Error in reads alignment

[summus-kong]

Hi, when i run hic-pro, i got error.

bin=/mnt/data/hwb/hi_c/GES82185/HiC-Pro-2.11.1/bin/HiC-Pro $bin -i fq/ -o result/ -c config-hicpro.txt

Run HiC-Pro 2.11.1

Thu Mar 25 02:26:47 EDT 2021 Bowtie2 alignment step1 ... Logs: logs/sample1/mapping_step1.log [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit /mnt/data/hwb/hi_c/GES82185/HiC-Pro-2.11.1/bin/../scripts//Makefile:85: recipe for target 'bowtie_global' failed make: *** [bowtie_global] Error 1

[nservant]

Hi, Please have a look in the logs folder and look for an error message in the bowtie output files. Best

[FengjuanjuanCMS]

I encountered the same error，R1_bowtie2.log error message：(ERR): Description of arguments failed! How do I correct this error? Thank you very much.

[RuoYinLee]

Run HiC-Pro 3.1.0

2022年 04月 14日 星期四 12:16:12 CST Bowtie2 alignment step1 ... Logs: logs/sample/mapping_step1.log [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit make: *** [/home/lishiyong/HI-C/HIC-PRO/HiC-Pro-3.1.0/HiC-Pro_3.1.0/bin/../scripts//Makefile:88: bowtie_global] Error 1

mapping_step1.log /home/lishiyong/HI-C/HIC-PRO/bowtie2-2.4.5/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample/HIC003_S2_L001_R1_hg19_index.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HIC003_S2_L001_R1 -p 1 -x reference/hg19_index -U rawdata/sample/HIC003_S2_L001_R1.fastq 2>> logs/sample/HIC003_S2_L001_R1_bowtie2.log| /home/lishiyong/HI-C/JUICER/samtools-1-15.1/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/sample/HIC003_S2_L001_R1_hg19_index.bwt2glob.bam /home/lishiyong/HI-C/HIC-PRO/bowtie2-2.4.5/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/sample/HIC003_S2_L001_R2_hg19_index.bwt2glob.unmap.fastq --rg-id BMG --rg SM:HIC003_S2_L001_R2 -p 1 -x reference/hg19_index -U rawdata/sample/HIC003_S2_L001_R2.fastq 2>> logs/sample/HIC003_S2_L001_R2_bowtie2.log| /home/lishiyong/HI-C/JUICER/samtools-1-15.1/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/sample/HIC003_S2_L001_R2_hg19_index.bwt2glob.bam

HIC003_S2_L001_R2_bowtie2.log

HiC-Pro mapping

(ERR): "reference/hg19_index" does not exist or is not a Bowtie 2 index Exiting now ...

I have the same problem, I re-built the hg19_index files, but same result.

is there less storage left for program? I have only 25Gb for it and I run this program in vmware-ubuntu.

thank you

[nservant]

Hi, Could you show me how you set up the INDEXES and GENOME in the configuration file please ?

[RuoYinLee]

Hi,

I found the problem, there was wrong index files I made. the index files the bowtie2 built is not right. I downloaded six of index files from the index files , then all goes right, the HiC-Pro runs well. I am not sure what goes wrong with my bowtie2, I am sure I installed it right, but the sizes of index files I made with my laptop is not the same with I downloaded. So I think this is the problem. Thank you so much.

At 2022-04-20 00:27:04, "Nicolas Servant" @.***> wrote:

Hi, Could you show me how you set up the INDEXES and GENOME in the configuration file please ?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[Jiangjiangzhang6]

I met the same error , how to debug

[RuoYinLee]

in bowtie2 web site download the six index files for your running not built index files by yourself

[elenadelpup]

I have run HiC pro in several species following the very same steps and scripts, including Bowtie2 index creation, and I have this same error occurring only in one species:

---

Bowtie2 alignment step1 ... Logs: logs/SRR12034715/mapping_step1.log [main_samview] fail to read the header from "-". [main_samview] fail to read the header from "-". Exit: Error in reads alignment - Exit

Log files are: /carnegie/binaries/centos7/conda/3.7/envs/HiC-Pro_3.1.0/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/SRR12034702/SRR12034702_1_bowtie2.bwt2glob.unmap.fastq --rg-id BMG --rg SM:SRR12034702_1 -p 4 -x /carnegie/data/Shared/Labs/Rhee/Everyone/ElenaDelPup/HiCdata/genomes/wheat/bowtie2 -U rawdata/SRR12034702/SRR12034702_1.fastq 2>> logs/SRR12034702/SRR12034702_1_bowtie2.log| /carnegie/binaries/centos7/conda/3.7/envs/HiC-Pro_3.1.0/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/SRR12034702/SRR12034702_1_bowtie2.bwt2glob.bam /carnegie/binaries/centos7/conda/3.7/envs/HiC-Pro_3.1.0/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/SRR12034702/SRR12034702_2_bowtie2.bwt2glob.unmap.fastq --rg-id BMG --rg SM:SRR12034702_2 -p 4 -x /carnegie/data/Shared/Labs/Rhee/Everyone/ElenaDelPup/HiCdata/genomes/wheat/bowtie2 -U rawdata/SRR12034702/SRR12034702_2.fastq 2>> logs/SRR12034702/SRR12034702_2_bowtie2.log| /carnegie/binaries/centos7/conda/3.7/envs/HiC-Pro_3.1.0/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/SRR12034702/SRR12034702_2_bowtie2.bwt2glob.bam

[elenadelpup]

I have tried experimenting with the options --noauto --large-index of Bowtie2, in the case the defaults were not good anymore for the large genome I am using now (Triticum aestivum) but it is still not working. Best, Elena

[shRDJr]

Hello, I also encountered the same error, checked that the index and genome path were correct, but it still showed that it does not exist or is not a Bowtie 2 index, and my genome was not a model species and could not be downloaded in bowtie2 web. What should I do?

I found a solution in another issue