BLAT call failed with Aligngraph

baoe / AlignGraph

Algorithm for secondary de novo genome assembly guided by closely related references

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BLAT call failed with Aligngraph #17

Open meetasunil opened 8 years ago

meetasunil commented 8 years ago

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error. How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find.. Please help.

Thanks, Meeta

baoe commented 8 years ago

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/17.

meetasunil commented 8 years ago

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

baoe commented 8 years ago

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Jut for your information, the commands.txt is:

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632.

meetasunil commented 8 years ago

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798.

baoe commented 8 years ago

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798.

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220.

meetasunil commented 8 years ago

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042 GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167371990.

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042 GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA m140524_192431_c36/108974/9965_15918_corrected2/0_4349 AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG m140524_192431_c36/108976/8078_14521_corrected2/2105_3641 CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA m140524_192431_c36/108983/3301_4821_corrected2/213_1519 TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG m140524_192431_c36/108986/17302_22021_corrected2/1719_3723 CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

baoe commented 8 years ago

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042 GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167371990.

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042 GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA m140524_192431_c36/108974/9965_15918_corrected2/0_4349 AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG m140524_192431_c36/108976/8078_14521_corrected2/2105_3641 CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA m140524_192431_c36/108983/3301_4821_corrected2/213_1519 TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG m140524_192431_c36/108986/17302_22021_corrected2/1719_3723 CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

— Reply to this email directly or view it on GitHubhttps://github.com/baoe/AlignGraph/issues/17#issuecomment-167485390.

meetasunil commented 8 years ago

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub <https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588 .

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167371990.

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167485390>.

— Reply to this email directly or view it on GitHub https://github.com/baoe/AlignGraph/issues/17#issuecomment-167696409.

meetasunil commented 8 years ago

Hi Bao, I'm seeing another issue now.. AlignGraph and plat are running but all the tmp/*.psl files being produced are empty. This is highly unlikely.. because the contigs and reference genome are for the same species. Any clues about this?

Also, It would be good to get a detailed log file for all the steps fie debugging..

Regards, Meeta Sunil

On 28 December 2015 at 19:14, Meeta Sunil meetasunil@gmail.com wrote:

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

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— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub <https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798 .

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137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167485390>.

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baoe commented 8 years ago

You mean the program is running, but all the files are empty? Maybe you could just wait for some time and check again?

Best, Bao

From: meetasunil [notifications@github.com] Sent: Tuesday, December 29, 2015 8:49 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Also, It would be good to get a detailed log file for all the steps fie debugging..

Regards, Meeta Sunil

On 28 December 2015 at 19:14, Meeta Sunil meetasunil@gmail.com wrote:

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

— Reply to this email directly or view it on GitHub < https://github.com/baoe/AlignGraph/issues/17#issuecomment-167176588>.

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub <https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798 .

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220>.

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137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

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meetasunil commented 8 years ago

Yes, both aligngraph and pblat are running. I was thinking that blat writes the output to psl only at the end of processing, so I was expecting tmp/_contigs_genome.1.psl to be empty until .2.psl will be created. But there are some 3000 scaffolds in reference genome so there should be 3000 psls created. Right now 999 have been created in almost two days. Another 2000 will take four more days to be created. And all these are empty so far. Not sure if all 3000 will be written together at the end.. I was thinking only the running blat job should create empty psl (_contigs_genome.999.psl right now) and all the psls till 998th job should have got the output. Am keeping an eye on this.

Best, Meets

On Wed, 30 Dec 2015 4:03 pm Bao notifications@github.com wrote:

You mean the program is running, but all the files are empty? Maybe you could just wait for some time and check again?

Best, Bao

From: meetasunil [notifications@github.com] Sent: Tuesday, December 29, 2015 8:49 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, I'm seeing another issue now.. AlignGraph and plat are running but all the tmp/*.psl files being produced are empty. This is highly unlikely.. because the contigs and reference genome are for the same species. Any clues about this?

Also, It would be good to get a detailed log file for all the steps fie debugging..

Regards, Meeta Sunil

On 28 December 2015 at 19:14, Meeta Sunil meetasunil@gmail.com wrote:

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

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137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

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meetasunil commented 8 years ago

Hi Bao, Wish you a very happy new year!

I see that AlignGraph is still running but I don't know if it's actually doing something.. All the pblat jobs are over and all the PSLs created in tmp/ are empty only. Do you think it would still be performing assembly based on bowtie-mapping or should I just kill it? It's been going on for almost 15 days now..

Thanks, Meeta

Regards, Meeta Sunil

On 30 December 2015 at 16:15, Meeta Sunil meetasunil@gmail.com wrote:

Yes, both aligngraph and pblat are running. I was thinking that blat writes the output to psl only at the end of processing, so I was expecting tmp/_contigs_genome.1.psl to be empty until .2.psl will be created. But there are some 3000 scaffolds in reference genome so there should be 3000 psls created. Right now 999 have been created in almost two days. Another 2000 will take four more days to be created. And all these are empty so far. Not sure if all 3000 will be written together at the end.. I was thinking only the running blat job should create empty psl (_contigs_genome.999.psl right now) and all the psls till 998th job should have got the output. Am keeping an eye on this.

Best, Meets

On Wed, 30 Dec 2015 4:03 pm Bao notifications@github.com wrote:

You mean the program is running, but all the files are empty? Maybe you could just wait for some time and check again?

Best, Bao

From: meetasunil [notifications@github.com] Sent: Tuesday, December 29, 2015 8:49 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, I'm seeing another issue now.. AlignGraph and plat are running but all the tmp/*.psl files being produced are empty. This is highly unlikely.. because the contigs and reference genome are for the same species. Any clues about this?

Also, It would be good to get a detailed log file for all the steps fie debugging..

Regards, Meeta Sunil

On 28 December 2015 at 19:14, Meeta Sunil meetasunil@gmail.com wrote:

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

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137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

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baoe commented 8 years ago

Hi, Meeta,

It looks weird that the files are empty. It means no contig has been aligned to the reference genome. But I remember you told me the contigs and the reference genome should be very close.

