Assembling single end reads in abyss

Dr. Gaurav Sablok

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Mar 5, 2012, 3:11:06 PM3/5/12

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Hi All,

I am assembling my single end read using the ABYSS. I have sequenced using illumina single end sequencing. I was assebling and I got this error. Any suggestion on how to resolve this error. As Shaun suggested earlier in a post that how to assemble the single end reads using paired end feature so i used the same.
---------------------------------------------------------------------------------------------
root@calculus:~/gaurav$ abyss-pe name=217 k=28 n=10 in=217.fastq assembly-3.fa
ABYSS -k28 -q3 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa 217.fastq
ABySS 1.3.2
ABYSS -k28 -q3 --coverage-hist=coverage.hist -s assembly-bubbles.fa -o assembly-1.fa 217.fastq
Reading `217.fastq'...
217.fastq:86206077: error: expected `+' and saw end-of-file
make: *** [assembly-1.fa] Error 1
------------------------------------------------------------------------------------------------

Thanks
Gaurav

Ka Ming Nip

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Mar 6, 2012, 12:36:41 PM3/6/12

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Hi Gaurav,

Can you report what is the last 8 lines of your FASTQ file?
tail -n 8 217.fastq

It's possible that your FASTQ file is truncated.

Ka Ming

Dr. Gaurav Sablok

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Mar 6, 2012, 12:41:02 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

Hi Ming,

Hes is the last lines
-------------------------------
root@calculus:~/gaurav/assembly/217$ tail -n 8 217.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
-----------------------------------------------
Thanks,
Gaurav

Ka Ming Nip

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Mar 6, 2012, 12:42:11 PM3/6/12

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Never mind about my last message, I saw your same message on another thread...

Dr. Gaurav Sablok

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Mar 6, 2012, 12:45:18 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

Hi Ming,

I am getting this problem again. How to solve this problem.

Best regards,
Gaurav

Ka Ming Nip

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Mar 6, 2012, 1:06:17 PM3/6/12

to abyss...@googlegroups.com, Ka Ming Nip, tray...@bcgsc.ca

Hi Gaurav,

Can you tell me how many lines are there in 217.fastq?
wc -l 217.fastq

Ka Ming

Dr. Gaurav Sablok

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Mar 6, 2012, 1:10:05 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

Hi Ming,
--------------------
root@calculus:~/gaurav/assembly/217$ wc -l 217.fastq
86206076 217.fastq
-----------------
Thanks,
Gaurav

Ka Ming Nip

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Mar 6, 2012, 1:16:45 PM3/6/12

to abyss...@googlegroups.com, Ka Ming Nip, tray...@bcgsc.ca

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

Dr. Gaurav Sablok

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Mar 6, 2012, 1:24:14 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

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

Ka Ming Nip

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Mar 6, 2012, 1:32:19 PM3/6/12

to abyss...@googlegroups.com, Ka Ming Nip, tray...@bcgsc.ca

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

Dr. Gaurav Sablok

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Mar 6, 2012, 2:00:05 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

Hi Ming,

I got this:
-----------------------------
root@calculus:~/gaurav/assembly/217$ tail -n 8 217removed.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
-------------------------

Thanks,
Gaurav

Ka Ming Nip

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Mar 6, 2012, 2:33:17 PM3/6/12

to abyss...@googlegroups.com, Ka Ming Nip, tray...@bcgsc.ca

Hi Gaurav,

Can you run this command?
tail -n 8 217.fastq | cat -e

If there are space characters in the last line, the dollar sign character '$' would be shifted like so:

@HWI-ST261:3:42:1600:139196#TGACCA/1$

AGAAGATCACGTCTGCTGAGGCTCGCAAGCTCAAGAAGGAGCGCATGGCACGGAAAAAGCGAGGCGGGGAGGAAACCGACGATGACGTGGAAAGAACACC$
+$
N^c^cddbf^ceccgcgcfafggdgdfWWfedeed_ccc\c^bccNcccbS]a\aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB$

$

If that is the case, then try this:
sed '/^ *$/d' 217.fastq > 217removed2.fastq
tail -n 8 217removed2.fastq

Ka Ming

Dr. Gaurav Sablok

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Mar 6, 2012, 2:38:41 PM3/6/12

to Ka Ming Nip, abyss...@googlegroups.com, tray...@bcgsc.ca

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

Tony Raymond

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Mar 6, 2012, 2:46:11 PM3/6/12

to Dr. Gaurav Sablok, Ka Ming Nip, abyss...@googlegroups.com

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]
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

Dr. Gaurav Sablok

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Mar 6, 2012, 3:02:15 PM3/6/12

to Tony Raymond, Ka Ming Nip, abyss...@googlegroups.com

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

Tony Raymond

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Mar 6, 2012, 3:07:26 PM3/6/12

to Dr. Gaurav Sablok, Ka Ming Nip, abyss...@googlegroups.com

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]

