xTea
xTea copied to clipboard
parklab
read 0 ALT contigs AND fail to open file "xxxx.clipped.fq"
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Command line :path-to-dir/xTea-master/bin/xtea -i normal_name.csv -b normal_name_bam.csv -x null -p ./normal_wes/5.TE_output/ -o ./normal_wes/5.TE_output/multiple_TE_output.sh -l path-to-dir/xTea-master/rep_lib_annotation/ -r ~/db/human_genome_index/hg38/hg38.fa -g path-to-dir/xTea-master/gencode.v33.hg38.annotation.gff3 --xtea path-to-dir/xTea-master/xtea/ -q short -f 1 -y 7 -n 8 -m 250
____________________________________________________________________________________________________
I used xTea-v0.1 to analysis my blood-wes dataset. however, I always get above error.Why I always can't get a corrrect clipped.fq files.
Could you change the relative path "-p ./normal_wes/5.TE_output/ " to the full path and have a try? Similarly for all other paths, use the full path.
Thank you so much, simoncchu. I used full path in my commmand, and solved the above problem. however, i get new error:
Blacklist file null does not exist!
+++++++++++++++++++++
+++++++++++++++++++++++++++++++
============================================ my command /home/liukai/biosoft/wes_script/xTea-master/bin/xtea2 -i /home/liukai/postd/wes/data/multiple_20_tumor_normal_name.csv -b /home/liukai/postd/wes/data/multiple_20_tumor_normal_name_bam.csv -x null -p /home/liukai/postd/wes/data/multiple_20_tumor_normal/5.TE_output/ -o /home/liukai/postd/wes/data/multiple_20_tumor_normal/5.TE_output/multiple_TE_output.sh -l /home/liukai/biosoft/wes_script/xTea-master/rep_lib_annotation/ -r ~/db/human_genome_index/hg38/hg38.fa -g /home/liukai/biosoft/wes_script/xTea-master/gencode.v33.hg38.annotation.gff3 --xtea /home/liukai/biosoft/wes_script/xTea-master/xtea/ -q short -f 5907 -y 7 -n 8 -m 25
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++ finally, i get the empty TE.vcf file
$ python /home/liukai/biosoft/wes_script/xTea-master/xtea/x_TEA_main.py -D -i /home/liukai/postd/we s/data/HR_48sample_normal/5.TE_output/C180245-N/Alu/candidate_list_from_clip.txt --nd 5 --ref /home/liukai/db/human_genome_ind ex/hg38/hg38.fa -a /home/liukai/biosoft/wes_script/xTea-master/rep_lib_annotation/Alu/hg38/hg38_Alu.out -b /home/liukai/postd /wes/data/HR_48sample_normal/5.TE_output/C180245-N/Alu/bam_list.txt -p /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_out put/C180245-N/Alu/tmp/ -o /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C180245-N/Alu/candidate_list_from_disc.tx t -n 8 Working on "disc" step! Ave coverage is 24.828: automatic parameters (clip, disc, clip-disc) with value (2, 4 ,1)
Discordant cutoff: 4 is used!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! Position chr19:9803399 has more than 1 annotation!!!! multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/liukai/biosoft/anaconda3/envs/gatk4/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/home/liukai/biosoft/anaconda3/envs/gatk4/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "/home/liukai/biosoft/wes_script/xTea-master/xtea/x_TEI_locator.py", line 564, in unwrap_self_filter_by_discordant_non_barcode return TELocator.run_filter_by_discordant_pair_by_chrom_non_barcode(*arg, **kwarg) File "/home/liukai/biosoft/wes_script/xTea-master/xtea/x_TEI_locator.py", line 1111, in run_filter_by_discordant_pair_by_chrom_non_barcode site_pos + iextend, i_is, f_dev, xannotation) File "/home/liukai/biosoft/wes_script/xTea-master/xtea/x_alignments.py", line 99, in cnt_discordant_pairs iter_alignmts = bamfile.fetch(chrm, start, end) File "pysam/libcalignmentfile.pyx", line 1081, in pysam.libcalignmentfile.AlignmentFile.fetch File "pysam/libchtslib.pyx", line 689, in pysam.libchtslib.HTSFile.parse_region ValueError: invalid coordinates: start (19177217) > stop (19177216) """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/liukai/biosoft/wes_script/xTea-master/xtea/x_TEA_main.py", line 472, in
===================================================================
I run the problem step alone, and get above error report
It's unclear to me which step triggered the error from what you posted here. Could you post the output files with size?