Maybe you could check if there is any problem with the input reference genome file?
Did you use the -fastMap option? If so, maybe you can run another copy of your data without this option for some time (one day or so), and see if the alignment files are still empty?

Happy new year! Bao

From: meetasunil [notifications@github.com] Sent: Saturday, January 09, 2016 9:31 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Wish you a very happy new year!

Thanks, Meeta

Regards, Meeta Sunil

On 30 December 2015 at 16:15, Meeta Sunil meetasunil@gmail.com wrote:

Yes, both aligngraph and pblat are running. I was thinking that blat writes the output to psl only at the end of processing, so I was expecting tmp/_contigs_genome.1.psl to be empty until .2.psl will be created. But there are some 3000 scaffolds in reference genome so there should be 3000 psls created. Right now 999 have been created in almost two days. Another 2000 will take four more days to be created. And all these are empty so far. Not sure if all 3000 will be written together at the end.. I was thinking only the running blat job should create empty psl (_contigs_genome.999.psl right now) and all the psls till 998th job should have got the output. Am keeping an eye on this.

Best, Meets

On Wed, 30 Dec 2015 4:03 pm Bao notifications@github.com wrote:

You mean the program is running, but all the files are empty? Maybe you could just wait for some time and check again?

Best, Bao

From: meetasunil [notifications@github.com] Sent: Tuesday, December 29, 2015 8:49 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, I'm seeing another issue now.. AlignGraph and plat are running but all the tmp/*.psl files being produced are empty. This is highly unlikely.. because the contigs and reference genome are for the same species. Any clues about this?

Also, It would be good to get a detailed log file for all the steps fie debugging..

Regards, Meeta Sunil

On 28 December 2015 at 19:14, Meeta Sunil meetasunil@gmail.com wrote:

Ohk thanks, I've re-merged the two fasta files I have and also removed thewhite spaces from the headers.. Now it's working fine Many thanks, Meeta

On Tue, 29 Dec 2015 7:24 am Bao notifications@github.com wrote:

Hi, Meeta,

Maybe you have an empty line somewhere in the file (probably between chaff contigs and long contigs)? AlignGraph scans the file and finishes when it meets an empty line. You can see lines between 3025 and 3038 in the code for more details.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Sunday, December 27, 2015 9:01 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Oh, I've attached them again. In case you don't receive them still, please see them here:

head head.txt

137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

head - 2 tail.txt

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAAT

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 15:55, Bao notifications@github.com wrote:

I can't find the attached file...

Bao

From: meetasunil [notifications@github.com] Sent: Saturday, December 26, 2015 6:51 AM

To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

ohk, I've attached the head -20 and tail outputs of my contigs.fasta; please see if it is ok for ALignGraph to process or how should I modify it..

It's actually a concatenation of contigs from one assembly ranging in length from 31 to several thousands (with fasta headers containing spaces), and very long pacbio reads.

Best, Meeta

Regards, Meeta Sunil

On 26 December 2015 at 20:01, Bao notifications@github.com wrote:

Hi, Meeta,

Maybe it's because the contig file's format is something I didn't expect when I was writing the software, e.g. it contains many spaces between two continuous contigs? Let me know about it.

Yes. If the _checkpoint.txt is empty, --resume doesn't work.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 10:20 PM To: baoe/AlignGraph Cc: Bao Subject: Re: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hi Bao, Thanks for your reply. I just noticed that the tmp/_contigs.fa which is called by blat/pblat is empty. Probably this is why the blat call fails and not due to any path issues (I even hard coded the full path to pblat in AlignGraph.cpp and got the same error).. Now I wonder why this is happening.. My input contigs.fasta is 5.3G, the tmp/_chaff.fa is 621M while the tmp/_contigs.fa is 0.

Jut for your information, the commands.txt is:

--read1 AhPE1_Yfil.seq --read2 AhPE2_Yfil.seq --contig contigs.fasta --genome AhG.fasta --distanceLow 75 --distanceHigh 1400 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa --insertVariation 200

Also, the tmp/_checkpoint.txt is empty.. Is that why --resume doesn't work for me? Any suggestions for resolving this as well?

Thanks again, Meeta

Regards, Meeta Sunil

On 24 December 2015 at 17:45, Bao notifications@github.com wrote:

Hi, Meeta,

This error message tells that neither PBLAT nor BLAT can be called, so I guess there would some problem in your $PATH. Maybe you can double check it.

Best, Bao

From: meetasunil [notifications@github.com] Sent: Thursday, December 24, 2015 3:20 AM To: baoe/AlignGraph Subject: [AlignGraph] BLAT call failed with Aligngraph (#17)

Hello Bao, My $PATH contains all the three tools - bowtie2, blat and pblat but I still get BLAT CALL FAILED! error How can I troubleshoot this? I'd like Aligngraph to use pblat preferably but it is trying to look for blat and that also it is not able to find Please help

Thanks, Meeta

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17>.

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https://github.com/baoe/AlignGraph/issues/17#issuecomment-167199632>.

— Reply to this email directly or view it on GitHub < https://github.com/baoe/AlignGraph/issues/17#issuecomment-167327798 .

— Reply to this email directly or view it on GitHub< https://github.com/baoe/AlignGraph/issues/17#issuecomment-167329220 .

