Comments (13)
EmanuelSoda
commented on June 27, 2024
I also used the docker version but I have the same problem it returns all zeros.
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
hi @EmanuelSoda did you solve this problem or get feedback from the authors?
@mtokuyama
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EmanuelSoda
commented on June 27, 2024
Unfortunately I wasn't able to solve the bug and I had to used another tool
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
Unfortunately I wasn't able to solve the bug and I had to used another tool
could you please share the other tool for ERV?
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EmanuelSoda
commented on June 27, 2024
Is this one
https://github.com/wyang17/SQuIRE
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
thanks for your sharing!
JG
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andreabc
commented on June 27, 2024
if it helps now, I was able to find ERVs (i.e. non-zero output) when I added 'chr' to the chromosome names in the ERVmap.bed file
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
if it helps now, I was able to find ERVs (i.e. non-zero output) when I added 'chr' to the chromosome names in the ERVmap.bed file
hi @andreabc could you please share your code and changed ERVmap.bed file？
I still got errors with docker https://hub.docker.com/r/eipm/ervmap
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andreabc
commented on June 27, 2024
I did awk 'BEGIN{OFS="\t"}$1="chr"$1' ERVmap.old.bed > ERVmap.bed (from https://stackoverflow.com/questions/18061606/add-string-in-each-line-at-the-begining-of-column). I converted the docker image to singularity but had to make sure the actual file was bound - e.g. -B /path/to/ERVmap.bed:/resources/ERVmap.bed
Here's the file I generated with chr prefixes: ERVmap.chr.bed.txt
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
hi @andreabc
this is my nohup output
GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820
200300
--read1
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] CPUs:(12)
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] Limit RAM:(151290751290)
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] Read1:(/home/zhou/raid/EGA/POPLAR/raw/GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820_1.fastq.gz)
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] Read2:(/home/zhou/raid/EGA/POPLAR/raw/GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820_2.fastq.gz)
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] OUT_PREFIX:(GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820)
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] MODE:(ALL)
[Wed Jan 11 13:26:24 CST 2023]: [INFO] -------- START (mode: ALL) ---------
[Wed Jan 11 13:26:24 CST 2023]: [INFO] ---- Alignment ----
[Wed Jan 11 13:26:24 CST 2023]: [DEBUG] total 0
drwxrwxr-x 2 zhou zhou 10 Jan 11 13:25 .
drwxr-xr-x 1 zhou zhou 100 Jan 11 13:26 ..
Jan 11 13:28:35 ..... started mapping
Jan 11 13:40:53 ..... finished mapping
Jan 11 13:40:57 ..... started sorting BAM
Jan 11 13:42:47 ..... finished successfully
[Wed Jan 11 13:42:54 CST 2023]: [INFO] ---- Alignment Complete ----
[Wed Jan 11 13:42:54 CST 2023]: [INFO] ---- Indexing
[Wed Jan 11 13:43:12 CST 2023]: [INFO] ---- Indexing Complete
[Wed Jan 11 13:43:12 CST 2023]: [INFO] ---- Finding ERVs ----
ERROR: chromomsome sort ordering for file /results/GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820Aligned.sortedByCoord.out.bam is inconsistent with other files. Record was:
chr10 47250 47300 HWI:1:X:1:2209:1361:14830/1 255 +
[Wed Jan 11 13:45:17 CST 2023]: [INFO] ---- Finding ERVs complete ----
[Wed Jan 11 13:45:17 CST 2023]: [INFO] -------- END (mode: ALL) ---------
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
mkdir -p ${i}
cd ./${i}
if [ ! -f ${dir}/CircRNA/STAR/${i}/${i}ERVresults.txt ]; then
singularity exec \
--bind ${dir}/raw:/data:ro \
--bind ${index}:/genome:ro \
--bind ${erv_bed}:/resources:ro \
--bind ${dir}/ERV.map/${i}:/results \
/home/zhou/raid/singularity/ervmap.1.2.1.sif /scripts/ERVmapping.sh \
--read1 ${dir}/raw/${i}_1.fastq.gz --read2 ${dir}/raw/${i}_2.fastq.gz \
--output ${i} \
--mode ALL \
--cpus 12 \
--limit-ram 151290751290
I already replaced ERVmap.chr.bed.txt, but
ERROR: chromomsome sort ordering for file /results/GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820Aligned.sortedByCoord.out.bam is inconsistent with other files. Record was:
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jianguozhouzunyimedicaluniversity
commented on June 27, 2024
GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820ERVresults.txt
Hi @andreabc thanks for your support. It's worked, please double-check my output.
Best，
JG
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YimingLiu000
commented on June 27, 2024
Hi!
@jianguozhouzunyimedicaluniversity I faced the same situation as you. Replacing ERVmap.bed didn't solve all the problems. Could you let me know how you solved the following error? Thanks for your help!
ERROR: chromosome sort ordering for file /results/GO28753_ngs_rna_targrna_rnaaccess_EA_f3251ce553_20150820Aligned.sortedByCoord.out.bam is inconsistent with other files.
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Related Issues (11)
- installation / usage instructions HOT 17
- Differential analysis HOT 2
- ERV normalisation questions
- Question about ERV family in ERVmap.bed file
- How was ERVmap.bed generated? HOT 1
- out of order record
- results fileter HOT 5
- Failed to run the jobs
- btrim - the requested version (0.3.0) is not available any more HOT 6
- /usr/bin/python2.7 htseq.script.count not found HOT 1
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