It's unclear to me which step triggered the error from what you posted here. Could you post the output files with size?
. ├── [ 23] Alu │ ├── [ 111] bam_list1.txt │ ├── [ 110] bam_list.txt │ ├── [ 0] candidate_disc_filtered_cns2.txt │ ├── [ 0] candidate_disc_filtered_cns2.txt.high_confident │ ├── [ 0] candidate_disc_filtered_cns_post_filtering.txt │ ├── [ 0] candidate_disc_filtered_cns.txt │ ├── [ 0] candidate_disc_filtered_cns.txt.before_calling_transduction │ ├── [ 0] candidate_disc_filtered_cns.txt.before_calling_transduction.sites_cov │ ├── [ 0] candidate_disc_filtered_cns.txt.before_filtering │ ├── [ 0] candidate_disc_filtered_cns.txt.gntp.features │ ├── [ 0] candidate_disc_filtered_cns.txt.gntp.features0.out │ ├── [ 0] candidate_disc_filtered_cns.txt.high_confident │ ├── [ 459] candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene.txt.arff │ ├── [ 0] candidate_disc_filtered_cns.txt.igv_sites │ ├── [ 8.7M] candidate_list_from_clip.txt │ ├── [ 143M] candidate_list_from_clip.txt_tmp │ ├── [ 0] candidate_list_from_disc.txt │ ├── [ 0] candidate_list_from_disc.txt.clip_sites_raw_disc.txt │ ├── [ 4.1K] run_xTEA_pipeline.sh │ ├── [ 9] sample_id.txt │ └── [ 15] tmp │ ├── [ 122] basic_cov_is_rlth_info.txt │ ├── [ 428K] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam_sq.txt │ ├── [ 0] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam.std_out │ ├── [ 3] clip │ │ └── [ 26] 0 │ │ ├── [ 23K] chr10.clip_realign_pos │ │ ├── [ 32K] chr11.clip_realign_pos │ │ ├── [ 31K] chr12.clip_realign_pos │ │ ├── [ 12K] chr13.clip_realign_pos │ │ ├── [ 18K] chr14.clip_realign_pos │ │ ├── [ 17K] chr15.clip_realign_pos │ │ ├── [ 22K] chr16.clip_realign_pos │ │ ├── [ 29K] chr17.clip_realign_pos │ │ ├── [ 9.2K] chr18.clip_realign_pos │ │ ├── [ 40K] chr19.clip_realign_pos │ │ ├── [ 58K] chr1.clip_realign_pos │ │ ├── [ 14K] chr20.clip_realign_pos │ │ ├── [ 5.8K] chr21.clip_realign_pos │ │ ├── [ 11K] chr22.clip_realign_pos │ │ ├── [ 42K] chr2.clip_realign_pos │ │ ├── [ 33K] chr3.clip_realign_pos │ │ ├── [ 23K] chr4.clip_realign_pos │ │ ├── [ 27K] chr5.clip_realign_pos │ │ ├── [ 26K] chr6.clip_realign_pos │ │ ├── [ 29K] chr7.clip_realign_pos │ │ ├── [ 19K] chr8.clip_realign_pos │ │ ├── [ 23K] chr9.clip_realign_pos │ │ ├── [ 19K] chrX.clip_realign_pos │ │ └── [ 799] chrY.clip_realign_pos │ ├── [ 1.2M] clip_peak_candidate.list │ ├── [ 137M] clip_reads_tmp0 │ ├── [ 8] cns │ │ ├── [ 0] all_disc_pos.disc_pos │ │ ├── [ 2] asm │ │ ├── [ 146] basic_cov_is_rlth_info.txt │ │ ├── [ 829] filtering_log.txt │ │ ├── [ 1.3K] temp_clip.sam │ │ └── [ 1.3K] temp_disc.sam │ ├── [ 74] disc │ │ ├── [ 51K] chr10.discord_pos.txt │ │ ├── [ 21K] chr10.discord_pos.txt.discdt │ │ ├── [ 51K] chr10.discord_pos.txt.raw.discdt │ │ ├── [ 70K] chr11.discord_pos.txt │ │ ├── [ 29K] chr11.discord_pos.txt.discdt │ │ ├── [ 69K] chr11.discord_pos.txt.raw.discdt │ │ ├── [ 67K] chr12.discord_pos.txt │ │ ├── [ 28K] chr12.discord_pos.txt.discdt │ │ ├── [ 67K] chr12.discord_pos.txt.raw.discdt │ │ ├── [ 26K] chr13.discord_pos.txt │ │ ├── [ 11K] chr13.discord_pos.txt.discdt │ │ ├── [ 26K] chr13.discord_pos.txt.raw.discdt │ │ ├── [ 39K] chr14.discord_pos.txt │ │ ├── [ 16K] chr14.discord_pos.txt.discdt │ │ ├── [ 39K] chr14.discord_pos.txt.raw.discdt │ │ ├── [ 36K] chr15.discord_pos.txt │ │ ├── [ 15K] chr15.discord_pos.txt.discdt │ │ ├── [ 37K] chr15.discord_pos.txt.raw.discdt │ │ ├── [ 49K] chr16.discord_pos.txt │ │ ├── [ 20K] chr16.discord_pos.txt.discdt │ │ ├── [ 49K] chr16.discord_pos.txt.raw.discdt │ │ ├── [ 64K] chr17.discord_pos.txt │ │ ├── [ 26K] chr17.discord_pos.txt.discdt │ │ ├── [ 64K] chr17.discord_pos.txt.raw.discdt │ │ ├── [ 20K] chr18.discord_pos.txt │ │ ├── [ 8.3K] chr18.discord_pos.txt.discdt │ │ ├── [ 20K] chr18.discord_pos.txt.raw.discdt │ │ ├── [ 85K] chr19.discord_pos.txt │ │ ├── [ 34K] chr19.discord_pos.txt.discdt │ │ ├── [ 84K] chr19.discord_pos.txt.raw.discdt │ │ ├── [ 119K] chr1.discord_pos.txt │ │ ├── [ 52K] chr1.discord_pos.txt.discdt │ │ ├── [ 123K] chr1.discord_pos.txt.raw.discdt │ │ ├── [ 31K] chr20.discord_pos.txt │ │ ├── [ 13K] chr20.discord_pos.txt.discdt │ │ ├── [ 31K] chr20.discord_pos.txt.raw.discdt │ │ ├── [ 12K] chr21.discord_pos.txt │ │ ├── [ 5.1K] chr21.discord_pos.txt.discdt │ │ ├── [ 12K] chr21.discord_pos.txt.raw.discdt │ │ ├── [ 25K] chr22.discord_pos.txt │ │ ├── [ 10K] chr22.discord_pos.txt.discdt │ │ ├── [ 25K] chr22.discord_pos.txt.raw.discdt │ │ ├── [ 89K] chr2.discord_pos.txt │ │ ├── [ 39K] chr2.discord_pos.txt.discdt │ │ ├── [ 92K] chr2.discord_pos.txt.raw.discdt │ │ ├── [ 70K] chr3.discord_pos.txt │ │ ├── [ 30K] chr3.discord_pos.txt.discdt │ │ ├── [ 72K] chr3.discord_pos.txt.raw.discdt │ │ ├── [ 49K] chr4.discord_pos.txt │ │ ├── [ 21K] chr4.discord_pos.txt.discdt │ │ ├── [ 50K] chr4.discord_pos.txt.raw.discdt │ │ ├── [ 54K] chr5.discord_pos.txt │ │ ├── [ 24K] chr5.discord_pos.txt.discdt │ │ ├── [ 56K] chr5.discord_pos.txt.raw.discdt │ │ ├── [ 54K] chr6.discord_pos.txt │ │ ├── [ 23K] chr6.discord_pos.txt.discdt │ │ ├── [ 56K] chr6.discord_pos.txt.raw.discdt │ │ ├── [ 57K] chr7.discord_pos.txt │ │ ├── [ 25K] chr7.discord_pos.txt.discdt │ │ ├── [ 59K] chr7.discord_pos.txt.raw.discdt │ │ ├── [ 40K] chr8.discord_pos.txt │ │ ├── [ 17K] chr8.discord_pos.txt.discdt │ │ ├── [ 42K] chr8.discord_pos.txt.raw.discdt │ │ ├── [ 48K] chr9.discord_pos.txt │ │ ├── [ 21K] chr9.discord_pos.txt.discdt │ │ ├── [ 50K] chr9.discord_pos.txt.raw.discdt │ │ ├── [ 41K] chrX.discord_pos.txt │ │ ├── [ 18K] chrX.discord_pos.txt.discdt │ │ ├── [ 42K] chrX.discord_pos.txt.raw.discdt │ │ ├── [ 1.5K] chrY.discord_pos.txt │ │ ├── [ 662] chrY.discord_pos.txt.discdt │ │ └── [ 1.6K] chrY.discord_pos.txt.raw.discdt │ ├── [ 218] discordant_reads_tmp0 │ ├── [ 0] disc_tmp.list │ ├── [ 3] igv │ │ └── [ 0] bamsnap_screenshot.txt │ ├── [ 1.4M] raw_discordant_reads_tmp0 │ └── [ 3] transduction │ └── [ 121] basic_cov_is_rlth_info.txt ├── [ 934] Alu.config ├── [ 10] L1 │ ├── [ 111] bam_list1.txt │ ├── [ 110] bam_list.txt │ ├── [ 459] candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene.txt.arff │ ├── [ 7.9M] candidate_list_from_clip.txt │ ├── [ 143M] candidate_list_from_clip.txt_tmp │ ├── [ 4.2K] run_xTEA_pipeline.sh │ ├── [ 9] sample_id.txt │ └── [ 12] tmp │ ├── [ 114] basic_cov_is_rlth_info.txt │ ├── [ 14K] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam_sq.txt │ ├── [ 0] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam.std_out │ ├── [ 3] clip │ │ └── [ 51] 0 │ │ ├── [ 29M] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.fq │ │ ├── [ 3.4M] chr10.clip_pos │ │ ├── [ 21K] chr10.clip_realign_pos │ │ ├── [ 5.1M] chr11.clip_pos │ │ ├── [ 29K] chr11.clip_realign_pos │ │ ├── [ 4.7M] chr12.clip_pos │ │ ├── [ 28K] chr12.clip_realign_pos │ │ ├── [ 1.5M] chr13.clip_pos │ │ ├── [ 11K] chr13.clip_realign_pos │ │ ├── [ 2.7M] chr14.clip_pos │ │ ├── [ 16K] chr14.clip_realign_pos │ │ ├── [ 2.7M] chr15.clip_pos │ │ ├── [ 15K] chr15.clip_realign_pos │ │ ├── [ 3.4M] chr16.clip_pos │ │ ├── [ 20K] chr16.clip_realign_pos │ │ ├── [ 4.7M] chr17.clip_pos │ │ ├── [ 26K] chr17.clip_realign_pos │ │ ├── [ 1.3M] chr18.clip_pos │ │ ├── [ 8.4K] chr18.clip_realign_pos │ │ ├── [ 5.5M] chr19.clip_pos │ │ ├── [ 34K] chr19.clip_realign_pos │ │ ├── [ 8.9M] chr1.clip_pos │ │ ├── [ 51K] chr1.clip_realign_pos │ │ ├── [ 2.2M] chr20.clip_pos │ │ ├── [ 13K] chr20.clip_realign_pos │ │ ├── [ 819K] chr21.clip_pos │ │ ├── [ 5.3K] chr21.clip_realign_pos │ │ ├── [ 1.9M] chr22.clip_pos │ │ ├── [ 10K] chr22.clip_realign_pos │ │ ├── [ 6.4M] chr2.clip_pos │ │ ├── [ 38K] chr2.clip_realign_pos │ │ ├── [ 5.2M] chr3.clip_pos │ │ ├── [ 30K] chr3.clip_realign_pos │ │ ├── [ 3.3M] chr4.clip_pos │ │ ├── [ 21K] chr4.clip_realign_pos │ │ ├── [ 3.9M] chr5.clip_pos │ │ ├── [ 24K] chr5.clip_realign_pos │ │ ├── [ 3.7M] chr6.clip_pos │ │ ├── [ 24K] chr6.clip_realign_pos │ │ ├── [ 4.0M] chr7.clip_pos │ │ ├── [ 27K] chr7.clip_realign_pos │ │ ├── [ 2.8M] chr8.clip_pos │ │ ├── [ 18K] chr8.clip_realign_pos │ │ ├── [ 3.6M] chr9.clip_pos │ │ ├── [ 21K] chr9.clip_realign_pos │ │ ├── [ 2.9M] chrX.clip_pos │ │ ├── [ 18K] chrX.clip_realign_pos │ │ ├── [ 130K] chrY.clip_pos │ │ └── [ 688] chrY.clip_realign_pos │ ├── [ 1.1M] clip_peak_candidate.list │ ├── [ 137M] clip_reads_tmp0 │ ├── [ 7] cns │ │ ├── [ 2] asm │ │ ├── [ 113] basic_cov_is_rlth_info.txt │ │ ├── [ 