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137 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTA 139 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTC 141 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTT 143 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACTG 145 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 147 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG 149 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTA 151 length 32 cvg_0.0_tip_0 AGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTC 153 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAA 155 length 32 cvg_0.0_tip_0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAATAC

m140524_192431_c36/108971/0_8213_corrected2/29_8042

GAAGAGTACATGCACAATAAAACCAGGCTAAAGAGAAACACAACTAATCCTGGTCAAGGAAACATGGCCTTGTCAAAAACTACAAGGATTTTTTGCATAAAATTTTCCATTGAAAAAAGAACAAGGTGTGAACAAAAAAAATTCCCCATGCACCTAAACTGTCAAGTGTCATACTATGCTCTACCAGATAGAATTGATTAGTTATCAAAAAAAAAAATCATAACTTGGTAAGTCATACATTATAAGTAGTTTGAGCTTAATGATGACACCAATAGCGGAAGTAACCTAAATGAAAACTGCTGAAGATAATTATGCAAAACACCATCAGAAAAATTTGAAGGCTAGACTAGTCAAGCAACATATAGAGGAACTAAACATTTTTCACACATCCAAGATTAAAGTCCCTACGTCCATTCTAGATGCTACATTAGGGGTTTTCACACCAATCATCTAATAATCTAGACAGGAGAAGAAAAAGCATCCCTAATTCCCACCATAGAGATTAGTAGGGTGTTGAGCCAAAAAGCCCAAGCAAGAATTTGCATCTGTGCAGAAAAGTGACAGAAAGAATGGTTTGGTCAATAATAAGGATATAAGTTTAGAGGACAGGATGCTGATGTCAAATAATAGGCCAAGATCGTTAAATAAGGTTACTAAGTTAGATAAGGACTGCGTGGCAGTCAGCCCCCCACCGACCCACCTAACCCATCGGGGACCCCCCAAACGTTTTAAGCAATGACCAACTTTTACATTCAAAAAGGATAACAATTACAATATATATATAACCCTAAGTATTGCAAATTAACATTAATTTCCTAAGCAAATATTAGATTATGTAATATATGTACTGTTAATACTCATCCTTTCCACTTTTAGCTTCTTATGTGCAATTCTTTGAGTTGTATACAACATATGCCATTCAAAAAGACTTGAGCCAACCACCTCCTCTCCTAAGAATACAACAATATTTCATTATCCAATTGGCTACCACCTTGGTGGGGTTTGGAAGGTCAAAAGTACATAACCTATTCCTATCAAAAATTATGTGCTACTCAACCTATGATGCACATCATCAACATGGAATTATTTCACTTTCCAAATACCACAAAATATGAGCAACATTTCAGATACAGCACCTGCACTTCAAAAGTTTTTCAAATAGAATTAGCCAGGAAAAAAATTTTCTCTGAAGTTTTCAAGCTGAATGGAGCTTAAGAAGCCCCAAAAACATGTACTAAAATACTAATAAAGATGAATTCAATGATAAAACAATAATCAATGCCCTTATGGGGGGGACAAGAATGAGGAATGGGACATAACTTTACCTGACAAAAATAAGGAATGAACAACTGATGTTATGAAAATTGAATGAGCTTTTTGCCAACTGGAACATTCAATGTAATGTTCAAGGGCCTTTGAAAGATCACCATAGTACTGATAGTACACAGCCTACACAGAATACATAAAAAATTTCAAGAAAAGTAGAGTAAGTCAGTAATGTTATATGAGTTTTCTTTAGAAAGTATTCAAAAAATAGCAGACTTGTCTGAGAATAAATAATTTCCAGTAGTTAAATGTCAAAGGTGCAAGAATACATCAGTTTAATTTTTAATTAATCTCTTATGTAAGTGCAGAAAATTATCTTATAAGCCTGTCTGTGAATGAGGGAATAAATCAGTGCTTGTGTAAGGAGCTAAAATATGCTTAGGAGTCTCTGTGGATGTCCGCAGCCATGAAAGAACACAAGTGCGAAGTGTGGCTCTTTACGCACATGTTTCCTTCAGTTTTTTCTCTCCATTTTGAGCAGTCAAGACAGTTGGGATTAAGGAAATTAAAAAATTTTGTAAAGGGTCCAACGAGAGATAATTTGAGTTTCATGAAAAGAAAAAACGTCACTTATAACACTTCATAGATACTAGGAAAGCAGTGCCGCTGTAGTACAAGGGAGCCAGGTCAACCCAGCTCGCAAACTATATTCTTCTTCCAAAAAGTTTTTCTATATCATCAACTCATACTCATACCTACTCATATAAAGATTTGGCCGACTAGATTTAGGTAGTTCTAAGATCCAGTTAGTTCTCTTTACAAAAACTTCCTTACCGTATAATCTTTCAGATATGACGTTCACAAATATTAGGAGTTAAAAGAAACATAATCATTCACAACTCTAAGATGACCAGCAAAAAGACCACAGCAGGAACAATTACTAGGTTTAAAGGTGTTAACATACAGTAGATTAAGAAAGGCAAAAGAAACCAAAATCGTTAGTCCATCTTTCTTTATAATCTGTTTCCACAAATCAGGTTTTCAAGCTCCCTCAGATCCTTAAGCCTGTTTCTTCGTACCCTCAAGGTTTTCAATAAACCAAATAAGTTTGATTATAAACCACATGAAACTTTTACCACTATCCCGTGTTTACAGATCACAACTCCCACTTCAACTACAGCTTACCCAACACCACCAAACCAACAAGTCAACAATATAGAGTCCAATCCTTACACCCATTAGGCATCTTGCTGCCCTCATTTATCAATGCCTATGAAAACCAATGCTGACAGCCAACTCAAATGGAGTGTAATGCATCACTAGAAACTAACTCATGCACAGTTATGATATCAAGCCAAAAGTCTGTTAATGCAATAATTTCTCACAAAAAGACACCGGCGGTACCCTCTATTATAGTGTCCGATTTAATGCACTTGCATGTAAATCTACAATTCAACCCTGCACGGACAAACATGGCAGGCAAGTTCCTGATCTGGAACCTCAAGCCAAACTTGATCACCAATGGATTGAAGATCACCCAACTGAATGTGGTGCGGCACCACACCAGTACAACATTATGGAGGTGAAGAAGCTTCTAAAGAGAGATGGAGATGGTGGTGGTTTCACTGTTTGATTGTCGTGACCTGCTGGTGCCTTGCTACTGACGTTGGTGATGGTTAATATGGTGGTTGACCACAGAAATGGTGACAATGTTCATTATTCATGATGGTGGAAAGCTATATTTTATAGTTGGTTGGTGGTGAATGGACAGCAGACAAACTAGCAGCTGTCATGAGTTAAATGTATTACAGATAATAGGTGGCTGAGAAAAACCAAGTCTTGCTGTAAGACTCATCCAAATGCTCGGTAAGTGGCGGAGTCTGTTATTCGAGTGTTAATAGCAGTCATGCTTCATCTCCAATTCTTGGCTCTTGCAAGGATGTGGATATACATCGATAAAACAATTCCGTGGTTCAATTTTGTAAAGTGCTGTACTTCTTTCTTTCAGGATAAGCATAATGTAATTTCCATAGGTGCAAATAAAAAGTTGATGAATTATTGAAAATAAAAATCCAGAGGTGTGCAATGAGATTATAAGTCCAAGAGATGAAGTTTGGATGAAATTTATGGGAGTTTGAATGTTTGATAATGATTGGTAAAATAAGATCGATCTTAGTCAAAACTTGATATGGAAAAGTATGAAATCTAAAAAAGTTGAATATTTTTTACTCTAAACAAGATGTGTAAGCTAAGGTTCTGAGGAATTTCATAATGAAAATCTAATCAGAGATTCAAGTCATACACAAATTTTATTCATGACCTGGCCTCATGAAATAGAAACCTAAAACTGTTTCCAATTAGAAGGAATGGAAAATTCTCTCTATTAAAACTATAGGTACTTTAAGGAGGTGCACAATAATTTAAAGAGGTATTAATTCTAGCAAGCTAAATTCAAAAATTAGAAATAATGATCGATATCTGAACAAGTAACAGTACATAGATAGTTTAGAAGCCAAAAGATATGGAATAAGAAAGTAGGAGGCAAAAGTAATGGGAAAGGGAGGTGAATCAAAACATGATCCATAGCTCATATGCAACCACTGCGAAGGAACACCCAACTCTTCAATAAATTTGCGCTGATCTTCTTGGGAACTCCAAGTATCACAATATTGGAACAAGATTTCTCGAATAACAGTGGAATGTAAGTAAGGAAAATCTTTACGGTAGGGCATGTGAAGAACAACATAAATAGCCCAATGACATTTTCCAAGACACAAAAGCTGGGAAACATATGCCATGTCAAGAATATGAAGATCACTAGAAGTAAAGGCACCTATTGCTTCAAGAATTCCACGCTGATGCCAAATCATATGGTAGTCAAGTGGATCATTAGTTGACGCAAAAGCACTGAACATGGATTTCAAGCCATCAAATTTACCATCTTCACTAGCATGAAGCAACATTAGATAATATGCAAGGTCGTACCGTCCCTCTGTAAAAACTTTACCAGTTTCGTCCACTGGTCCCTCATCAATATAAACTGGAACCGGGTAAGGAGCCTTGCCTTCAGTAAGAAGATGTTGATATGTGTGAAAAATAGAGGGTAAGGGAGTGCCTGGTGGCAATTCATACCACATCAACAACCCCAAGAACCTTTTCCAGTCAACCCTTTTTCCAGCCAAGCACTGTGAATGTTACCTGAAAGTAATTCATAAAGCCGTATCCTGTCCTTTTCAATGAAATTCATGTCCATTCCATTAATTCTCCACAGTTCTAACTGCTGAGCTACATCAGAACGGTTCACCATAGACCCACCAGCCTCTCCTAGTAAGCAGGCCAGCCTAACATCCCCTCCAGAAGCAGCCAATTCAACAGCAGCATCCAATTGTTTCCCAGTCATTAAAAGAAATAATTGCTCCAGATCATCAGACTCACTCACGCAGCTCAAATCTTCTTGCACACGGTGGTAAACACTCTCTTGTAACCAATAACTAAACTCTGCCCTCCGCATTAAAGGAAGTGCTTCAGGGTCAAATTCTGAACGACTGACTTTTCCATCCAACATCATATCTTCCTCAAGGTCATCTACCCCATGCTCTGTCTGTCCACTAGTCTCTTTTTCAGAGAAAAGAACTTTAATTAGCTCCCATACAATGACTTGATGCATCAAAGACACACGAACAGATGCCACCATATCAGTAACCTCTAGTTGCTTCTCCACTACATCTATATATCGCCGACATATATCAGACAGAATTAAGCGATCACATACGACTTTTTGAAGGCTTAATTTCGAGGAACCAACTTCAACTTCTAGTATTCTACGATTCAAAGACTTATGTAAATCCAAGGGAGAATCAAAAAGCAAATCAATTGCTTCCTTTTTCACTTCATTAGTTTCATCTCGAGTGACTTTGTCTATTGCAACCTTTTCAAGAGTGATAACGGAAGAAAGCATTCCTTGGCGAGCGTTACCAACAGGTACACCACTATGAATAAGGAGACCATTAGGTCCCCACCCAACACGAAATGACCTACCCATGAACAATCCTGCATCAACTATATTGCGTGAATGGTAATCAGAGACTGGTGTTTCTTGCTTAAAATTAAGCTTGAAACCTACTGGATTAACCATCCTCACAGGTGATCCTTTATTCTTCTGGGAAAGTACAAGAGCTCCAGGAGAATTTACATCAAAATCTTTCCATTTGTACTCGAGCAAGGGTACTGGAGTCTTCCTGGGTGGGGCAGGACTCGGTTTATAATCAACCATTAGCCCTGAGTTATACAAAGGAGACTTTTCTCGGTGAGCTACTTGTTTCTCGTAAGAAGGAAACCCGGAATTATCTTCAATGTCATTGCCGTCATCAGAAAACATTAACATTTTCATCTCCTTCATTCTATCAGGATCAAGGCCAAGAAAAGTAGGAAGTGAGTGAGAAAGATCAGGACCATTTTGGCCCATATCGAATCTGTCACTACCAATGCCCTCATCCTCACCAACATCATCATTCATCTCAACACAATTCTCAACTGGGTCCGCATCCGCGTCATCCATCACAATGTCATCCTCATCGTCTACACTTAATCCAAATCGACTAAAATGTTGAACCAAAAACATCCATTCTCCACTCAATGGATCATACGAAATGAACTCAGCTCCTTGCTTTTCAGCAGTAGCTCTCAACCTATCAACAATCTTACACAATCTATCACCTTCAAAATCCAACCTTCCTAACTTCAAAACCAAAGTCACAACAGCAGGCTTGTTTAATCCTTCCCCAACAGGAGGTTTACAACTCTCATCTTCGTAAACAACAACTTCATGCCTATTAAACTTAACAATCTCCATCACATCCAACTCCAGCATGGTCTCGCCCAGCAGGAACCTCACACATCCCGAAATCCATCTGGCCACGCGGTTAAAATCCCTAACTTTACAACTGTCTCTAGCATTAACACCCTCTATTTCTGTTAAATCTTTCAATGACGGTTCAGTATAATATTCTGAATCAATGGTGGCGGCCACCATGTATGGGGGAAAAGGTACCAACATTATAAATTATTCACCAATGATCCGAATGTCCAGTGTAATCCCAAATTTTACCGAGCACAAGAACCTGTAAATTGAACTCTCAAATTCACACAATCAAAATTAAGCAATAAAATTCATACTACACTGTTACCACTCCAAGTATAACTCAGTAACTCATAAACACAACCTTAATACTATAATTTGCCCCTAATTTGAGTTTGAAACCCTCAATTTCCCCAAAAAAAACTCGGTGTATTTCACTAGATGCTACGAAACTCCAAATAGCTAAAAAATGTGAGATCTGTAAAACTAAAAGAATAAATTAGGTATCAACAATCAAATGTAAAGAAATTGAAGTTACTTGCTCAAGAGAATAAAGTGAAATAAAGAGAAGAACTTACTTACTACGTCGACAATGGCTGCTTGCCGCGCCTAGTTGCCTGCTTGCATGAAGGGTTTGAATAAAAAGAACAGTTACTTCGGTCGCATAAAGGAAAAACGATTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTATTTTTTTTTTTTGTTTTTTATTTTTTTTTTTTTTTGATTTTCCTCTTTAATCGCCTCTCTGTGTTTCTGAGATATTAAATATGGGAGGCAATTAGTTTGCATTTAAAAAATGAATTTGATTTGATTAATAATTCTATAATTATAGAATCATACGATACAATCATACAACTATAAAATTTGTTGGGAAATTATGAGCGTCATTCTCTTACGATATAACAAATATAATTATTTTATTAGAAAACAAATATAATAATTTTATTAGAAAAGAATCGATTACATTACAATATTTACTTAATATAGAATTTAATTATCTTTAAAATTAGAGTTAAATTAGGTATAGTAATAGTATGGAGTATGATTTATTATAGCAATTCTATATAACTAACCTAAAATTGATATATTTAATTGAATAAAAAAGTGATTGCATTTAATAAATAATTTTAAAAACATTTGTATTTAATTTTGTGCTTTAAAAATGTCACGTGTTCGATAAATTTAACACTAATAATGTATACTTGGCATATTCTTTTAAGTTTTATTTTTATATATTTCATACCCATAAATTCATATATTGCACGAATTTATATACTAATATCTAATATCTAATCTAATGTATACTAATCTCAAACTTATAAAATGGTGATAAGTGAGTTAGACCGGTGAAGACGTGATTGAGAAGTTGTGCACAACAAAATACTGCTCCCTCCTATTCTACCTATTA

