I am trying to run pizzly with the following chain of commands:
kallisto index -i index.idx -k 31 Homo_sapiens.GRCh37.68.cdna.all.fa.gz
kallisto quant -i index.idx --fusion -o output ../SRR6796292_gz/SRR6796292_1.fastq.gz ../SRR6796292_gz/SRR6796292_2.fastq.gz
pizzly -k 31 --gtf Homo_sapiens.GRCh37.68.gtf --cache index.cache.txt --align-score 2 --insert-size 400 --fasta Homo_sapiens.GRCh37.68.cdna.all.fa.gz --output test output/fusion.txt
The first two steps run fine, but the third fails with the following output:
terminate called after throwing an instance of 'seqan::ParseError'
what(): The key field of an attribute is empty!
Aborted
Any advice on how to debug this would be appreciated! Below is my complete command line output:
`$ kallisto index -i index.idx -k 31 Homo_sapiens.GRCh37.68.cdna.all.fa.gz
[build] loading fasta file Homo_sapiens.GRCh37.68.cdna.all.fa.gz
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 1385 target sequences
[build] counting k-mers ... done.
[build] building target de Bruijn graph ... done
[build] creating equivalence classes ... done
[build] target de Bruijn graph has 1002451 contigs and contains 101485755 k-mers
$
$ kallisto quant -i index.idx --fusion -o output ../SRR6796292_gz/SRR6796292_1.fastq.gz ../SRR6796292_gz/SRR6796292_2.fastq.gz
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 176,927
[index] number of k-mers: 101,485,755
[index] number of equivalence classes: 672,665
[quant] running in paired-end mode
[quant] will process pair 1: ../SRR6796292_gz/SRR6796292_1.fastq.gz
../SRR6796292_gz/SRR6796292_2.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 31,558,619 reads, 24,517,027 reads pseudoaligned
[quant] estimated average fragment length: 171.611
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 1,170 rounds
$ pizzly -k 31 --gtf Homo_sapiens.GRCh37.68.gtf --cache index.cache.txt --align-score 2 --insert-size 400 --fasta Homo_sapiens.GRCh37.68.cdna.all.fa.gz --output test output/fusion.txt
terminate called after throwing an instance of 'seqan::ParseError'
what(): The key field of an attribute is empty!
Aborted`
I am trying to run pizzly with the following chain of commands:
kallisto index -i index.idx -k 31 Homo_sapiens.GRCh37.68.cdna.all.fa.gz
kallisto quant -i index.idx --fusion -o output ../SRR6796292_gz/SRR6796292_1.fastq.gz ../SRR6796292_gz/SRR6796292_2.fastq.gz
pizzly -k 31 --gtf Homo_sapiens.GRCh37.68.gtf --cache index.cache.txt --align-score 2 --insert-size 400 --fasta Homo_sapiens.GRCh37.68.cdna.all.fa.gz --output test output/fusion.txt
The first two steps run fine, but the third fails with the following output:
terminate called after throwing an instance of 'seqan::ParseError'
what(): The key field of an attribute is empty!
Aborted
Any advice on how to debug this would be appreciated! Below is my complete command line output:
`$ kallisto index -i index.idx -k 31 Homo_sapiens.GRCh37.68.cdna.all.fa.gz
[build] loading fasta file Homo_sapiens.GRCh37.68.cdna.all.fa.gz
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 1385 target sequences
[build] counting k-mers ... done.
[build] building target de Bruijn graph ... done
[build] creating equivalence classes ... done
[build] target de Bruijn graph has 1002451 contigs and contains 101485755 k-mers
$
$ kallisto quant -i index.idx --fusion -o output ../SRR6796292_gz/SRR6796292_1.fastq.gz ../SRR6796292_gz/SRR6796292_2.fastq.gz
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 176,927
[index] number of k-mers: 101,485,755
[index] number of equivalence classes: 672,665
[quant] running in paired-end mode
[quant] will process pair 1: ../SRR6796292_gz/SRR6796292_1.fastq.gz
../SRR6796292_gz/SRR6796292_2.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 31,558,619 reads, 24,517,027 reads pseudoaligned
[quant] estimated average fragment length: 171.611
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 1,170 rounds
$ pizzly -k 31 --gtf Homo_sapiens.GRCh37.68.gtf --cache index.cache.txt --align-score 2 --insert-size 400 --fasta Homo_sapiens.GRCh37.68.cdna.all.fa.gz --output test output/fusion.txt
terminate called after throwing an instance of 'seqan::ParseError'
what(): The key field of an attribute is empty!
Aborted`