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

Dr. Gaurav Sablok

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Mar 6, 2012, 3:52:39 PM3/6/12

to Tony Raymond, Ka Ming Nip, abyss...@googlegroups.com

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

Tony Raymond

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Mar 6, 2012, 3:56:23 PM3/6/12

to Dr. Gaurav Sablok, Ka Ming Nip, abyss...@googlegroups.com

`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 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

esteban429

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Jun 18, 2014, 6:33:13 PM6/18/14

to abyss...@googlegroups.com, sab...@gmail.com, km...@bcgsc.ca

Hi all,

I am currently attempting Abyss for the first time and am experiencing the same problem. I have two .fastq files (one for forward short read data and one for revere), and gave the command [abyss-pe k=21 n=10 in='PJX022.removed.fastq PJX022.2point5Percent.R2.fastq' name=2.5percnt.k21c], without the [] of course, and repeatedly get the error message that states: [PJX022.removed.fastq:4902297: error: expected `+' and saw end-of-file]. I tried truncating the fast files, as per your suggestions, but I still get the error code. I would like to note that these fastq files did work for Velvet and Soap deNovo. Any help would be greatly appreciated.

Stephen

On Tuesday, March 6, 2012 3:56:23 PM UTC-5, tray...@bcgsc.ca wrote:

`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 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: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

Ka Ming Nip

unread,

Jun 18, 2014, 7:00:13 PM6/18/14

to esteban429, abyss...@googlegroups.com, sab...@gmail.com

Hi Stephen,

Thanks for using ABySS.

You would see this error when the last read of the FASTQ file is incomplete.
Can you please run the following commands report the results?

tail -n8 PJX022.removed.fastq PJX022.2point5Percent.R2.fastq
wc -l PJX022.removed.fastq PJX022.2point5Percent.R2.fastq

The number of lines of the FASTQ files should be a multiple of 4 and the last 4 lines should be in this format:

@example
ATCGATCG
+
BBCCDDEE

It is likely that your FASTQ files were truncated, which could happen when the FASTQ generation process was interrupted.

Thanks,
Ka Ming
________________________________________
From: esteban429 [esteb...@gmail.com]
Sent: June 18, 2014 3:33 PM
To: abyss...@googlegroups.com
Cc: sab...@gmail.com; Ka Ming Nip

Subject: Re: Assembling single end reads in abyss

Hi all,
I am currently attempting Abyss for the first time and am experiencing the same problem. I have two .fastq files (one for forward short read data and one for revere), and gave the command [abyss-pe k=21 n=10 in='PJX022.removed.fastq PJX022.2point5Percent.R2.fastq' name=2.5percnt.k21c], without the [] of course, and repeatedly get the error message that states: [PJX022.removed.fastq:4902297: error: expected `+' and saw end-of-file]. I tried truncating the fast files, as per your suggestions, but I still get the error code. I would like to note that these fastq files did work for Velvet and Soap deNovo. Any help would be greatly appreciated.

Stephen

On Tuesday, March 6, 2012 3:56:23 PM UTC-5, tray...@bcgsc.ca wrote:
`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<javascript:>]

Sent: Tuesday, March 06, 2012 12:52 PM
To: Tony Raymond

Cc: Ka Ming Nip; abyss...@googlegroups.com<javascript:>

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<javascript:><mailto:tray...@bcgsc.ca<javascript:>>> 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<javascript:><mailto:sab...@gmail.com<javascript:>>]

Sent: Tuesday, March 06, 2012 12:02 PM
To: Tony Raymond

Cc: Ka Ming Nip; abyss...@googlegroups.com<javascript:><mailto:abyss...@googlegroups.com<javascript:>>

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<javascript:><mailto:tray...@bcgsc.ca<javascript:>><mailto:tray...@bcgsc.ca<javascript:><mailto:tray...@bcgsc.ca<javascript:>>>> 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<javascript:><mailto:sab...@gmail.com<javascript:>><mailto:sab...@gmail.com<javascript:><mailto:sab...@gmail.com<javascript:>>>]

Sent: Tuesday, March 06, 2012 11:38 AM
To: Ka Ming Nip

Cc: abyss...@googlegroups.com<javascript:><mailto:abyss...@googlegroups.com<javascript:>><mailto:abyss...@googlegroups.com<javascript:><mailto:abyss...@googlegroups.com<javascript:>>>; 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<javascript:><mailto:km...@bcgsc.ca<javascript:>><mailto:km...@bcgsc.ca<javascript:><mailto:km...@bcgsc.ca<javascript:>>><mailto:km...@bcgsc.ca<javascript:><mailto:km...@bcgsc.ca<javascript:>><mailto:km...@bcgsc.ca<javascript:><mailto:km...@bcgsc.ca<javascript:>>>>> 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

Elena Bushmanova

unread,

Jun 2, 2017, 1:58:15 PM6/2/17

to ABySS, esteb...@gmail.com, sab...@gmail.com

"sed '$d' reads.fq > reads.removed.fq" helps me!

четверг, 19 июня 2014 г., 2:00:13 UTC+3 пользователь Ka Ming Nip написал:

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