m140524_192431_c36/108974/9965_15918_corrected2/0_4349

AAAATCCAAATCATATTTCTTATTTGTCTTGGATTGGTTTGATTTGCCTGCCAATGAGGAAGAAGTGAGTCCCCTCAAATATTGAGTGCCTGCCAACAAAAAACATGTAAAAGTTTCATTCCTACTACATTTTTAATTGCAAAAAAATTATTATTCACATATGAATTATTTCATATGGATAAAAGAGAATATATCACTTTATAATTGATAATTGACTGGGCTTCAAAAAATTTATAAGAGTTCAAAAGGGTTTAAATAAGATTAAGTAGCATTGTTTTTCACTAATTTTTAAAATGAAACGGTCTCACAGTAAGACTATCTCTATTGGGTTGGCCCAATACACACCTTCTTTCTTAAAGTGATCATTTATATTTTTAAAATATTTTTTTCCTATAGTGTTAGAGTACTACTTATAACCTTAAAACGATAACTTATAATGTTCAAGTGGTGACTTGTAATTTTAAAATAATTAATTTTTATTGTTTTAGAGTGATTACTTATAACCTTAAAACGATCACTTACGATCATAAAGTGAATAAGCAAATGGGCTAATATATACCCATCTTGTGGTGAGACAGTCTCATACAAGACAAGCTGGTTTTTTAGGGAAATTCCAGCAGTGGGAGCGATCCCAGTTTTAATGAAATGTCAATTCACTTTTTAAAGAAAATTTCATGTATATGGTAGCATCCAGTTTATGCACGATCAAACTGTCGTAGCATTTTTCGTTAATTTCTTGTCAAATTCCATTTAATTCATATACTTGTAGTTTTTTCTCCCACATGGTAAGTATCCCAGTTTTCCTGTTTAATTAGCCCAATTTAACTTTTTATTCACGGCATTATAATGTTTAGATATCAAGCGCGCCCGTTTAAGTTTATTAACGGGCCGATAAAATGTTTAACAATTTTATTGGATAAAATTATAAATACTAACCTAATCATGATAAGTCTATTTGCAAAAAACTAACTAATCTGATATATTTACTTGCAAATGACTCCCACTTCACGGAAAACGTTAGTGGACCGTTAAGTTTGAAGGTTTGACTAATTTGAGAGTTTAAGTTGTCTATGTGGCAATATCTCATTAGTCCTCATATTTGTAAATAATTTAAATTTAAAAACAATAAATTAACAAAATAAATATAAAATATATTTAACGTCATTTTAATCCATCATAACGATTTTTTTCCAAAAAAGCGGACGTCGTGATTACCTTTATAGTGTACCTCTTTCGAAAATCCAAGCGAAACAAGTACTTATTGCGCCGATTTTCTTATGTGGATAAACTTTTTCGAAAATCCGATCAAAACAAGTATCTTATTCGAAAAGAGTACTTTTTCGGACGGAAAGTTAAATATTTAAATGATAATTAAGCGTAAAATTATTTTTTCGCAGTGAATATTTAACAATTATAATCTTTACATAAAATTATTAAATATTTATGGGCTTTAATGAATTAAACATTAAAATAGTAAATTAAACAAAAACTGGATGCTAACCAATGTGGAAAAAACTATACAAAAATGATAAATTTAAACGGAATTTAACAAGAAATTAACAGAAAATGCTACGGCAATTAGGTAGCGCATCAACTGGGTGATATCATGTGGAATTTTCTTTAAAAAGTGCTACGACTAGCATTTCATTAAAACTGAATACTACCATGTGAAATTTCCCTTTTTTATAATGAAAACTAATAACAACAAATCTTGAATTCAATGGCCTCGCACCTGCGACCAGCCCAGTCCAATTATATTGTTTATTTTTTTAAAATATATCAATTCTAAGCTTTTAAACACTCGTTTGAAGACTTGAAATGCCCATTTTAAGGCTTAAAAAACTCCTACTCCAAGCCTTAACATTCCTTTTTCAAAGGCTTCACTATATTTGTAAGCCTAAGAATGGGCATTTTTAGCTTACTTCAACAGTTAAATTGTTAATTTTAAAGCTTAAAATTTTTAGTTTATTGCTTATAGTCCCTACTTTAAGGCTTGAAAAATGTCGTATATTATTTTAGTAAGCAAGTTTAGCATTGAAATGGTTTATACTAATGTTGTTTTCTCTCTTTGATCAAGCATGATACGTCTTTGAATATGATTTTTAAGTTTTGGAATTATCAGTTTGAGACTTGGAATAGACCTTGTATTCATTTAAGGTAGTATTCGATGCTTGGTTGTCTGTTAAGGCTTGAAATTGGCCATTTAAGGCTTAGATTTGGCATTTGACGGTTTGTAATACATATTAAATGCATGCTTAGAATAGGCTTTTTTAAATCTTAAAAATTGATCTTTTAAGCCTTGAAGTTGTCAATATAAGGCTAGAAATTAACCATTTAAGGTTTGAAAATTGACATTTTAAGGTTTGAAGTATATTGAATGACTTTTACAAATGTATTCATTTTTATAGTTGTGAAATTTTTGCATCAAAGTTTTAATTTGCTAACTTAAAATACAAGAAGATATTGAGTACAAAATTTTAAATATGATCAACACTAAACTTGAGAACAAGATAACACTTTTCTAGACTATTTACATTTACACCAACAAACTACAATACATGAGATTAACATTTTTATTGGGACTACGTATGAATGGTCGTGCTCGACATTGGTGCATGAAGTGGTTATGGAGAAGAGGACATCATAGACTCAGGGTGATTGCAAATTTTTTAGGTGAAGAAAGTCATTGATTTTGTGTAAAAAGCTTAAGTGATATTAGTGAGGAAGAAGTCTTTTTTAGTTTTGTATTTTATGATAATGGGCTACCAAACCCATACTAATGCAGTCGTACAACGACTGTCGCAGACAAGTTTTAGTCAACTAATAAAATATTTTGGGCTTATGCAGTGTTTGTTTATCAGCTCATTATATTTCTTCATAAATTAAATAAGAGAAATTACCTCTTACCCTAATTATTACTAATATAGGTATCCCTTATTTCTTTAACTGGTATTTTGCCTACACATATTTTTTTTGAATCACAGAAATTGTCTCTGTCCCTTTTCATACTCTTCTAAACTGCTCAATTCGTTTGATAATTAATATCCAATTTCAATCCATTTTTGTCCCTTTTTTTTTTTTTTTTTTTTGGTCGGTCATAAACAATGACAAACCTACTCTCGCTACTCGATCCCCTTGACGTCATTCATGGCCAAAGAAAGGTAATTCTTTGAATCTTCTTTTTTTTTTTCATTTTGTTTATTTTTTTCTTTTCTTTACCAATTGTCCTTGGTGTTGCTTAATTATTGTAATATATATACAGGAATCGTTAAGATCTGCTTAAACATTCACGTCATGTTATTATATTATATTTATTTATTTATTTATTATTAATATTTATTTATTTCTTATTATGGCTTTAAGCGATGATTTCCTTTTAATAGGCATTAACGTGATGATTCATGTGGGATGATATGTTTAGGACTATAGGAGATAACGAGGGTTGTTACCATTGTTATCAAAATCGCGATTCTGATCTACGATTTTACGGTTTTATGATCAAAAAATAAATGTGCTATTCATTTGTAAGAAGATTTAATCTGATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTTTCTAATGATTTAACGATCCATCATAATCTATTCTTAATTATAGATTTAATGATTTAACGATCCATCATAATCTAGTTATTTTTCTAATGATTGTAAGAAGATTTAATCTAATTATTATATAATCTATTCTTAATTATAATTATTTTTTCTAATGATTTAACCGATGCCATCATCATATTAGGTTTAAAAAATAAGACTTCATTGGTATGAAGATTTAAACTAATTATTAAATAATTTTTTGTTTCATTCTTAAATATATAGTCAAAGAAAGTTTAATTAATAAACTTAAACTTTTGAGATAAATAACTATTAGAGATTACAAATTTAAGTTTATTGTAGAATCTTACGATCCTACGATTCGATTCCACCTCTTTCGATGATTCCAAGTAGAATCTCGATTTTAACAACTTTGGTTATTACTAATCAAAGTATTATTAATCTAATCAAAGTATTATATGACAAAATGTATATCGACTCAATTACCATTATTAATTGATATACTATCTGGTTCATTACATGAATTCGTAGAGGAAGTTTTTTAGTTATCTTAAGTTCTTACCAGATGTTAGTGATTG