0] candidate_sites_all_clip.fq │ │ ├── [ 0] candidate_sites_all_disc.fa │ │ └── [ 64] filtering_log.txt │ ├── [ 26] disc │ │ ├── [ 47K] chr10.discord_pos.txt │ │ ├── [ 64K] chr11.discord_pos.txt │ │ ├── [ 62K] chr12.discord_pos.txt │ │ ├── [ 24K] chr13.discord_pos.txt │ │ ├── [ 36K] chr14.discord_pos.txt │ │ ├── [ 34K] chr15.discord_pos.txt │ │ ├── [ 45K] chr16.discord_pos.txt │ │ ├── [ 59K] chr17.discord_pos.txt │ │ ├── [ 19K] chr18.discord_pos.txt │ │ ├── [ 76K] chr19.discord_pos.txt │ │ ├── [ 108K] chr1.discord_pos.txt │ │ ├── [ 29K] chr20.discord_pos.txt │ │ ├── [ 12K] chr21.discord_pos.txt │ │ ├── [ 23K] chr22.discord_pos.txt │ │ ├── [ 81K] chr2.discord_pos.txt │ │ ├── [ 65K] chr3.discord_pos.txt │ │ ├── [ 45K] chr4.discord_pos.txt │ │ ├── [ 50K] chr5.discord_pos.txt │ │ ├── [ 50K] chr6.discord_pos.txt │ │ ├── [ 53K] chr7.discord_pos.txt │ │ ├── [ 37K] chr8.discord_pos.txt │ │ ├── [ 45K] chr9.discord_pos.txt │ │ ├── [ 39K] chrX.discord_pos.txt │ │ └── [ 1.3K] chrY.discord_pos.txt │ ├── [ 2] igv │ └── [ 3] transduction │ └── [ 120] basic_cov_is_rlth_info.txt ├── [ 1.0K] L1.config ├── [ 3] pub_clip │ └── [ 27] 0 │ ├── [ 141] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.fq -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.fq │ ├── [ 97] chr10.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr10.clip_pos │ ├── [ 97] chr11.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr11.clip_pos │ ├── [ 97] chr12.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr12.clip_pos │ ├── [ 97] chr13.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr13.clip_pos │ ├── [ 97] chr14.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr14.clip_pos │ ├── [ 97] chr15.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr15.clip_pos │ ├── [ 97] chr16.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr16.clip_pos │ ├── [ 97] chr17.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr17.clip_pos │ ├── [ 97] chr18.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr18.clip_pos │ ├── [ 97] chr19.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr19.clip_pos │ ├── [ 96] chr1.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr1.clip_pos │ ├── [ 97] chr20.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr20.clip_pos │ ├── [ 97] chr21.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr21.clip_pos │ ├── [ 97] chr22.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr22.clip_pos │ ├── [ 96] chr2.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr2.clip_pos │ ├── [ 96] chr3.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr3.clip_pos │ ├── [ 96] chr4.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr4.clip_pos │ ├── [ 96] chr5.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr5.clip_pos │ ├── [ 96] chr6.