pseudogenes insertion from pacbio bam

[AhmedArslan]

Hi,
I am facing a problem in identifying "pseudogenes" insertion from pacbio reads; I am using the following command:

python3 xTea/bin/xtea_long -i sample_id -b bam -r GRCh38_latest_genomic.primary.fa -g GRCh38_latest_genomic.gff --xtea=tools/xTea/xtea_long -o exons -y 64 --rep=tools/xTea/

sh run_xTEA_pipeline.sh

And I am getting the following error:

Running command: minimap2 -k11 -w5 --sr --frag=yes -A2 -B4 -O4,8 -E2,1 -r150 -p.5 -N5 -n1 -m20 -s30 -g200 -2K50m --MD --heap-sort=yes --secondary=no --cs -a -t 10 tools/xTea/consensus_mask_lrd/Psudogene.fa ./all_ins_seqs.fa.after_polyA_round.fa | samtools view -hSb - | samtools sort -o ./tmp/classification/Psudogene_cns.bam -

Running command: samtools index ./tmp/classification/Psudogene_cns.bam

Traceback (most recent call last):
File "tools/xTea/xtea_long/l_main.py", line 311, in
lrc.classify_ins_seqs(sf_rep_ins, sf_ref, flk_lenth, sf_rslt)
File "tools/xTea/xtea_long/l_rep_classification.py", line 175, in classify_ins_seqs
self.get_unmasked_seqs(sf_rep_ins_tmp, sf_tmp_out, sf_new_tmp)
File "ools/xTea/xtea_long/l_rep_classification.py", line 288, in get_unmasked_seqs
with open(sf_slcted) as fin_slcted:
FileNotFoundError: [Errno 2] No such file or directory: ''

Feedback is appreciated.
Thanks.