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Xinglab / isoCirc

isoCirc
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Issues of not generating correct file by using isoCirc #8

Closed taffy-miao closed 2 years ago

taffy-miao commented 2 years ago

I’m using the isoCirc from your lab, it worked on your test data. But when I download your data from ebi (https://www.ebi.ac.uk/ena/browser/view/PRJNA594380?show=reads) and using isoCirc by the following command (I downloaded the data and put it straight into the pipeline without other steps):

ref=/home/fengyige/data/star/hg19/hg19.fa

gtf=/home/fengyige/data/star/hg19/gencode.v21.annotation.gtf

circ=/home/fengyige/data/circRNA/hsa_hg19_circRNA.bed

input=/home/fengyige/20220826_circrna/fastq/SRR10612056_1.fastq.gz

isocirc -t 20 ${input} ${ref} ${gtf} ${circ} ../SRR10612056/

It did generate isocirc.bed and isocirc.out, but it didn't generate isocirc_stats.out. And the *out file only contains the header line. I wonder if the data downloaded from ebi need some pre-processing? Or I just miss some critical steps？

Thanks for your help!

yangao07 commented 2 years ago

Can you paste all the output information when running isocirc?

taffy-miao commented 2 years ago

I ran it twice, this is the log message for the first time, the second time ended accidentally:

