Lachesis failed at the step of LoadDenovoCLMSFromSAMs.

[shendurelab]

Lachesis failed at the step of LoadDenovoCLMSFromSAMs.

[tangerzhang]

Hi,
Have you solved this problem? I have the same issue when using LACHESIS. I am wondering how to solved this problem. Could you please provide any clue about this?
Thanks!

[lamz138138]

Hi,

I remembered the problem was result from un-sorted bam. Maybe it is a problem of SortSam.jar in picard (so I change it to SortSame). Or you had to sort the bam before the step of "samtools flagstat" (I had a new file called *consistent.bam). It's a long time since I solve this problem and I couldn't get the files. So I would give the relate code that was used to revised the file of PreprocessSAMs.pl blow, Hope it would help.

By the way, you could sorted bam file before "samtools flagstat", then continue the following process if it failed without repeat the previously steps.

export reSite="AAGCTT"
export bedtoolsPath="/tools/bedtools2-2.20.1/bin/bedtools"
export samtoolsPath="/tools/samtools-0.1.19/samtools"
export picardPath="/tools/picard/picard.jar"
export memSize="64G"
export filterInconsistentPath="/tools/NGS/bin/filterInconsistentPairReads.pl"
sed -i "/^my \$RE_site/s#'.*'#'$reSite'#; \
    /^my \$make_bed_around_RE_site_pl/s#'.*'#'$outputDir/preprocessSAMs/make_bed_around_RE_site.pl'#; \
    /^my \$bedtools/s#'.*'#'$bedtoolsPath'#; \
    /^my \$samtools/s#'.*'#'$samtoolsPath'#; \
    /^#my \$mem/s#\".*\"#\"$memSize\"#;/^#my \$mem/s/#//; 
    /^#my \$picard_head/s#\/.*\/#$picardPath#;/^#my \$picard_head/s/#//;
    /#run_cmd( \"\${picard_head}SortSam.jar/s/SortSam.jar/ SortSam/;
    /#run_cmd( \"\${picard_head} SortSam/s/^#//;
    /#run_cmd( \"\${picard_head}MarkDuplicates.jar/s/MarkDuplicates.jar/ MarkDuplicates/;
    /#run_cmd( \"\${picard_head} MarkDuplicates/s/^#//;
    /run_cmd( \"\${picard_head} MarkDuplicates/s#true\"#true READ_NAME_REGEX=null TMP_DIR=$outputDir/preprocessSAMs/temp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000\"#;
    /^my $nodups/s#\"\"#\".nodups\"#;
    /run_cmd( \"\$samtools view -F12/a run_cmd( \"\$filterInconsistentPath \$head.REduced\$nodups.paired_only.bam | \$samtools view -bS - -o \$head.consistent.bam\" );
    /run_cmd( \"\$samtools flagstat/s#\$head.REduced.*flagstat#\$head.consistent.bam > \$head.consistent.flagstat#;
    /^\/\//s#^//#\#//#" PreprocessSAMs.pl
 sed -i "/^my \$samtools/a my \$filterInconsistentPath = '$filterInconsistentPath';" PreprocessSAMs.pl
 sed -i "/^\/\//s#^//#\#//#" make_bed_around_RE_site.pl

[tangerzhang]

Hi, Thanks for your message.
I will try to solve this problem with your script :-)

[Epigenetics-Wang]

Hi,

I remembered the problem was result from un-sorted bam. Maybe it is a problem of SortSam.jar in picard (so I change it to SortSame). Or you had to sort the bam before the step of "samtools flagstat" (I had a new file called *consistent.bam). It's a long time since I solve this problem and I couldn't get the files. So I would give the relate code that was used to revised the file of PreprocessSAMs.pl blow, Hope it would help.

By the way, you could sorted bam file before "samtools flagstat", then continue the following process if it failed without repeat the previously steps.

export reSite="AAGCTT"
export bedtoolsPath="/tools/bedtools2-2.20.1/bin/bedtools"
export samtoolsPath="/tools/samtools-0.1.19/samtools"
export picardPath="/tools/picard/picard.jar"
export memSize="64G"
export filterInconsistentPath="/tools/NGS/bin/filterInconsistentPairReads.pl"
sed -i "/^my \$RE_site/s#'.*'#'$reSite'#; \
    /^my \$make_bed_around_RE_site_pl/s#'.*'#'$outputDir/preprocessSAMs/make_bed_around_RE_site.pl'#; \
    /^my \$bedtools/s#'.*'#'$bedtoolsPath'#; \
    /^my \$samtools/s#'.*'#'$samtoolsPath'#; \
    /^#my \$mem/s#\".*\"#\"$memSize\"#;/^#my \$mem/s/#//; 
    /^#my \$picard_head/s#\/.*\/#$picardPath#;/^#my \$picard_head/s/#//;
    /#run_cmd( \"\${picard_head}SortSam.jar/s/SortSam.jar/ SortSam/;
    /#run_cmd( \"\${picard_head} SortSam/s/^#//;
    /#run_cmd( \"\${picard_head}MarkDuplicates.jar/s/MarkDuplicates.jar/ MarkDuplicates/;
    /#run_cmd( \"\${picard_head} MarkDuplicates/s/^#//;
    /run_cmd( \"\${picard_head} MarkDuplicates/s#true\"#true READ_NAME_REGEX=null TMP_DIR=$outputDir/preprocessSAMs/temp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000\"#;
    /^my $nodups/s#\"\"#\".nodups\"#;
    /run_cmd( \"\$samtools view -F12/a run_cmd( \"\$filterInconsistentPath \$head.REduced\$nodups.paired_only.bam | \$samtools view -bS - -o \$head.consistent.bam\" );
    /run_cmd( \"\$samtools flagstat/s#\$head.REduced.*flagstat#\$head.consistent.bam > \$head.consistent.flagstat#;
    /^\/\//s#^//#\#//#" PreprocessSAMs.pl
 sed -i "/^my \$samtools/a my \$filterInconsistentPath = '$filterInconsistentPath';" PreprocessSAMs.pl
 sed -i "/^\/\//s#^//#\#//#" make_bed_around_RE_site.pl

Hi,@lamz138138,
I got the same problem, and i try to sovle the problem by using your code. I have a question about where can i get the script of filterInconsistentPairReads.pl? Is this problem caused by not sorting the sam file ? I am wondering how to solved this problem. Could you please provide any clue about this?
Thanks!

[lamz138138]

@Epigenetics-Wang Hi, I remember it was caused by failing to sort the bam, that is the output bam isn't sorted by name as expected. And I think filterInconsistentPairReads.pl is my script, but I forget what is used for (it's a pity I can't find this scripts now).

I had solved this problem by running the PrepocessSAMs.pl step by step, then figure out whether bam is sorted by name. Then if it still failed to work, try to find read that make "c2.tid == c1.mtid" is false (read name is different which may result from failing to sort bam), then write filterInconsistentPairReads.pl.

Hope this useful.

[Epigenetics-Wang]

@Epigenetics-Wang Hi, I remember it was caused by failing to sort the bam, that is the output bam isn't sorted by name as expected. And I think filterInconsistentPairReads.pl is my script, but I forget what is used for (it's a pity I can't find this scripts now).

I had solved this problem by running the PrepocessSAMs.pl step by step, then figure out whether bam is sorted by name. Then if it still failed to work, try to find read that make "c2.tid == c1.mtid" is false (read name is different which may result from failing to sort bam), then write filterInconsistentPairReads.pl.

Hope this useful.

Hi,@lamz138138,
Thanks for your message.
I will try to solve this problem with your advice :-)