JinfengChen
commented
5 years ago Can you share the reads, reference genome, TE annotation that are used for the RelocaTE2 run? I can test where is the problem.
Open sunliang3361 opened 5 years ago
JinfengChen
commented
5 years ago Can you share the reads, reference genome, TE annotation that are used for the RelocaTE2 run? I can test where is the problem.
sunliang3361
commented
5 years ago Hi Jinfeng, Thank you for your kind replay. Could you give me hint how to give you the big data set? Thanks
Liang
On Tue, Sep 11, 2018 at 5:23 PM, JinfengChen notifications@github.com wrote:
Can you share the reads, reference genome, TE annotation that are used for the RelocaTE2 run? I can test where is the problem.
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-- Liang Sun Ph.D Bioinformatics&Systems Biology University of Delaware http://bigbird.anr.udel.edu/sunliang/resume/home.php http://bigbird.anr.udel.edu/sunliang/project_web/
I am very interesting in using your relocaTE2 but get the following errors. Could you give me some hints what my problems are? Thanks.
Running on node14.cluster. It is started Mon Aug 27 15:57:30 CDT 2018. testing if bam exists: /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.at10_mut500_sim5x1.te_repeat.flankingReads.fq_1.te_repeat.flankingReads.bwa.mates.bam bam not exists, preceed with bwa to map the reads [bwa_aln_core] convert to sequence coordinate... 0.08 sec [bwa_aln_core] refine gapped alignments... 0.02 sec [bwa_aln_core] print alignments... 0.15 sec [bwa_aln_core] 46233 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /opt/apps/bwa/0.6.2/bin/bwa samse /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/Athaliana_447_TAIR10.fa /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.at10_mut500_sim5x1.te_repeat.flankingReads.bwa.single.sai /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/flanking_seq/at10_mut500_sim5x1.te_repeat.flankingReads.fq [main] Real time: 0.956 sec; CPU: 0.379 sec [bwa_aln_core] convert to sequence coordinate... 0.08 sec [bwa_aln_core] refine gapped alignments... 0.01 sec [bwa_aln_core] print alignments... 0.14 sec [bwa_aln_core] 46316 sequences have been processed. [main] Version: 0.6.2-r126 [main] CMD: /opt/apps/bwa/0.6.2/bin/bwa samse /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/Athaliana_447_TAIR10.fa /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.at10_mut500_sim5x2.te_repeat.flankingReads.bwa.single.sai /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/flanking_seq/at10_mut500_sim5x2.te_repeat.flankingReads.fq [main] Real time: 0.811 sec; CPU: 0.337 sec [W::bam_merge_core2] No @HD tag found. mergeing bam file: 2/2 files mergeing fullread bam file: 0/0 files [E::hts_open_format] Failed to open file /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam Existing TE file does not exists or zero size fullread bam: /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam Traceback (most recent call last): File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1826, in
main()
File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1810, in main
read_junction_reads_align(align_file_f, read_repeat, teJunctionReads)
File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1649, in read_junction_reads_align
fsam = pysam.AlignmentFile(align_file_f, 'rb')
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.cinit (pysam/libcalignmentfile.c:11004)
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:13714)
IOError: [Errno 2] could not open alignment file
main()
File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1810, in main
read_junction_reads_align(align_file_f, read_repeat, teJunctionReads)
File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1649, in read_junction_reads_align
fsam = pysam.AlignmentFile(align_file_f, 'rb')
File "pysam/libcalignmentfile.pyx", line 734, in pysam.libcalignmentfile.AlignmentFile.cinit (pysam/libcalignmentfile.c:11004)
File "pysam/libcalignmentfile.pyx", line 933, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:13714)
IOError: [Errno 2] could not open alignment file
/gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam: No such file or directory [E::hts_open_format] Failed to open file /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam Existing TE file does not exists or zero size fullread bam: /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam Traceback (most recent call last): File "/opt/apps/relocate2/2.0.2-b1464b4/bin/relocaTE_insertionFinder.py", line 1826, in/gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam: No such file or directory [E::hts_open_format] Failed to open file /gpfs/home/lsun/vm/TDNAscan/simulation_compare/relocate2/5x/5x/repeat/bwa_aln/Athaliana_447_TAIR10.repeat.fullreads.bwa.sorted.bam Existing TE file does not exists or zero size