Open lipikakalson opened 5 months ago
Hi, I have been trying to use ISOWN but facing errors while so.
perl ../bin/database_annotation.pl /home/isilon/patho_anemone-meso/mutect-slurm/D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated/D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered.vcf D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf annotating input file with ANNOVAR ...NOTICE: Output files are written to D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.annovar.vcf.temp.convert2annovar.variant_function, D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.annovar.vcf.temp.convert2annovar.exonic_variant_function NOTICE: Reading gene annotation from ../bin/../external_tools/annovar/humandb_hg38/hg38_refGene.txt ... Done with 88819 transcripts (including 21511 without coding sequence annotation) for 28307 unique genes NOTICE: Processing next batch with 3098593 unique variants in 3098593 input lines NOTICE: Finished analyzing 1000000 query variants NOTICE: Finished analyzing 2000000 query variants NOTICE: Finished analyzing 3000000 query variants NOTICE: Reading FASTA sequences from ../bin/../external_tools/annovar/humandb_hg38/hg38_refGeneMrna.fa ... Done with 25826 sequences WARNING: A total of 606 sequences will be ignored due to lack of correct ORF annotation NOTICE: Variants with invalid input format are written to D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.annovar.vcf.temp.convert2annovar.invalid_input annotating input file with dbSNP ... ../bin/qpipeline tabix -m 2020 -d ../bin/../external_databases/00-All.modified.vcf.gz -A -E -p dbSNP_00-All -i D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.annovar.vcf -f ../bin/../external_databases/hg38_random.fa > D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.dbSNP.vcf Segmentation fault annotating input file with COSMIC ... ../bin/qpipeline tabix -m 2020 -d ../bin/../external_databases/Cosmic.vcf.gz -A -E -p COSMIC_99 -i D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.dbSNP.vcf -f ../bin/../external_databases/hg38_random.fa > D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.cosmic.vcf annotating input file with ExAC ... ../bin/qpipeline tabix -m 2020 -d ../bin/../external_databases/ExAC.r1.sites.vep.vcf.gz -A -E -p ExAC.r1.database -i D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.cosmic.vcf -f ../bin/../external_databases/hg38_random.fa > D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.exac.vcf [my_tabix.c:51] - failed to load tabix index file '../bin/../external_databases/ExAC.r1.sites.vep.vcf.gz' annotating input file with MutationAccessor ... ../bin/qpipeline tabix -m 2020 -d ../bin/../external_databases/MA_scores_rel3_hg38_full.tar.gz -A -E -p MA_scores_rel3_hg38_full -i D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.exac.vcf -f ../bin/../external_databases/hg38_random.fa > D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf.temp.ma.vcf [my_tabix.c:51] - failed to load tabix index file '../bin/../external_databases/MA_scores_rel3_hg38_full.tar.gz' annotating input file with PolyPhen ... annotating input file with sequence context ... calculating flanking region ... final reformatting ... cleanup: deleting temporary files ( D6608-2__D6608-2_S26_230907_A01664_0193_BHG25CDRX3_merged_dedup_BQSRecalibrated_filtered_isown.vcf*.temp.* ) ...
I have tried everything which has been discussed in previous issues so far for "Segmentation fault". Anyone had any success with it?
Thanks, Lipika
Hi, I have been trying to use ISOWN but facing errors while so.
I have tried everything which has been discussed in previous issues so far for "Segmentation fault". Anyone had any success with it?
Thanks, Lipika