Hi!
I am experiencing an issue trying to call pseudogenes from long reads data.
The error I get is:
[E::sam_hrecs_update_hashes] Duplicate entry "hg38_yale_pseudogenes_PABPC1P1" in sam header
samtools view: failed to add PG line to the header
samtools sort: failed to read header from "-"
Traceback (most recent call last):
File "/martina/xTea/LR/xTea/xtea_long/l_main.py", line 316, in <module>
lrc.classify_ins_seqs(sf_rep_ins, sf_ref, flk_lenth, sf_rslt)
File "/martina/xTea/LR/xTea/xtea_long/l_rep_classification.py", line 200, in classify_ins_seqs
self.get_unmasked_seqs(sf_rep_ins_tmp, sf_tmp_out, sf_new_tmp)
File "/martina/xTea/LR/xTea/xtea_long/l_rep_classification.py", line 318, in get_unmasked_seqs
with open(sf_slcted) as fin_slcted:
FileNotFoundError: [Errno 2] No such file or directory:
This is what my run_xTEA_pipeline.sh looks like this:
PREFIX=/martina/xTea/LR/sample/
############
############
REF=/martina/data/reference/GRCh38/genome.fa
XTEA_PATH=/martina/xTea/LR/xTea/xtea_long/
BAM_LIST=${PREFIX}"bam_list.txt"
TMP=${PREFIX}"tmp/"
REP_LIB=/martina/xTea/rep_lib_annotation/
SVA_REF_COPY=null
############
############
python ${XTEA_PATH}"l_main.py" -C -b ${BAM_LIST} -r ${REF} -p ${TMP} -o ${PREFIX}"candidate_list_from_clip.txt" -n 8 -w 75
python ${XTEA_PATH}"l_main.py" -A -b ${BAM_LIST} -r ${REF} -p ${TMP} -i ${PREFIX}"candidate_list_from_clip.txt" -o ${PREFIX}"all_ins_seqs.fa" --rep ${REP_LIB} -n 8
python ${XTEA_PATH}"l_main.py" -N -b ${BAM_LIST} -r ${REF} -p ${TMP}"ghost" -o ${PREFIX}"ghost_reads.fa" --rmsk /martina/xTea/rep_lib_annotation/LINE/hg38/hg38_L1_larger_500_with_all_L1HS.out --cns /martina/xTea/rep_lib_annotation/consensus/LINE1.fa --min 4000 -n 8
python ${XTEA_PATH}"l_main.py" -Y -i ${PREFIX}"all_ins_seqs.fa" -r ${REF} -p ${TMP}"classification" --rep ${REP_LIB} -y 80 -o ${PREFIX}"classified_results.txt" -n 8
python ${XTEA_PATH}"l_main.py" --clean -b ${BAM_LIST} -r ${REF} -p ${TMP} -i ${PREFIX}"candidate_list_from_clip.txt" -n 8
I tried using -y 80 to include also another class to see if that could help but the error does not change.
Is there anything I could try to solve this?
Thank you!
Hi!
I am experiencing an issue trying to call pseudogenes from long reads data.
The error I get is:
This is what my run_xTEA_pipeline.sh looks like this:
I tried using
-y 80to include also another class to see if that could help but the error does not change.Is there anything I could try to solve this?
Thank you!