m140524_192431_c36/108976/8078_14521_corrected2/2105_3641

CTTATAAAGACAGTCTCTCAGAAGAGGCATTGTATGCTCAATTAAAAAACTGGGTTTATATGTGAGGGTGAGTGTTGGAAAAATAACCTAGATGTAATCCCATATCAAAGATTTAGAGAAAGATTTACCAATGTATATATAATCTTAATGGACTACTTTTATCATCAATTAATTATATAATGAAAACTCATTAAACTTATGTGCAATTAACAGCTAGTCTCCTGAGAGACCGTTTTTGTCTGAGAGACGTCTCCAGCGCCCCAATCCATTAAAGGCTTATTGCCGTATATTATCTAGCATTTTTCCCTAATGGGTCCAACCCCAATTGAAGAGATGGTACTCTCAAAGAGACCGTCTCTCACAGGAATTTGTAATTAACTATTCTCTTATATGGGTAATGTCATAATGCATAACATAACAAATTTGAACATGTCGGACTGATTCAAGGAAACGTTGGAGTGAATGATCAATGATCTTAAAGATTTTGTTGTAGCGTGGACGGCTGATTTCCTCCTAAATACAACTATACTATACGACTATACCCAGAGATTCAAACACACCGTTTCAAGAAAGACGTTGACTTATGTAAACTGGCACAAGGTTGACTTTGTAAAATTCAATTAACTTTGGATAGCTTATCCCTATTTTTAGTATTTTATTTATAAAATCGTTGTTGTTGACTTTGAAACAAAAAATATTATTTCGTTCTGTAAAGTTGTTGTTATTTGTCATTTAAATTAAGTTGTTTTATTAAAATACTTTAATAGTTTATCTAAATTTAATAGTTGCTACAGTTTCTATAGCAACTTTTGTTCATCAACTGATTTTATTAAGTGCTACATATTTGTCCATGTATATTTTAAAATATAGTCAAGTGAAATTTGGTTTAATTTTGTCTTAAACGCATATTTTCATAATACTAACTTTTTTTGAATTTTTATAATATAAAATTAAAGATATTAAAGATTAAAATCGTGCATTTCCTCACATACTTTCGACTAACATCGTTTTAATATTGTTATATTTTTGCGGTCTTCACATGTTTTCCACTAACTTTATCAAACTTTTTTTTAATGATTGTGGTCCCATCACTACAAAAAAATAATGAAATGGCGACACCGTTTCCATTGCCATTTGGAAGCTAAATGGTCAAAAAGTGGTATTGGCGACGGGAGGGCGACGAGCTATGAGTGGACGCCAAAATGCTGGACGCTAAACTAAAACATGGACGCTAATTGGACGCCATTTTACGTTGACCACTGGGCGACCACCTGGCGACCAAATACCTCATCGCCTGAAATGAAGCTGTCTGGCGACCAAAAATCTCGTCGCCAGCCCATAGCCATTATATTTTAGATTTTGTATTTTTTTTTTTTGCTTTTTTTCGTGCATATATATATATATATATATATA

m140524_192431_c36/108983/3301_4821_corrected2/213_1519

TGGTGGAAGAATTTCATATTGACACTAACTAGCATGGCACAAAGATGGGCACAAAGCCTCCTTGAAGGCTCAATTACTTCATTTGATGAACTTTCCGAAAAGTTCAAAGGCCATTTTTCTTCAAGGACTGCCAGATCTAAGCAGTCCACTGATATGATGAACATTATACAAGGAAAAGATGAATCCCTCAGAAATTATGTGTCCAGGTTCGACAAAGAAATTCTGTAGGTGCTGAACCCTGAAGAGAACATCCTCACATTCGCTTTCAGGCAAGGTCTGAATTCTGAAAGGCCTGAAAGTCAAGCCTTAAAATTCAGCAATCAGTGGACTTATATGAAAACAATGAATGAAATCAGGGGAGTATGCACAATCCCATGTTGATGGAGCAGAAAAGCAAACCCCCTGAAAGAAGCAGCAGAAAGCCATCTGAAAGGCAGGATAGCGGGAAGAAACTGATGAGAAATGAAGATGTTGATGTTCCTGGGCTCCATAATTATACTCATTATACACCACTCAAAGAGTCCAAGGCCAAAATCTTCAATGTACATATGCAAGATATTAGGTGGTAGAGGCTTGTCCAAAGGAAAATGGTTGGATAGAACCCAAATGCGTATTACAAATTTCATGAATGTCCAGGTCATCGGACAGAGCATTGTGAATCTCTAAAGAACAATATTGAAGATATGATCTAGAGAAGGTATCTCCAACAGTATAAACAAGATAAAGCTGTTGGTAAAAGACAAACCAGCAACACATCTAGACAGACCAGGGGCAACACTGATCGGGATCTAAAGAAAAGAAAAGAAATTCTTATGATATACCAAGAATCAGGTTATCAAATAATGAAACACACTTAAGAGCAGCAACAGCTCCAAGCTGATGGAGGTGATGGATCAGGAAGAACCACCGTATCTACTAGATATGACCTTCACTAGGGAGGATTGCAATAGGATATCTTACCCTCATTCAGATCCCTAGTAATGGTAGTTGACATTACCGACCGGTCTCTACACAGGATCCTGCTGGATAGAGGTGCTGAAATAAATGTCAGCTGAAATAAATGTCATTTATAAATCTTGTTGGGATCAAATGGATTTAGATGACAAAGTTTTTAGAAAATCAATCACACCAATTGTGGGGTATCTAGTGAGTCAGTTCTAGCATAAGGGAAAATTACTCTACCAGTTACTATCACCGATGTATAGGGGATTACCGTAACTGTCCCCCATGAATTTTATATTCTGGATGCTCCTACAAGATATAATTGCATTCTG

