Sent: Tuesday, March 06, 2012 12:02 PM
To: Tony Raymond
Cc: Ka Ming Nip; abyss...@googlegroups.com<mailto:abyss...@googlegroups.com>
Subject: Re: Assembling single end reads in abyss
Hi Tony,
I tried again
--------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217removed2.fastq
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG
+
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-ST261:3:42:1600:139196#TGACCA/1
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC
+
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 7:46 PM, Tony Raymond <tray...@bcgsc.ca<mailto:traymo...@bcgsc.ca><mailto:traymond@bcgsc.ca<mailto:tray...@bcgsc.ca>>> wrote:
Hi Gaurav,The file is truncated. The last line is actually "@HWI-ST" without a new line character at the end of it so it is getting merged with "gauravs@calculus:~/gaurav/assembly/217$". You will need to regenerate the file.
Tony
________________________________________
From: Dr. Gaurav Sablok [sab...@gmail.com<mailto:sablo...@gmail.com><mailto:sab...@gmail.com<mailto:sab...@gmail.com>>]
Sent: Tuesday, March 06, 2012 11:38 AM
To: Ka Ming Nip
Cc: abyss...@googlegroups.com<mailto:abyss...@googlegroups.com><mailto:abyss-us...@googlegroups.com<mailto:abyss...@googlegroups.com>>; Tony Raymond
Subject: Re: Assembling single end reads in abyss
Hi Ming,
I got this :
--------------------------------------
gauravs@calculus:~/gaurav/assembly/217$ tail -n 8 217.fastq | cat -e
CATTGAAGCAGATGGTGCCGTAGTTGGTTGAGAAGGAAAGAGGGTGGACCTCGACACCGAGAGTAGCGATGTATTTTTTCTCGAATTCACCGTTCAACAG$
+$
ffeefccfeefcdefaefef^bcbdeccTaVWUY^bbaaaQ_a`GZXO`U_ZT_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-ST261:3:42:1600:139196#TGACCA/1$
AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC$
+$
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$
@HWI-STgauravs@calculus:~/gaurav/assembly/217$
------------------------------------
Thanks,
Gaurav
On Tue, Mar 6, 2012 at 6:32 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>><mailto:km...@bcgsc.ca<mailto:kmn...@bcgsc.ca><mailto:km...@bcgsc.ca<mailto:km...@bcgsc.ca>>>> wrote:
Hi Gaurav,Yes, let's give that a shot. After that, please try `tail -n 8 217removed.fastq` and see if you are getting 8 lines now.
Ka Ming
On Tuesday, March 6, 2012 10:24:14 AM UTC-8, Gaurav wrote:
Hi Ming,I removed the empty line using sed '/^$/d' 217.fastq > 217removed.fastq. Is it OK or I should use any other method.
Best,
Gaurav