Could you look at the reference you mapped against and make sure that each entry ends in something like ref0000000/1234? Also, can you look at your mapping.m4 file and ensure that the same ref\d{7}/\d+ structure is reported in the target column (col 2). PBJelly adds identifiers to your scaffold sequences during the setup step, and this error is saying that the scaffold id is not on the end of this target name.
--
Thanks,
~/Adam English
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I am not sure if this a formatting or functionality question.
I am testing on EColi test dataset. My short read assembly has only contigs and no scaffolds.
I have renamed the contigs to the mentioned format >EColi|ref0000000/1234. After running setup, the names in the fasta file were automatically changed to >EColi|ref0000000/582|ref0000001 and the contigs were reordered within the file.
All stages run without any errors. Ultimately the assembly stage just 'assembled' one particular contig. Am I using the right representation and is there a way to find adjacencies between distinct contigs and filling in the respective gaps?
Thanks,
Viraj
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The setup step performs two functions. 1) It identifies gaps in your reference. 2) It renames your reference with the ref ids you see for PBJelly's internal use.
This second function is why you see your reference being renamed. PBJelly doesn't care what the initial name is, it will add the ref-id tag.
But! Your real problem here is that PBJelly currently doesn't fill inter-scaffold gaps. I've been working on that version, and it's first pass is nearly completed. Until then, you're limited to captured gaps (i.e. within scaffolds).
--
Have a great day,
~/Adam Engish
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I have already checked the reference ids and the ids in .m4 file and they are exactly the same (the one re-name by setup stage). Why do these warnings appear, then? How can I solve it?
Thank you so much in advance,
Regards,
Cristina Osuna
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Dear all,
I have a problem running jelly support. i get this errors
2013-03-21 21:27:40,684 [INFO] Running /home/faino001/programs/PBJelly_12.9.14/SupportGaps.py /media/data1/V_TRIC/PBJelly/mapping/pacbio.fasta.m4 /media/data1/V_TRIC/a5_pipeline/test.final.scaffolds.gapInfo.bed /media/data1/V_TRIC/PBJelly/support/pacbio.fasta.gapCans
2013-03-21 21:27:40,710 [WARNING] Missed adapter in read! 12023371_9
2013-03-21 21:27:40,711 [WARNING] Missed adapter in read! 12057770_6
2013-03-21 21:27:40,711 [WARNING] Missed adapter in read! 12036692_2
2013-03-21 21:27:40,713 [WARNING] Missed adapter in read! 12065490_4
2013-03-21 21:27:40,713 [WARNING] Missed adapter in read! 12025689_2
2013-03-21 21:27:40,717 [WARNING] Missed adapter in read! 12049219_2
2013-03-21 21:27:40,717 [WARNING] Missed adapter in read! 12049219_2
2013-03-21 21:27:40,718 [WARNING] Missed adapter in read! 12061942_2
2013-03-21 21:27:40,718 [WARNING] Missed adapter in read! 12009410_6
2013-03-21 21:27:40,719 [WARNING] Missed adapter in read! 12026940_2
2013-03-21 21:27:40,724 [WARNING] Missed adapter in read! 12059316_2
Traceback (most recent call last):
File "/home/faino001/programs/PBJelly_12.9.14/SupportGaps.py", line 573, in <module>
runner.run()
File "/home/faino001/programs/PBJelly_12.9.14/SupportGaps.py", line 557, in run
self.options.spanOnly)
File "/home/faino001/programs/PBJelly_12.9.14/SupportGaps.py", line 422, in classifyReads
oscafName, scaffold, contig = refParser.match(read.tname).groups()
AttributeError: 'NoneType' object has no attribute 'groups'
these errors are not there when i test the lambda data.
thanks
Luigi
Hello Luigi,
Could you look at the reference you mapped against and make sure that each entry ends in something like ref0000000/1234? Also, can you look at your mapping.m4 file and ensure that the same ref\d{7}/\d+ structure is reported in the target column (col 2). PBJelly adds identifiers to your scaffold sequences during the setup step, and this error is saying that the scaffold id is not on the end of this target name.
--
Thanks,
~/Adam English
Dear PBJelly community,
I am not sure if this a formatting or functionality question.
I am testing on EColi test dataset. My short read assembly has only contigs and no scaffolds.
I have renamed the contigs to the mentioned format >EColi|ref0000000/1234. After running setup, the names in the fasta file were automatically changed to >EColi|ref0000000/582|ref0000001 and the contigs were reordered within the file.
All stages run without any errors. Ultimately the assembly stage just 'assembled' one particular contig. Am I using the right representation and is there a way to find adjacencies between distinct contigs and filling in the respective gaps?
Thanks,
Viraj
Hello Viraj,
The setup step performs two functions. 1) It identifies gaps in your reference. 2) It renames your reference with the ref ids you see for PBJelly's internal use.
This second function is why you see your reference being renamed. PBJelly doesn't care what the initial name is, it will add the ref-id tag.
But! Your real problem here is that PBJelly currently doesn't fill inter-scaffold gaps. I've been working on that version, and it's first pass is nearly completed. Until then, you're limited to captured gaps (i.e. within scaffolds).
--
Have a great day,
~/Adam Engish
Dear all,
I observed a similar WARNING messages in my err file from support stage running:
2017-02-18 01:04:42,080 [INFO] Running /software/shared/apps/x86_64/PBJelly/12.9.14/SupportGaps.py /scratch/seminavis/17-new_assemblies_D6/PBjelly/mapping/SCall_corrected.fasta.m4 /scratch/seminavis/17-new_assemblies_D6/cleaning/D6_gapClosed-1000/D6_gapClosed-1000-hdhd_hhdd-85-75-20_2017-02-07_175833/D6_gapClosed-1000-hdhd_hhdd-85-75-20.gapInfo.bed /scratch/seminavis/17-new_assemblies_D6/PBjelly/support/SCall_corrected.fasta.gapCans
[...]
2017-02-18 01:04:59,153 [WARNING] Missed adapter in read! m150824_141845_42202_c100846352550000001823188212311525_s1_p0/84342/26285_30155
2017-02-18 01:04:59,154 [WARNING] Missed adapter in read! m150828_055617_42202_c100821182550000001823174411031573_s1_p0/119124/4144_19249
2017-02-18 01:04:59,154 [WARNING] Missed adapter in read! m150828_101837_42202_c100821182550000001823174411031574_s1_p0/142212/2618_9553
2017-02-18 01:04:59,154 [WARNING] Missed adapter in read! m150825_032048_42202_c100814532550000001823181311031530_s1_p0/62493/2181_17365
2017-02-18 01:04:59,154 [WARNING] Missed adapter in read! m150825_032048_42202_c100814532550000001823181311031530_s1_p0/62493/2181_17365
2017-02-18 01:04:59,154 [WARNING] Missed adapter in read! m150825_032048_42202_c100814532550000001823181311031530_s1_p0/62493/2181_17365
2017-02-18 01:07:37,803 [INFO] Finished Support!
I have already checked the reference ids and the ids in .m4 file and they are exactly the same (the one re-name by setup stage). Why do these warnings appear, then? How can I solve it?
Thank you so much in advance,
Regards,
Cristina Osuna