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr6.clip_pos │ ├── [ 96] chr7.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr7.clip_pos │ ├── [ 96] chr8.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr8.clip_pos │ ├── [ 96] chr9.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chr9.clip_pos │ ├── [ 96] chrX.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chrX.clip_pos │ └── [ 96] chrY.clip_pos -> /home/liukai/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/L1/tmp/clip/0/chrY.clip_pos ├── [ 10] SVA │ ├── [ 111] bam_list1.txt │ ├── [ 110] bam_list.txt │ ├── [ 459] candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene.txt.arff │ ├── [ 9.5M] candidate_list_from_clip.txt │ ├── [ 143M] candidate_list_from_clip.txt_tmp │ ├── [ 4.2K] run_xTEA_pipeline.sh │ ├── [ 9] sample_id.txt │ └── [ 12] tmp │ ├── [ 113] basic_cov_is_rlth_info.txt │ ├── [ 121K] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam_sq.txt │ ├── [ 0] C150021-N.sorted.MarkDuplicates.BQSR.sorted.bam.clipped.sam.std_out │ ├── [ 3] clip │ │ └── [ 26] 0 │ │ ├── [ 25K] chr10.clip_realign_pos │ │ ├── [ 36K] chr11.clip_realign_pos │ │ ├── [ 34K] chr12.clip_realign_pos │ │ ├── [ 13K] chr13.clip_realign_pos │ │ ├── [ 20K] chr14.clip_realign_pos │ │ ├── [ 18K] chr15.clip_realign_pos │ │ ├── [ 25K] chr16.clip_realign_pos │ │ ├── [ 33K] chr17.clip_realign_pos │ │ ├── [ 10K] chr18.clip_realign_pos │ │ ├── [ 46K] chr19.clip_realign_pos │ │ ├── [ 64K] chr1.clip_realign_pos │ │ ├── [ 15K] chr20.clip_realign_pos │ │ ├── [ 6.3K] chr21.clip_realign_pos │ │ ├── [ 13K] chr22.clip_realign_pos │ │ ├── [ 46K] chr2.clip_realign_pos │ │ ├── [ 36K] chr3.clip_realign_pos │ │ ├── [ 26K] chr4.clip_realign_pos │ │ ├── [ 29K] chr5.clip_realign_pos │ │ ├── [ 28K] chr6.clip_realign_pos │ │ ├── [ 33K] chr7.clip_realign_pos │ │ ├── [ 21K] chr8.clip_realign_pos │ │ ├── [ 26K] chr9.clip_realign_pos │ │ ├── [ 21K] chrX.clip_realign_pos │ │ └── [ 883] chrY.clip_realign_pos │ ├── [ 1.3M] clip_peak_candidate.list │ ├── [ 137M] clip_reads_tmp0 │ ├── [ 7] cns │ │ ├── [ 2] asm │ │ ├── [ 113] basic_cov_is_rlth_info.txt │ │ ├── [ 0] candidate_sites_all_clip.fq │ │ ├── [ 0] candidate_sites_all_disc.fa │ │ └── [ 64] filtering_log.txt │ ├── [ 26] disc │ │ ├── [ 55K] chr10.discord_pos.txt │ │ ├── [ 76K] chr11.discord_pos.txt │ │ ├── [ 73K] chr12.discord_pos.txt │ │ ├── [ 28K] chr13.discord_pos.txt │ │ ├── [ 42K] chr14.discord_pos.txt │ │ ├── [ 40K] chr15.discord_pos.txt │ │ ├── [ 54K] chr16.discord_pos.txt │ │ ├── [ 70K] chr17.discord_pos.txt │ │ ├── [ 22K] chr18.discord_pos.txt │ │ ├── [ 93K] chr19.discord_pos.txt │ │ ├── [ 130K] chr1.discord_pos.txt │ │ ├── [ 34K] chr20.discord_pos.txt │ │ ├── [ 13K] chr21.discord_pos.txt │ │ ├── [ 27K] chr22.discord_pos.txt │ │ ├── [ 