About Picard

Jin Pan · 12-01-2011, 07:40 AM

When I run the software, it returns an error.
you can see it in the attachment, please give me some suggestion.
thank you very much.

spapillon · 12-01-2011, 10:56 AM

As the error states, "Sequence must start with @: >@ ..." Meaning that Picard is trying to read the sequence and is failing. It calls the method FastqToSam but the file you gave it is in fasta format. You need to convert it beforehand (remove the '>' at the beginning of lines)

Jin Pan · 12-01-2011, 05:56 PM

I open and detect my data file, But i don't find ">".
This is a sequence in my data file.
@HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0:
TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA
+
FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

Jin Pan · 12-01-2011, 06:03 PM

I open and detect my data file, But i don't find ">".
This is a sequence in my data file.
@HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0:
TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA
+
FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

Jin Pan · 12-01-2011, 06:04 PM

I opened and detected my data file, But i didn't find ">".
This is a sequence in my data file.
@HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0:
TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA
+
FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

skycreative · 12-01-2011, 06:21 PM

would you try plat text file , not the gz file?

Jin Pan · 12-01-2011, 06:27 PM

It's OK. Thanks a lot.

Jin Pan · 12-01-2011, 07:01 PM

If I run Estimatelibrarycomplexity.jar, it seems that the data format is wrong again.

ERROR: Error parsing SAM header. Unrecognized header record type. Line: @HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0:

Lv Ray · 07-15-2014, 05:55 AM

how do you solved your hard problem?

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12-01-2011, 10:56 AM	#2
spapillon Junior Member Location: Montreal, Canada Join Date: Nov 2011 Posts: 4	As the error states, "Sequence must start with @: >@ ..." Meaning that Picard is trying to read the sequence and is failing. It calls the method FastqToSam but the file you gave it is in fasta format. You need to convert it beforehand (remove the '>' at the beginning of lines)

12-01-2011, 05:56 PM	#3
Jin Pan Junior Member Location: China Join Date: Dec 2011 Posts: 7	I open and detect my data file, But i don't find ">". This is a sequence in my data file. @HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0: TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA + FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

12-01-2011, 06:03 PM	#4
Jin Pan Junior Member Location: China Join Date: Dec 2011 Posts: 7	I open and detect my data file, But i don't find ">". This is a sequence in my data file. @HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0: TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA + FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

12-01-2011, 06:04 PM	#5
Jin Pan Junior Member Location: China Join Date: Dec 2011 Posts: 7	I opened and detected my data file, But i didn't find ">". This is a sequence in my data file. @HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0: TGCAGAACAAGGTTTTTGCCTCATTTTGAAAGGAGAAAATCAATTTAAGTTGCTGCTTCAATGCCAGATCAAGGGTCTCCAAAGAGCACAGCAGA + FFFHHHHHJJJJIIJJJIJJJJIJJJJJHIIJJJJFGIJJJGIJJJJIJGIJJJIJJJGGIEEHJEGIGFEHDFFEFEEEEDECDDDDDDDDDD<

12-01-2011, 06:21 PM	#6
skycreative Member Location: GuangXi China Join Date: Jan 2010 Posts: 27	would you try plat text file , not the gz file?

12-01-2011, 06:27 PM	#7
Jin Pan Junior Member Location: China Join Date: Dec 2011 Posts: 7	It's OK. Thanks a lot.

12-01-2011, 07:01 PM	#8
Jin Pan Junior Member Location: China Join Date: Dec 2011 Posts: 7	If I run Estimatelibrarycomplexity.jar, it seems that the data format is wrong again. ERROR: Error parsing SAM header. Unrecognized header record type. Line: @HWI-ST298:282:C05BGACXX:4:1101:6099:2249 1:N:0:

07-15-2014, 05:55 AM	#9
Lv Ray Member Location: GZ,China Join Date: Jun 2014 Posts: 42	how do you solved your hard problem?