error while running QuEST_2.4

[Theodore Georgomanolis]

First of all, sorry if this is a double post. But I cannot found anywhere my previous one.

I'm running the following command and I get the following errors:


The following fasta files were found in your reference path:

genome.fa

Evaluating the size of the genome. This may take several minutes.

Found the following contigs:

chr1: 247249719 bps
chr2: 490200868 bps
chr3: 689702695 bps
chr4: 880975758 bps
chr5: 1061833624 bps
chr6: 1232733616 bps
chr7: 1391555040 bps
chr8: 1537829866 bps
chr9: 1678103118 bps
chr10: 1813477855 bps
chr11: 1947930239 bps
chr12: 2080279773 bps
chr13: 2194422753 bps
chr14: 2300791338 bps
chr15: 2401130253 bps
chr16: 2489957507 bps
chr17: 2568732249 bps
chr18: 2644849402 bps
chr19: 2708661053 bps
chr20: 2771097017 bps
chr21: 2818041340 bps
chr22: 2867732772 bps
chrX: 3022646526 bps
chrY: 3080419480 bps
chrM: 3080436051 bps

Your genome looks fine and does not appear to contain any
duplicated chromosome entries.

Estimated size of the genome is 50000789.9 Kb ( 50.00 Gbps ).

Converting ChIP reads file into the QuEST format.
If the counter below stays at zero, the program can't
match the ChIP alignments to the reference genome that you provided.
In this case check that the sequences you have provided match the formats
accepted by QuEST (see README.txt) and that names of contigs in the alignment
files are *exactly* the same as in your genome or genome table.

Warning:
couldn't parse the parameter: ChIP-seq
skipping
Warning:
couldn't parse the parameter: [CCC-113]/Sample_665_LIB3776_LDI3264/2-3_0min_LIB3776.fastq
skipping
Warning:
couldn't parse the parameter: ChIP-seq
skipping
Warning:
couldn't parse the parameter: [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//data/ChIP_uncollapsed.QuEST
skipping
Warning:
couldn't parse the parameter: ChIP-seq
skipping
Warning:
couldn't parse the parameter: [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//parameters/genome_table
skipping
Warning:
couldn't parse the parameter: ChIP-seq
skipping
Warning:
couldn't parse the parameter: [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//data/ChIP_read_num_uncollapsed.txt
skipping
Warning:
couldn't parse the parameter: ChIP-seq
skipping
Warning:
couldn't parse the parameter: [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//module_outputs/align_2_QuEST_ChIP.report.txt
skipping
Could not understand param:


Error during the execution of /home/trotos/Desktop/QuEST_2.4/align_2_QuEST align_file=/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264//2-3_0min_LIB3776.fastq output_file=/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//data/ChIP_uncollapsed.QuEST genome_table=/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//parameters/genome_table align_type=solexa_align report_file=/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//data/ChIP_read_num_uncollapsed.txt error_report_file=/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/Quest//module_outputs/align_2_QuEST_ChIP.report.txt. Error code: 256.

I'm using the following command:

./generate_QuEST_parameters.pl -solexa_align_ChIP '/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/2-3_0min_LIB3776.fastq' -solexa_align_RX_noIP '/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3774_LDI3262/Input_LIB3774.fastq' -rp '/media/trotos/4TB/WORK/UCSC/hg18/Sequence/hg18_reference/' -ap '/media/trotos/4TB/WORK/archive/ChIP-seq [CCC-113]/Sample_665_LIB3776_LDI3264/Quest/'

Any feddback is appreciated

[Anton]

Hi Theodore,

you probably should not be using -solexa_align unless its one of the very early ChIP-Seq datasets generated in 2006-2007.

I also noticed that you tried to use fastq file. You need to first align it to the reference genome (e.g. with BWA or novoalign), since fastq files contain sequence reads and not alignments to the reference genome.

Best, Anton 

[Theodore Georgomanolis]

Hi Anton,

Thank you for your answer, from the manual I thought that it was sufficient to provide it with fastq files... well I should have thought that those should first be aligned.
Also, I've somewhat doublepost, so I'll continue to the newer one as I now by using sam files I got the same problems.

Theodore

[Anton]

See my response to another thread.