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FenyoLab / L1EM

Estimate locus specific human LINE-1 expression.
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[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.al.aln.bam' #9

Open Biojenifer opened 2 years ago

Biojenifer commented 2 years ago

Hi!

After running the following command, according to the wiki:

bash -e run_L1EM_unstranded.sh /fullpathto/sampleA.bam /fullpathto/L1EM /fullpathto/hg38.fa

I get these errors:

[main] CMD: /opt/software/Compiler/gcccore/system/bwa/0.7.17/bin/bwa sampe -n 10000000 -N 10000000 /mnt/netapp2/conda_python_envs/py_envs/L1EM//annotation/L1EM.400.fa L1.ab.R1.aln.sai L1.ab.R2.aln.sai L1.fq1.ab L1.fq2.ab
[main] Real time: 17.741 sec; CPU: 9.017 sec
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.af.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.aj.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ab.aln.bam'
[E::idx_find_and_load] [E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.am.aln.bam'Could not retrieve index file for '../split_fqs/../split_fqs/L1.ap.a
ln.bam'

[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ak.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.an.aln.bam'
[E::idx_find_and_load] [E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ai.aln.bam'Could not retrieve index file for '../split_fqs/../split_fqs/L1.ad.a
ln.bam'

[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ao.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ac.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ae.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.aa.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ag.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.ah.aln.bam'
[E::idx_find_and_load] Could not retrieve index file for '../split_fqs/../split_fqs/L1.al.aln.bam'

This is the content of split_fqs directory:

L1.aa.aln.bam     L1.ac.R1.aln.sai  L1.ae.R2.aln.sai  L1.ah.aln.bam     L1.aj.R1.aln.sai  L1.al.R2.aln.sai  L1.ao.aln.bam     L1.fq1.ab  L1.fq1.ai  L1.fq1.ap  L1.fq2.ag  L1.fq2.an
L1.aa.R1.aln.sai  L1.ac.R2.aln.sai  L1.af.aln.bam     L1.ah.R1.aln.sai  L1.aj.R2.aln.sai  L1.am.aln.bam     L1.ao.R1.aln.sai  L1.fq1.ac  L1.fq1.aj  L1.fq2.aa  L1.fq2.ah  L1.fq2.ao
L1.aa.R2.aln.sai  L1.ad.aln.bam     L1.af.R1.aln.sai  L1.ah.R2.aln.sai  L1.ak.aln.bam     L1.am.R1.aln.sai  L1.ao.R2.aln.sai  L1.fq1.ad  L1.fq1.ak  L1.fq2.ab  L1.fq2.ai  L1.fq2.ap
L1.ab.aln.bam     L1.ad.R1.aln.sai  L1.af.R2.aln.sai  L1.ai.aln.bam     L1.ak.R1.aln.sai  L1.am.R2.aln.sai  L1.ap.aln.bam     L1.fq1.ae  L1.fq1.al  L1.fq2.ac  L1.fq2.aj
L1.ab.R1.aln.sai  L1.ad.R2.aln.sai  L1.ag.aln.bam     L1.ai.R1.aln.sai  L1.ak.R2.aln.sai  L1.an.aln.bam     L1.ap.R1.aln.sai  L1.fq1.af  L1.fq1.am  L1.fq2.ad  L1.fq2.ak
L1.ab.R2.aln.sai  L1.ae.aln.bam     L1.ag.R1.aln.sai  L1.ai.R2.aln.sai  L1.al.aln.bam     L1.an.R1.aln.sai  L1.ap.R2.aln.sai  L1.fq1.ag  L1.fq1.an  L1.fq2.ae  L1.fq2.al
L1.ac.aln.bam     L1.ae.R1.aln.sai  L1.ag.R2.aln.sai  L1.aj.aln.bam     L1.al.R1.aln.sai  L1.an.R2.aln.sai  L1.fq1.aa         L1.fq1.ah  L1.fq1.ao  L1.fq2.af  L1.fq2.am

As you can see, there are no indexes for *.aln.bam files. Do you know how can I solve this? Thanks!