brianjohnhaas
commented
8 years ago Hi
It wants a single file, not a set of files. If these all correspond to the same condition, then you'll want to merge them into single files. If they are different conditions, you'll want to run kallisto on each pair separately.
If kallisto has built-in functionality to handle multiple files, please let me know and I'll see if we can support it somehow.
best,
~b
On Mon, Apr 11, 2016 at 7:45 AM, bprabin notifications@github.com wrote:
I tried to run kallisto but get followling error. I need a help
prabinb@biolab:/data/Prabin_trinity/Jonsok_complete_trinity> /data/trinityrnaseq-2.1.1/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz,Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz,Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz --right Jonsok10daysR1CGATGTR2.fastq.P.qtrim.gz,Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz,Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz --est_method kallisto --trinity_mode --prep_reference --output_dir J96KCMD: kallisto quant -i /data/Prabin_trinity/Jonsok_complete_trinity/Trinity.fasta.kallisto_idx -o J96K <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz) <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR2.fastq.P.qtr im.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz)
Error: file not found /dev/fd/63,/dev/fd/62,/dev/fd/61 Error: file not found /dev/fd/60,/dev/fd/59,/dev/fd/58
Usage: kallisto quant [arguments] FASTQ-files
Required arguments: -i, --index=STRING Filename for the kallisto index to be used for quantification -o, --output-dir=STRING Directory to write output to
Optional arguments: --bias Perform sequence based bias correction -b, --bootstrap-samples=INT Number of bootstrap samples (default: 0) --seed=INT Seed for the bootstrap sampling (default: 42) --plaintext Output plaintext instead of HDF5 --single Quantify single-end reads -l, --fragment-length=DOUBLE Estimated average fragment length -s, --sd=DOUBLE Estimated standard deviation of fragment length (default: value is estimated from the input data) -t, --threads=INT Number of threads to use (default: 1) --pseudobam Output pseudoalignments in SAM format to stdout Error, cmd: kallisto quant -i /data/Prabin_trinity/Jonsok_complete_trinity/Trinity.fasta.kallisto_idx -o J96K <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz) <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz) died with ret: 256 at /data/trinityrnaseq-2.1.1/util/ align_and_estimate_abundance.pl line 714.
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
bprabin
I tried to run kallisto but get followling error. I need a help
prabinb@biolab:/data/Prabin_trinity/Jonsok_complete_trinity> /data/trinityrnaseq-2.1.1/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz,Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz,Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz --right Jonsok10daysR1CGATGTR2.fastq.P.qtrim.gz,Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz,Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz --est_method kallisto --trinity_mode --prep_reference --output_dir J96KCMD: kallisto quant -i /data/Prabin_trinity/Jonsok_complete_trinity/Trinity.fasta.kallisto_idx -o J96K <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz) <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz)
Error: file not found /dev/fd/63,/dev/fd/62,/dev/fd/61 Error: file not found /dev/fd/60,/dev/fd/59,/dev/fd/58
Usage: kallisto quant [arguments] FASTQ-files
Required arguments: -i, --index=STRING Filename for the kallisto index to be used for quantification -o, --output-dir=STRING Directory to write output to
Optional arguments: --bias Perform sequence based bias correction -b, --bootstrap-samples=INT Number of bootstrap samples (default: 0) --seed=INT Seed for the bootstrap sampling (default: 42) --plaintext Output plaintext instead of HDF5 --single Quantify single-end reads -l, --fragment-length=DOUBLE Estimated average fragment length -s, --sd=DOUBLE Estimated standard deviation of fragment length (default: value is estimated from the input data) -t, --threads=INT Number of threads to use (default: 1) --pseudobam Output pseudoalignments in SAM format to stdout Error, cmd: kallisto quant -i /data/Prabin_trinity/Jonsok_complete_trinity/Trinity.fasta.kallisto_idx -o J96K <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR1.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR1.fastq.P.qtrim.gz) <(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR1CGATGTR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR2CAGATCR2.fastq.P.qtrim.gz),<(gunzip -c /data/Prabin_trinity/Jonsok_complete_trinity/Jonsok10daysR3GTGAAAR2.fastq.P.qtrim.gz) died with ret: 256 at /data/trinityrnaseq-2.1.1/util/align_and_estimate_abundance.pl line 714.