96K] chr2.discord_pos.txt │ │ ├── [ 75K] chr3.discord_pos.txt │ │ ├── [ 53K] chr4.discord_pos.txt │ │ ├── [ 58K] chr5.discord_pos.txt │ │ ├── [ 58K] chr6.discord_pos.txt │ │ ├── [ 62K] chr7.discord_pos.txt │ │ ├── [ 44K] chr8.discord_pos.txt │ │ ├── [ 53K] chr9.discord_pos.txt │ │ ├── [ 45K] chrX.discord_pos.txt │ │ └── [ 1.6K] chrY.discord_pos.txt │ ├── [ 2] igv │ └── [ 3] transduction │ └── [ 113] basic_cov_is_rlth_info.txt └── [ 1022] SVA.config
This is the output files of one samples
Error triggered at the second step. Could you post the content of this file? run_xTEA_pipeline.sh
Just noticed you have run that step. Not sure why trigger this error ValueError: invalid coordinates: start (19177217) > stop (19177216). Is this WES? Could you test on HG002 (WGS) and see whether you can go through?
Just noticed you have run that step. Not sure why trigger this error
ValueError: invalid coordinates: start (19177217) > stop (19177216). Is this WES? Could you test on HG002 (WGS) and see whether you can go through?
Yes, it;s a WES dataset.
run_xTea_pipeline.sh in directory: Alu.
PREFIX=/home/liukxx/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/Alu/
############
############
ANNOTATION=/home/liukxx/biosoft/wes_script/xTea-master/rep_lib_annotation/Alu/hg38/hg38_Alu.out
ANNOTATION1=/home/liukxx/biosoft/wes_script/xTea-master/rep_lib_annotation/Alu/hg38/hg38_Alu.out
REF=/home/liukxx/db/human_genome_index/hg38/hg38.fa
GENE=/home/liukxx/biosoft/wes_script/xTea-master/gencode.v33.hg38.annotation.gff3
BLACK_LIST=/home/liukxx/db/human_genome_index/hg38/S33266340_Regions.bed
L1_COPY_WITH_FLANK=/home/liukxx/biosoft/wes_script/xTea-master/rep_lib_annotation/Alu/hg38/hg38_AluJabc_copies_with_flank.fa
SF_FLANK=null
L1_CNS=/home/liukxx/biosoft/wes_script/xTea-master/rep_lib_annotation/consensus/ALU.fa
XTEA_PATH=/home/liukxx/biosoft/wes_script/xTea-master/xtea/
BAM_LIST=${PREFIX}"bam_list.txt"
BAM1=${PREFIX}"10X_phased_possorted_bam.bam"
BARCODE_BAM=${PREFIX}"10X_barcode_indexed.sorted.bam"
TMP=${PREFIX}"tmp/"
TMP_CLIP=${PREFIX}"tmp/clip/"
TMP_CNS=${PREFIX}"tmp/cns/"
TMP_TNSD=${PREFIX}"tmp/transduction/"
############
############
python ${XTEA_PATH}"x_TEA_main.py" -C -i ${BAM_LIST} --lc 3 --rc 3 --cr 1 -r ${L1_COPY_WITH_FLANK} -a ${ANNOTATION} --cns ${L1_CNS} --ref ${REF} -p ${TMP} -o ${PREFIX}"candidate_list_from_clip.txt" -n 8 --cp /home/liukxx/postd/wes/data/HR_48sample_normal/5.TE_output/C150021-N/pub_clip/
python ${XTEA_PATH}"x_TEA_main.py" -D -i ${PREFIX}"candidate_list_from_clip.txt" --nd 5 --ref ${REF} -a ${ANNOTATION} -b ${BAM_LIST} -p ${TMP} -o ${PREFIX}"candidate_list_from_disc.txt" -n 8
python ${XTEA_PATH}"x_TEA_main.py" -N --cr 3 --nd 5 -b ${BAM_LIST} -p ${TMP_CNS} --fflank ${SF_FLANK} --flklen 3000 -n 8 -i ${PREFIX}"candidate_list_from_disc.txt" -r ${L1_CNS} --ref ${REF} -a ${ANNOTATION} -o ${PREFIX}"candidate_disc_filtered_cns.txt"
