ERVresults.txt didn't detect any ERVmap

[JianGuoZhou3]

Hi @mtokuyama I didn't detect any ERVmap.
I used docker https://hub.docker.com/r/eipm/ervmap

 singularity exec \
    --bind ${dir}/raw:/data:ro \
    --bind ${index}:/genome:ro \
    --bind ${erv_bed}:/resources:ro \
    --bind ${dir}/ERV.map/results/${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} -m ALL \
    --cpus 12 --limit-ram 151290751290 -d

But those two samples didn't detect any ERV.

SRR3083781Log.final.out.txt
SRR3083781ERVresults.txt
SRR10899987Log.final.out.txt
SRR10899987ERVresults.txt
Could you please help me to check this issue?
Best,
JG

[EmanuelSoda]

I also used the docker version but I have the same problem it returns all zeros.

[JianGuoZhou3]

hi @EmanuelSoda did you solve this problem or get feedback from the authors?
@mtokuyama

[EmanuelSoda]

Unfortunately I wasn't able to solve the bug and I had to used another tool

[JianGuoZhou3]

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?

[EmanuelSoda]

Is this one

https://github.com/wyang17/SQuIRE

[JianGuoZhou3]

https://github.com/wyang17/SQuIRE

thanks for your sharing!
JG

[andreabc]

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

[JianGuoZhou3]

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

[andreabc]

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

[JianGuoZhou3]

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) ---------

[JianGuoZhou3]

    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:

[JianGuoZhou3]

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

[YimingLiu000]

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.