[M::mm_idx_gen::84.4691.92] collected minimizers [M::mm_idx_gen::97.1702.66] sorted minimizers [M::main::97.1702.66] loaded/built the index for 24 target sequence(s) [M::mm_mapopt_update::101.6712.58] mid_occ = 654 [M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 24 [M::mm_idx_stat::103.6012.55] distinct minimizers: 166959269 (35.52% are singletons); average occurrences: 5.868; average spacing: 3.160; total length: 3095677412 [M::worker_pipeline::1586.3857.65] mapped 1218705 sequences [M::worker_pipeline::3042.4877.82] mapped 1215707 sequences [M::worker_pipeline::4495.8677.88] mapped 1213095 sequences [M::worker_pipeline::5802.347*7.88] mapped 1099061 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -ax splice -ub --MD --eqx -t 8 /home/fengyige/data/star/hg19/hg19.fa ./SRR10612050//cons.fa [M::main] Real time: 5802.786 sec; CPU: 45743.837 sec; Peak RSS: 22.140 GB == 17:02:13-Sep-12-2022 == [check_dependencies] Checking dependencies ... == 17:02:13-Sep-12-2022 == [check_dependencies] Checking dependencies done! == 17:02:13-Sep-12-2022 == [Tandem-Repeats-Finder] Finding tandem repeats with TRF ... == 17:02:13-Sep-12-2022 == [fxtools] fxtools qa ../fastq/SRR10612050_1.fastq.gz > ./SRR10612050//long_reads.fa 2> /dev/null == 17:07:36-Sep-12-2022 == [fxtools] fxtools sx ./SRR10612050//long_reads.fa 8 /home/fengyige/20220826_circrna/iso_out/SRR10612050/ == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.1 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.1; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.1 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.2 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.2; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.2 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.3 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.3; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.3 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.4 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.4; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.4 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.5 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.5; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.5 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.6 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.6; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.6 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.7 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.7; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.7 == 17:08:10-Sep-12-2022 == [Tandem Repeats Finder] trf409.legacylinux64 /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.8 2 7 7 80 10 100 2000 -h -ngs > ./SRR10612050//trf.out.8; rm /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.8 == 10:53:51-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.1 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.1 == 10:54:08-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.2 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.2 == 10:54:29-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.3 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.3 == 10:54:51-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.4 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.4 == 10:55:10-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.5 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.5 == 10:55:28-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.6 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.6 == 10:55:52-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.7 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.7 == 10:56:14-Sep-13-2022 == [Tandem Repeats Finder] cat ./SRR10612050//trf.out.8 >> ./SRR10612050//trf.out; rm ./SRR10612050//trf.out.8 == 10:56:35-Sep-13-2022 == [fxtools] fxtools lp ./SRR10612050//long_reads.fa > /home/fengyige/20220826_circrna/iso_out/SRR10612050/long_reads.fa.len 2> /dev/null == 11:27:17-Sep-13-2022 == [Tandem-Repeats-Finder] Finding tandem repeats with TRF done! == 11:27:17-Sep-13-2022 == [Mapping] Mapping consensus sequence to genome ... == 11:27:17-Sep-13-2022 == [Mapping] minimap2 -ax splice -ub --MD --eqx /home/fengyige/data/star/hg19/hg19.fa ./SRR10612050//cons.fa -t 8 > ./SRR10612050//cons.fa.sam == 13:04:01-Sep-13-2022 == [Mapping] Mapping consensus sequence to genome done! == 13:04:01-Sep-13-2022 == [Classifying] Classifying consensus alignment ... == 13:04:01-Sep-13-2022 == [classify_bam_core] Processing ./SRR10612050//cons.fa.sam ... == 13:04:06-Sep-13-2022 == [classify_bam_core] 100000 BAM records done ... == 13:04:10-Sep-13-2022 == [classify_bam_core] 200000 BAM records done ... == 13:04:14-Sep-13-2022 == [classify_bam_core] 300000 BAM records done ... == 13:04:19-Sep-13-2022 == [classify_bam_core] 400000 BAM records done ... == 13:04:23-Sep-13-2022 == [classify_bam_core] 