m140524_192431_c36/108986/17302_22021_corrected2/1719_3723

CCCAAAGATACGAGGAGGAAGAGAATGAGATGAGGGAACAGAACAATGAGTAGAAAGGGTAGCGAGGGGGGTCTTAAAGGTTAGAGACTTTGTGGGAAGGCGGTTGGTCAAATAGTTGGCTGTGGCAAGGGCTTCAGGCCAATAGGAGGCGGGAACATGAGACTCAAACATAAGGGCACGAGATATTTCTAGCAAAGTACGGTTTTTCCGTTCAGCAACCCCATTTTGCTGTGGTGTGTCAGGGCAAGTAGTCTGATGGATCATCCCATGCTCATGAAAGAAACGACTCATGGCATGAGACACATATTCCCCACCATTATCTGAGCGTAGGATTTTCAAGGGGGTATGAAACTGGGTAAGGATCATGTTATAAAATTTAACAAAGACATCAAAAACCTCAGATTTGTGTTTAAGAAAATAAATCCAGCTCATACGGGTACAATCATCCACAAATAACACAAAATACGATAAACAATGAGAATTAATATCGGGAGCAGGACCCCACACATTAGAATGAATCAAAGCAAAAGGTTTATCAGTCTTAAGTTAAACTAGTACAGTACGAATGTTTATGGCTCTTGGCCAATACGCAAGTTTCACAATCCAAAGACAAATTACAACTACCAAAAAAGGGAAAAAGACGTTTAAGGTAACCTAGTGATGGATGACCTAAACGTCTATGCCACTTCCATAATTGTTGTGTGGGAGACCTGCGAGCAAGCATAGTATGACCTTTTTGAATCGTCTCATCCATAGTAGTATAGTCACCCTGACCCGCTCAGTACACTCCGGCCAACGCAGCCCAACGAATGCGTCCCCGGTCCGAGCATCCTACACAAGACAACCATTAGAAGTCAAAACCACAGTACAATCAAGTTCCTTGGTTAATTGACTAACAGAAAGCAGTTTATGAGAGAGACTCGGGATCAACAAGCAATTTTTAAGACGAAGGGAGGAGGAAATATCAATAGGACCAGCTTTATCAACGGATACATATTCCCTATTAGCTGTTTGGACATGGGTATAGGAGGTGGGAGTAACGGAGGATATGGTCTTGTGGATCAAAGGTCATAGTGTCCGGTAGCCCCGCAGTCAGAAATCCATTGTGATGTTTTATTTTGACTAAGGAGACAAAAGATGGGATTTTGATTTGGGCTTGTGTGTACACGTGGGCTTGTACAAGGTTTGGGAATATTTAAGTGGGTTTTTTGTTTTTGTGGGAGTAAGGTTAGGTGAGGAGTTGGCTTGGTGTACACGTGGGCTTGTGGGTTTATTTAACTGGGTTTTTTGTTTTTGTGAGAGTAGGGTTAGGTGAGTGGGTTTTGGGGTTTCATTATAAAATGAAGGAAAAGGAAAGTAATTTCTTTCTCCTCCCTCAATAGAGCCGGCTGCACTTTCTCTCTCCTCACCTTCATTTCTTGCTTCTGGTCCATTAATGGAGGTACTCCAATGGTTCCTTTCATACCTGATTTTTCAAGTGAAGATGATGGGATCTCACCGGCTTGATCTACATATGCTAGGTTGGCCTTGCCGCCGGTCCGGTGAGACGGTGCCTTGGTGGCGGCCTTCCTTCTTTGTAGTTCATCCCACCAATCGGGGTAGCCTACTAACTTGAAACACCCTTCCTTAGTGTGCCGCGTACCACCGCAGTGGCTACACCTTAGCTTACGCCGGTCATCTTCTTCACGGTGACGAGGAAGGGGCCTGTTTTGCATGGCTAGACCCGATCCAAGATTTGAGGGCCCTGAGCCCAATGATGATACGCCGGCCATAATTTTCCGGCGAGAAATTTCCCGGCGAATGGTGGCGTAAGCGACCTCCACCGTCGGCAGTGGTTCCATGTTAAGCAAGTCCCTCCTTTCTTTGTCTAAATTTTCATTTATGCCCGTAAGAAATTGATACAATCTTTGCCTTTGAATAAAGCAGTTAAA

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rop14009 commented 8 years ago

Dear Bao, I have been trying to use the aligngraph for assembling scaffolds from SOAPdenovo2 with hg19 human genome as reference. I am getting the same error "BLAT CALL FAILED!". I have BLAT, pBLAT, bowtie and mummer in the installation path. Yet, its giving me the same error. Can you tell me what might be the possible problem?

My syntax is as follows:

$HOME/AlignGraph/AlignGraph/AlignGraph --read1 TCGA-A7-A0CE-10A-01D-A017-09.paired1.fasta --read2 TCGA-A7-A0CE-10A-01D-A017-09.paired2.fasta --contig graph_prefix.scafSeq --genome /N/dc2/projects/radovlab/robin_06-17-2016/TCGA-A7-A0CE-01A-11R-A00Z-07/lincRNA/multo/MULTo1.0/src/hg19genome.fasta --distanceLow 550 --distanceHigh 1550 --extendedContig extendedContigs.fa --remainingContig remainingContigs.fa

rop14009 commented 8 years ago

Can you tell me which version of blat you used when you wrote Aligngraph?

baoe commented 8 years ago

Hi,

It should be a version before v35. Please see FAQ 4 for details.

Best, Bao

From: rop14009 [notifications@github.com] Sent: Sunday, July 24, 2016 12:37 PM To: baoe/AlignGraph Cc: Bao; Comment Subject: Re: [baoe/AlignGraph] BLAT call failed with Aligngraph (#17)

Can you tell me which version of blat you used when you wrote Aligngraph?

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