Comments (7)
GuipengLi
commented on July 20, 2024
Hi, are you using short reads data? Try with "-d 1" option for short reads.
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tiagochst
commented on July 20, 2024
Hi,
Thanks it worked! But, now I have a problem in step 5 now.
[04-06 21:27:56] Running Step 5: Detect Interactions ...
extendpeak output/out_peaks.narrowPeak 500 output/out_peaks.slopPeak
Running extendpeak...
bedtools slop -i output/out_peaks.narrowPeak -g hg38.chrom.sizes -b 500 | bedtools merge -d 256 > output/out_peaks.slopPeak
awk 'BEGIN{OFS="\t";i=1}{print $1,$2,$3,"peak_"i;i=i+1}' output/out_peaks.slopPeak > tmp.bed; mv tmp.bed output/out_peaks.slopPeak
peak_depth2 output/out.rmdup.bedpe.tag 100 output/out_peaks.slopPeak output/out.peaks.depth
Running peakdepth...
psort output/out.rmdup.bedpe.tag output/out.rmdup.bedpe.tag.sorted > /dev/null 2>&1
bedtools coverage -sorted -b output/out.rmdup.bedpe.tag.sorted -a output/out_peaks.slopPeak -counts > output/out.peaks.depth
ERROR: Sort order was unspecified, and file output/out.rmdup.bedpe.tag.sorted is not sorted lexicographically.
Please re-reun with the -g option for a genome file.
See documentation for details.
hg38.chrom.sizes is this file: https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes
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GuipengLi
commented on July 20, 2024
This error seems to be caused by psort. Could you check if the file output/out.rmdup.bedpe.tag.sorted is empty or damaged?
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tiagochst
commented on July 20, 2024
It is not empty
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tiagochst
commented on July 20, 2024
The last 3 lines were responsible for the error. If I delete them I can run it bedtools.
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tiagochst
commented on July 20, 2024
I erased those lines manully and continue the pipeline.
But then I got:
[04-07 14:49:12] Running Step 6: QCplots ...
Please check input or Rerun step 6
[04-07 14:49:12] Running Step 7: MICC ...
Rscript /home/tiagochst/bin/ChIA-PET2_0.9.2/bin/MICC2.R output/out.interactions.intra.bedpe output/out.interactions.inter.bedpe output/out.interactions.MICC 2
Loading required package: VGAM
Loading required package: methods
Loading required package: stats4
Loading required package: splines
Running MICC...
Loading intra data...
Loading inter data...
Cacluating...
Error: Don't have enough confident interactions to learn the model.
Please could you help me? I'm not sure if I did something wrong.
My --forward and --reverse files are both fastq in Biological replicate 1 (https://www.encodeproject.org/experiments/ENCSR000CAA/)
For --genome I was using GDC files
For --bedtoolsgenome I used this file
As you said -d is 1 due to the short reads
My final command was:
ChIA-PET2 -g GRCh38.d1.vd1.fa -b hg38.chrom.sizes -f ENCFF000LAF.fastq.gz -r ENCFF000KZT.fastq.gz -d 1 -s 1
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tiagochst
commented on July 20, 2024
I removed the psort and the -sort argument and continue step 5 manually. One of the replicates worked.
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Related Issues (20)
- Unable to start CPT2 HOT 10
- Download ChIA-PET2.tar.gz Url HOT 5
- enough confident interactions to learn the model HOT 3
- stopped at 4th stage HOT 3
- std::bad_alloc error HOT 4
- extend parameter not used? HOT 2
- BWA issue
- error when run MICC.R HOT 8
- bug in trimLinker -h HOT 3
- MayBe error for the main bedpe2Phased HOT 2
- How can we get the significant Interactions? HOT 4
- Runnung Error in Step2,input error HOT 1
- need remove -sorted in the latest version of bedtools
- ERROR: The input file is neither a BAM file nor a SAM file.
- Solution to ld missing -lz during make
- Truncated .tag.sort file error: rmdup.bedpe.tag.sorted has 3 fields, but 6 were expected. HOT 1
- MICC error: there is no package called 'VGAM' HOT 4
- Sam file is not written HOT 2
- bedpe2Interaction core dumped HOT 2
- macs2 callpeaks
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