500000 BAM records done ... == 13:04:27-Sep-13-2022 == [classify_bam_core] 600000 BAM records done ... == 13:04:31-Sep-13-2022 == [classify_bam_core] 700000 BAM records done ... == 13:04:35-Sep-13-2022 == [classify_bam_core] 800000 BAM records done ... == 13:04:39-Sep-13-2022 == [classify_bam_core] 900000 BAM records done ... == 13:04:44-Sep-13-2022 == [classify_bam_core] 1000000 BAM records done ... == 13:04:48-Sep-13-2022 == [classify_bam_core] 1100000 BAM records done ... == 13:04:53-Sep-13-2022 == [classify_bam_core] 1200000 BAM records done ... == 13:04:57-Sep-13-2022 == [classify_bam_core] 1300000 BAM records done ... == 13:05:01-Sep-13-2022 == [classify_bam_core] 1400000 BAM records done ... == 13:05:05-Sep-13-2022 == [classify_bam_core] 1500000 BAM records done ... == 13:05:10-Sep-13-2022 == [classify_bam_core] 1600000 BAM records done ... == 13:05:14-Sep-13-2022 == [classify_bam_core] 1700000 BAM records done ... == 13:05:18-Sep-13-2022 == [classify_bam_core] 1800000 BAM records done ... == 13:05:23-Sep-13-2022 == [classify_bam_core] 1900000 BAM records done ... == 13:05:27-Sep-13-2022 == [classify_bam_core] 2000000 BAM records done ... == 13:05:31-Sep-13-2022 == [classify_bam_core] 2100000 BAM records done ... == 13:05:36-Sep-13-2022 == [classify_bam_core] 2200000 BAM records done ... == 13:05:40-Sep-13-2022 == [classify_bam_core] 2300000 BAM records done ... == 13:05:44-Sep-13-2022 == [classify_bam_core] 2400000 BAM records done ... == 13:05:48-Sep-13-2022 == [classify_bam_core] 2500000 BAM records done ... == 13:05:53-Sep-13-2022 == [classify_bam_core] 2600000 BAM records done ... == 13:05:57-Sep-13-2022 == [classify_bam_core] 2700000 BAM records done ... == 13:06:01-Sep-13-2022 == [classify_bam_core] 2800000 BAM records done ... == 13:06:06-Sep-13-2022 == [classify_bam_core] 2900000 BAM records done ... == 13:06:10-Sep-13-2022 == [classify_bam_core] 3000000 BAM records done ... == 13:06:14-Sep-13-2022 == [classify_bam_core] 3100000 BAM records done ... == 13:06:19-Sep-13-2022 == [classify_bam_core] 3200000 BAM records done ... == 13:06:23-Sep-13-2022 == [classify_bam_core] 3300000 BAM records done ... == 13:06:27-Sep-13-2022 == [classify_bam_core] 3400000 BAM records done ... == 13:06:31-Sep-13-2022 == [classify_bam_core] 3500000 BAM records done ... == 13:06:35-Sep-13-2022 == [classify_bam_core] 3600000 BAM records done ... == 13:06:40-Sep-13-2022 == [classify_bam_core] 3700000 BAM records done ... == 13:06:44-Sep-13-2022 == [classify_bam_core] 3800000 BAM records done ... == 13:06:48-Sep-13-2022 == [classify_bam_core] 3900000 BAM records done ... == 13:06:52-Sep-13-2022 == [classify_bam_core] 4000000 BAM records done ... == 13:06:56-Sep-13-2022 == [classify_bam_core] 4100000 BAM records done ... == 13:07:01-Sep-13-2022 == [classify_bam_core] 4200000 BAM records done ... == 13:07:05-Sep-13-2022 == [classify_bam_core] 4300000 BAM records done ... == 13:07:09-Sep-13-2022 == [classify_bam_core] 4400000 BAM records done ... == 13:07:13-Sep-13-2022 == [classify_bam_core] 4500000 BAM records done ... == 13:07:17-Sep-13-2022 == [classify_bam_core] 4600000 BAM records done ... == 13:07:21-Sep-13-2022 == [classify_bam_core] 4700000 BAM records done ... == 13:07:26-Sep-13-2022 == [classify_bam_core] 4800000 BAM records done ... == 13:07:30-Sep-13-2022 == [classify_bam_core] 4900000 BAM records done ... [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//high.bam' [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//high.bam' [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//high.bam' [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//high.bam' [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//high.bam' [E::idx_find_and_load] Could not retrieve index file for './SRR10612050//low.bam' == 13:07:34-Sep-13-2022 == [classify_bam_core] 5000000 BAM records done ... == 13:07:38-Sep-13-2022 == [classify_bam_core] 5100000 BAM records done ... == 13:07:42-Sep-13-2022 == [classify_bam_core] 5200000 BAM records done ... == 13:07:46-Sep-13-2022 == [classify_bam_core] 5300000 BAM records done ... == 13:07:51-Sep-13-2022 == [classify_bam_core] 5400000 BAM records done ... == 13:07:55-Sep-13-2022 == [classify_bam_core] 5500000 BAM records done ... == 13:07:59-Sep-13-2022 == [classify_bam_core] 5600000 BAM records done ... == 13:08:03-Sep-13-2022 == [classify_bam_core] 5700000 BAM records done ... == 13:08:07-Sep-13-2022 == [classify_bam_core] 5800000 BAM records done ... == 13:08:12-Sep-13-2022 == [classify_bam_core] 5900000 BAM records done ... == 13:08:16-Sep-13-2022 == [classify_bam_core] 6000000 BAM records done ... == 13:08:20-Sep-13-2022 == [classify_bam_core] 6100000 BAM records done ... == 13:08:24-Sep-13-2022 == [classify_bam_core] 6200000 BAM records done ... == 13:08:28-Sep-13-2022 == [classify_bam_core] 6300000 BAM records done ... == 13:08:33-Sep-13-2022 == [classify_bam_core] 6400000 