I'm struggling with getting the PAGIT toolkit to run correctly. I know it's a relatively common pipeline so I'm hoping someone here has encountered similar issues and worked them out.
First, I'm consistently running into issues with ICORN. With no meddling, it appears to pass the example test except that the results it reports are actually 0 (The output of out.icorn.txt is below). Even the "best" outcome I've been able to piece together has resulted in segmentation faults.
Transforming the read of PAGIT_test_2.fastq Transform the two fastq file to the correct fileformat for SSAHA-pileup ICORN will do iteration 1 of 2 Doing iteration 1. Please wait... $PAGIT_HOME/ICORN//pileup.NoPile.csh -rtype solexa -insertSizeRange 100,700 ../PAGIT_test.mate.fastq Res.image.fa.1 PAGIT_test perl $PAGIT_HOME/ICORN//icorn.Correct.pl ../Res.image.fa.1 PAGIT_test.snp PAGIT_test.del PAGIT_test.ins PAGIT_test.fastq ../Res.image.fa.2 1 ../PAGIT_test.SNPomatic.fastq 76 350 ../small.fastq 76 350 ../Res.image.fa.1.shift.txt 3 1 60 version is 3 Readpair = 1 Reading all chromosomes from ../Res.image.fa.1 ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../PAGIT_test.SNPomatic.fastq ... scanned 22500 solexa reads, 8721 (38.76%) matched , 8750 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.1 ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../small.fastq ... scanned 1 solexa reads, 1 (100.00%) matched , 1 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.2.tmp ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../PAGIT_test.SNPomatic.fastq ... scanned 22500 solexa reads, 8721 (38.76%) matched , 8750 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.2.tmp ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../small.fastq ... scanned 1 solexa reads, 1 (100.00%) matched , 1 total matches, 0 skipped. gzip: PAGIT_test.cigar: No such file or directory ICORN will do iteration 2 of 2 Doing iteration 2. Please wait... perl $PAGIT_HOME/ICORN//icorn.Correct.pl ../Res.image.fa.2 PAGIT_test.snp PAGIT_test.del PAGIT_test.ins PAGIT_test.fastq ../Res.image.fa.3 1 ../PAGIT_test.SNPomatic.fastq 76 350 ../small.fastq 76 350 ../Res.image.fa.2.shift.txt 3 2 60 version is 3 Readpair = 1 Reading all chromosomes from ../Res.image.fa.2 ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../PAGIT_test.SNPomatic.fastq ... scanned 22500 solexa reads, 8721 (38.76%) matched , 8750 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.2 ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../small.fastq ... scanned 1 solexa reads, 1 (100.00%) matched , 1 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.3.tmp ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../PAGIT_test.SNPomatic.fastq ... scanned 22500 solexa reads, 8721 (38.76%) matched , 8750 total matches, 0 skipped. Reading all chromosomes from ../Res.image.fa.3.tmp ... read 1 chromosomes. Indexing 1 chromosomes ... sorting ... done. Reading solexa pair data from ../small.fastq ... scanned 1 solexa reads, 1 (100.00%) matched , 1 total matches, 0 skipped. Found old shift fiel file! save new gzip: PAGIT_test.cigar: No such file or directory cat: *.ordered_selected.gff: No such file or directory Use of uninitialized value in subtraction (-) at $PAGIT_HOME/ICORN//icorn.prettyResult.pl line 45, <f> line 3. Argument "genome Size" isn't numeric in subtraction (-) at $PAGIT_HOME/ICORN//icorn.prettyResult.pl line 45, <f> line 3.
Results of ICORN: ICORN ran 2 on the genome file Res.image.fa. Correction of 1base pair substitutions errors 0 Correction of 1-3base pair insertion errors 0 Correction of 1-3base pair deletion errors 0 Amount of heterozygous sites in the last iteration 0 Rejected 1 bp corrections in the last iteration 0 Rejected 1-3bp insertions in the last iteration 0 Rejected 1-3bp deletions in the last iteration 0 Correction per iteration Iteration 1bp substition insertion deletion 1 0 0 0 2 0 0 0
% of genome that has at least 10x coverage of uniquely mapping reads %GeC >= 10x % of genome that has at least 20x coverage of uniquely mapping reads
% of genome that has at least 5x coverage perfect mapping reads (does map into repeats) 93.0144
% of read pairs mapped in last iteration 0 % of read pairs mapped uniquely in last iteration 0 The size of the genome changed (in bp) 0 Increase of reads mapped between the first and last iteration 0
However, after some meddling these seem to be primarily the outcome of an error in statistics fetching, as the actual output does exist.
When I run the program with my own files, however, the necessary fasta files are not even created, because SNPomatic runs in a segmentation fault.