python ${XTEA_PATH}"x_TEA_main.py" --transduction --cr 3 --nd 5 -b ${BAM_LIST} -p ${TMP_TNSD} --fflank ${SF_FLANK} --flklen 3000 -n 8 -i ${PREFIX}"candidate_disc_filtered_cns.txt" -r ${L1_CNS} --ref ${REF} --input2 ${PREFIX}"candidate_list_from_disc.txt.clip_sites_raw_disc.txt" --rtype 2 -a ${ANNOTATION1} -o ${PREFIX}"candidate_disc_filtered_cns2.txt"
python ${XTEA_PATH}"x_TEA_main.py" --sibling --cr 3 --nd 5 -b ${BAM_LIST} -p ${TMP_TNSD} --fflank ${SF_FLANK} --flklen 3000 -n 8 -i ${PREFIX}"candidate_disc_filtered_cns2.txt" -r ${L1_CNS} --ref ${REF} --input2 ${PREFIX}"candidate_list_from_disc.txt.clip_sites_raw_disc.txt" --rtype 2 -a ${ANNOTATION1} --blacklist ${BLACK_LIST} -o ${PREFIX}"candidate_sibling_transduction2.txt"
python ${XTEA_PATH}"x_TEA_main.py" --postF --rtype 2 -p ${TMP_CNS} -n 8 -i ${PREFIX}"candidate_disc_filtered_cns2.txt" -a ${ANNOTATION1} -o ${PREFIX}"candidate_disc_filtered_cns_post_filtering.txt"
python ${XTEA_PATH}"x_TEA_main.py" --postF --rtype 2 -p ${TMP_CNS} -n 8 -i ${PREFIX}"candidate_disc_filtered_cns2.txt.high_confident" -a ${ANNOTATION1} --blacklist ${BLACK_LIST} -o ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering.txt"
python ${XTEA_PATH}"x_TEA_main.py" --gene -a ${GENE} -i ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering.txt" -n 8 -o ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene.txt"
python ${XTEA_PATH}"x_TEA_main.py" --gntp_classify -i ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene.txt" -n 1 --model ${XTEA_PATH}"genotyping/DF21_model_1_2" -o ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt"
python ${XTEA_PATH}"x_TEA_main.py" --gVCF -i ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering_with_gene_gntp.txt" -o ${PREFIX} -b ${BAM_LIST} --ref ${REF} --rtype 2
python ${XTEA_PATH}"x_TEA_main.py" --igv --single_sample -p ${PREFIX}"tmp/igv" -b ${PREFIX}"bam_list1.txt" -i ${PREFIX}"candidate_disc_filtered_cns.txt" --ref ${REF} -e 1000 -n 8 -o ${PREFIX}"tmp/igv/bamsnap_screenshot.txt"
python ${XTEA_PATH}"x_TEA_main.py" --igv --single_sample -p ${PREFIX}"tmp/igv" -b ${PREFIX}"bam_list1.txt" -i ${PREFIX}"candidate_disc_filtered_cns.txt.high_confident.post_filtering.txt" --ref ${REF} -e 1000 -n 8 -o ${PREFIX}"tmp/igv/bamsnap_screenshot_hc.txt"
I remember a similar issue was reported on WES before. xTea is mainly developed for WGS, and is not tested that much on WES. I will test more and see how to solve this.
any updates on this issue? It was an error during my data preprocessing that resulted in this issue. I had only utilized the 5'-end of the paired-end sequencing fastq files. After making the necessary adjustments, it is now running smoothly.