error during excution
RuslanAlali opened this issue · comments
The tool looks very nice and helpful. I am afraid that I need some help with it.
I tried to run the code with both BAM and FastQs. However, I keep getting an error on line 13 of isolate_relevant_pairs(_fq).
**python surveyor.py X_R1_001.fastq.gz,X_R2_001.fastq.gz results2 hg19.fa HHV6_seq.fa HHV6_hg19.fa --fq --dust sdust/sdust**
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 200000 sequences (30101423 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 85345, 4, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (248, 318, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 716)
[M::mem_pestat] mean and std.dev: (329.80, 118.11)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 872)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 200000 reads in 111.685 CPU sec, 11.204 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 10 HHV6_hg19.fa results2/head_1.fq results2/head_2.fq
[main] Real time: 62.164 sec; CPU: 116.315 sec
Executing: isolate_relevant_pairs_fq X_R1_001.fastq.gz X_R2_001.fastq.gz hg19.fa HHV6_seq.fa results2 results2/bam_0/
isolate_relevant_pairs_fq: line 13: syntax error near unexpected token `gzFile,'
isolate_relevant_pairs_fq: line 13: `KSEQ_INIT(gzFile, gzread)'
Executing: bwa mem -t 10 HHV6_hg19.fa results2/bam_0//retained-pairs_1.fq results2/bam_0//retained-pairs_2.fq | samtools view -b -F 2304 > results2/bam_0//retained-pairs.remapped.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `results2/bam_0//retained-pairs_1.fq'.
[main_samview] fail to read the header from "-".
Executing: samtools sort -@ 10 results2/bam_0//retained-pairs.remapped.bam -o results2/bam_0//retained-pairs.remapped.cs.bam
samtools sort: failed to read header from "results2/bam_0//retained-pairs.remapped.bam"
Executing: extract_clips HHV6_seq.fa results2 results2/bam_0/
extract_clips: line 15: syntax error near unexpected token `int,'
extract_clips: line 15: `KSEQ_INIT(int, read)'
Thanks in advance
Hi,
That looks really weird. isolate_relevant_pairs_fq is a binary exec, so I am not sure why it would give a syntax error. It is clearly not being executed as a binary executable.
What happens if you run
./isolate_relevant_pairs_fq X_R1_001.fastq.gz X_R2_001.fastq.gz hg19.fa HHV6_seq.fa results2 results2/bam_0/
?
Can you also ls the content of the SurVirus folder?
It produces the same error
(mypython3) [root@ip-10-11-5-10 SurVirus]# ./isolate_relevant_pairs_fq (path)/X_R1.fasq.gz (path)/X_R2.fasq.gz hg19.fa ../../HPVDetector_v1.0/HHV/HHV6_seq results2 results2/bam_0/
./isolate_relevant_pairs_fq: line 13: syntax error near unexpected token `gzFile,'
./isolate_relevant_pairs_fq: line 13: `KSEQ_INIT(gzFile, gzread)'
As for the contents of the folder:
CMakeCache.txt HHV6_seq.pac bp_region_consensus_builder.cpp filter hg19.fa.ann host_virus.fa.bwt isolate_relevant_pairs_fq random_pos_generator.py sam_utils.h
CMakeFiles HHV6_seq.sa build_libs.sh filter.cpp hg19.fa.bwt host_virus.fa.fai isolate_relevant_pairs_fq.cpp random_pos_generator.pyc sdust
CMakeLists.txt HHV6_seq_no_repeat.fa build_region-reads_associations filter_by_qname hg19.fa.fai host_virus.fa.pac ks-test.h reads_categorizer sparsehash-sparsehash-2.0.3
HHV6_seq HHV6_seq_no_repeat.fa.fai build_region-reads_associations.cpp filter_by_qname.cpp hg19.fa.pac host_virus.fa.sa libs reads_categorizer.cpp sparsehash-sparsehash-2.0.3.zip
HHV6_seq.amb LICENSE cmake_install.cmake get-realignments-for-qname hg19.fa.sa htslib-1.11 max_is_calc.py remapper surveyor.py
HHV6_seq.ann Makefile config.h get-realignments-for-qname.cpp host_virus.fa htslib-1.11.zip max_is_calc.pyc remapper.cpp sw_utils.h
HHV6_seq.bwt README.md extract_clips hg19.fa host_virus.fa.amb isolate_relevant_pairs merge_retained_reads results utils.h
HHV6_seq.fai bp_region_consensus_builder extract_clips.cpp hg19.fa.amb host_virus.fa.ann isolate_relevant_pairs.cpp merge_retained_reads.cpp results2
I think it is about installing. I got this error when I tried to cmake the script. I tried to install it on Centos server and on Ubuntu. I still have the error when compiling "NOTFOUNT".
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
HTS_LIB
linked by target "get-realignments-for-qname" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "filter" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "remapper" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "isolate_relevant_pairs_fq" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "filter_by_qname" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "bp_region_consensus_builder" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "reads_categorizer" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "build_region-reads_associations" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "extract_clips" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "isolate_relevant_pairs" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
linked by target "merge_retained_reads" in directory /mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus
-- Configuring incomplete, errors occurred!
See also "/mnt/fileshare/Temp/Virus_detection/SurVirus/test2/SurVirus/CMakeFiles/CMakeOutput.log".
I am not sure what is going on, I have never seen anything like that. It seems like it failed compiling because it cannot find htslib (did it compile correctly?), yet you seem to have executables (notice that for every cpp file you have what appears to be the related executable, without extension).
It seems like the executables are being executed as bash scripts.
If you run
head isolate_relevant_pairs_fq
what do you see?