BAM records done ... == 13:08:37-Sep-13-2022 == [classify_bam_core] 6500000 BAM records done ... == 13:08:42-Sep-13-2022 == [classify_bam_core] 6600000 BAM records done ... == 13:08:46-Sep-13-2022 == [classify_bam_core] 6700000 BAM records done ... == 13:08:50-Sep-13-2022 == [classify_bam_core] 6800000 BAM records done ... == 13:08:54-Sep-13-2022 == [classify_bam_core] 6900000 BAM records done ... == 13:08:59-Sep-13-2022 == [classify_bam_core] 7000000 BAM records done ... == 13:09:03-Sep-13-2022 == [classify_bam_core] 7100000 BAM records done ... == 13:09:07-Sep-13-2022 == [classify_bam_core] Processing ./SRR10612050//cons.fa.sam done. == 13:09:07-Sep-13-2022 == [Classifying] Classifying consensus alignment done! == 13:10:40-Sep-13-2022 == [gtfToGenePred] gtfToGenePred -genePredExt -ignoreGroupsWithoutExons /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene_pred == 13:10:46-Sep-13-2022 == [genePredToBed] genePredToBed /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene_pred /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed == 13:10:47-Sep-13-2022 == [get_transcript_from_bed12] Loading transcript from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene_pred ... == 13:10:49-Sep-13-2022 == [get_transcript_from_gene_pred] Loading transcript from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene_pred done! == 13:10:49-Sep-13-2022 == [get_splice_site_from_bed12] Loading splice site from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed ... == 13:10:51-Sep-13-2022 == [get_splice_site_from_bed12] Loading splice site from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed done! == 13:10:51-Sep-13-2022 == [get_splice_junction_from_bed12] Loading splice junction from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed ... == 13:10:53-Sep-13-2022 == [get_splice_junction_from_bed12] Loading splice junction from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed done! == 13:10:53-Sep-13-2022 == [get_exon_from_bed12] Loading exon from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed ... == 13:10:55-Sep-13-2022 == [get_exon_from_bed12] Loading exon from /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed done! == 13:10:55-Sep-13-2022 == [get_back_splice_junction_from_bed] Loading splice junction from /home/fengyige/data/circRNA/hsa_hg19_circRNA.bed ... == 13:10:55-Sep-13-2022 == [get_back_splice_junction_from_bed] Loading splice junction from /home/fengyige/data/circRNA/hsa_hg19_circRNA.bed done! == 13:11:04-Sep-13-2022 == [read_wise_eval] Generating read-wise evaluation result ... == 13:14:02-Sep-13-2022 == [high_quality] 100000 high mapping quality BAM records have been processed ... == 13:17:10-Sep-13-2022 == [high_quality] 200000 high mapping quality BAM records have been processed ... == 13:20:19-Sep-13-2022 == [high_quality] 300000 high mapping quality BAM records have been processed ... == 13:23:28-Sep-13-2022 == [high_quality] 400000 high mapping quality BAM records have been processed ... == 13:26:32-Sep-13-2022 == [high_quality] 500000 high mapping quality BAM records have been processed ... == 13:29:35-Sep-13-2022 == [high_quality] 600000 high mapping quality BAM records have been processed ... == 13:32:34-Sep-13-2022 == [high_quality] 700000 high mapping quality BAM records have been processed ... == 13:35:33-Sep-13-2022 == [high_quality] 800000 high mapping quality BAM records have been processed ... == 13:38:32-Sep-13-2022 == [high_quality] 900000 high mapping quality BAM records have been processed ... == 13:41:32-Sep-13-2022 == [high_quality] 1000000 high mapping quality BAM records have been processed ... == 13:44:33-Sep-13-2022 == [high_quality] 1100000 high mapping quality BAM records have been processed ... == 13:47:32-Sep-13-2022 == [high_quality] 1200000 high mapping quality BAM records have been processed ... == 13:50:34-Sep-13-2022 == [high_quality] 1300000 high mapping quality BAM records have been processed ... == 13:53:34-Sep-13-2022 == [high_quality] 1400000 high mapping quality BAM records have been processed ... == 13:56:34-Sep-13-2022 == [high_quality] 1500000 high mapping quality BAM records have been processed ... == 13:59:35-Sep-13-2022 == [high_quality] 1600000 high mapping quality BAM records have been processed ... == 14:02:35-Sep-13-2022 == [high_quality] 1700000 high mapping quality BAM records have been processed ... == 14:05:36-Sep-13-2022 == [high_quality] 1800000 high mapping quality BAM records have been processed ... == 14:06:16-Sep-13-2022 == [read_wise_eval] Generating read-wise evaluation result done! == 14:06:16-Sep-13-2022 == [filter_circRNA_read] Filtering back-splice-junctions ... == 14:07:06-Sep-13-2022 == [filter_circRNA_read] Filtering back-splice-junctions done! == 14:07:06-Sep-13-2022 == [rescue_reads] Rescuing reads using reliable back-splice-junctions ... == 14:07:33-Sep-13-2022 == [rescue_reads] Rescuing reads using reliable back-splice-junctions done! == 14:07:33-Sep-13-2022 == [uniq_isoform_with_unsorted_coors] Generating isoform-wise evaluation result ... == 14:07:33-Sep-13-2022 == [uniq_isoform_with_unsorted_coors] Generating isoform-wise evaluation result done! == 14:07:34-Sep-13-2022 == [bed2exonGtf] bed2exonGtf ./SRR10612050//isocirc.bed ./SRR10612050//isocirc.bed.exon.gtf == 14:07:35-Sep-13-2022 == [exonGtf] awk -v OFS="\t" '($3=="exon"){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.exon.gtf == 14:07:38-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="gene"){print $1,$4-1,$5}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene.bed == 14:07:39-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="CDS"){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.cds.gtf == 14:07:42-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="UTR" || $3=="five_prime_utr" || $3=="three_prime_utr"){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.utr.gtf == 14:07:44-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="exon" && ($0 ~ /gene_biotype "lincRNA"/ || $0 ~ /gene_type "lincRNA"/)){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.lincRNA.gtf == 14:07:46-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="exon" && ($0 ~ /gene_biotype "antisense"/ || $0 ~ /gene_type "antisense"/)){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.antisense.gtf == 14:07:47-Sep-13-2022 == [gtf2bed] awk -v OFS="\t" '($3=="exon" && ($0 ~ /gene_biotype "rRNA"/ || $0 ~ /gene_type "rRNA"/)){print}' /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf > /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.rRNA.gtf == 14:08:00-Sep-13-2022 == [bed2exonGtf] bed2exonGtf ./SRR10612050//isocirc.bed.five.site.bed ./SRR10612050//isocirc.bed.five.site.exon.gtf == 14:08:01-Sep-13-2022 == [bed2exonGtf] bed2exonGtf ./SRR10612050//isocirc.bed.three.site.bed ./SRR10612050//isocirc.bed.three.site.exon.gtf == 14:08:03-Sep-13-2022 == [bed2exonGtf] bed2exonGtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.five.site.bed /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.five.site.exon.gtf == 14:08:06-Sep-13-2022 == [bed2exonGtf] bed2exonGtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.three.site.bed /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.three.site.exon.gtf == 14:08:09-Sep-13-2022 == [itst_gtf_gtf] itst_gtf_gtf ./SRR10612050//isocirc.bed.five.site.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.five.site.exon.gtf ./SRR10612050//isocirc.bed.five.site.gene.out == 14:08:10-Sep-13-2022 == [itst_gtf_gtf] itst_gtf_gtf ./SRR10612050//isocirc.bed.three.site.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.three.site.exon.gtf ./SRR10612050//isocirc.bed.three.site.gene.out == 14:08:11-Sep-13-2022 == [gtf2gene] gtf2gene ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf ./SRR10612050//isocirc.bed.ovlp.gene.out == 14:08:14-Sep-13-2022 == [itst_gtf_bed] itst_gtf_bed ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.cds.gtf ./SRR10612050//isocirc.bed.CDS.out == 14:08:15-Sep-13-2022 == [itst_gtf_bed] itst_gtf_bed ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.utr.gtf ./SRR10612050//isocirc.bed.UTR.out == 14:08:16-Sep-13-2022 == [itst_gtf_bed] itst_gtf_bed ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.lincRNA.gtf ./SRR10612050//isocirc.bed.lincRNA.out == 14:08:17-Sep-13-2022 == [itst_gtf_bed] itst_gtf_bed ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.antisense.gtf ./SRR10612050//isocirc.bed.antisense.out == 14:08:18-Sep-13-2022 == [itst_gtf_bed] itst_gtf_bed ./SRR10612050//isocirc.bed.exon.gtf /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.rRNA.gtf ./SRR10612050//isocirc.bed.rRNA.out == 14:08:19-Sep-13-2022 == [itst_intron] bedtools intersect -v -a ./SRR10612050//isocirc.bed.exon.gtf -b /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.bed -split > ./SRR10612050//isocirc.bed.intron.out == 14:08:22-Sep-13-2022 == [itst_intergenic] bedtools intersect -v -a ./SRR10612050//isocirc.bed.exon.gtf -b /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.gene.bed > ./SRR10612050//isocirc.bed.intergenic.out == 14:08:29-Sep-13-2022 == [itst_exon] bedtools intersect -a ./SRR10612050//isocirc.bed.exon.gtf -b /home/fengyige/20220826_circrna/iso_out/SRR10612050/gencode.v21.annotation.gtf.exon.gtf -wa -wb > ./SRR10612050//isocirc.bed.exon.out == 14:08:31-Sep-13-2022 == [get_block_anno] No "exon_number" found in record.

yangao07 commented 2 years ago

Seems like the exon_number tag is missing from the GTF file you specify. Can you try the command grep exon_number /home/fengyige/data/star/hg19/gencode.v21.annotation.gtf | head?

taffy-miao commented 2 years ago

Turns out that my GTF file from UCSC has lost some message. I'm now using the GTF file from ensembl and it finally work successfully. Thanks for your help!

yangao07 commented 2 years ago

Great!