Alignment failed

[cherryDAP]

I used juicer1.6 and juicer2 to assemble the hic data respectively, but both reported errors in the comparison step. I downloaded the latest juicer-tools.

The download code is as follows: cd juicer-1.6/ ln -s CPU scripts cd scripts/common wget https://github.com/aidenlab/Juicebox/releases/download/v2.17.00/juicer_tools_2.17.00.jar ln -s juicer_tools_2.17.00.jar juicer_tools.jar

The running code is as follows： nohup bash /ME4012_Vol0002/dengaiping/software/juicer/scripts/juicer.sh -g SanyaOcu -z /ME4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi.fa/reference/SanyaOcu.fa -y /ME4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi.fa/restriction_sites/SanyaOcu_DpnII.txt -p /ME4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi.fa/restriction_sites/SanyaOcu.chrom.size -s DpnII -D /ME4012_Vol0002/dengaiping/software/juicer/CPU -t 25 &> juicer.log &

The two errors are: [M::mem_pestat] (25, 50, 75) percentile: (513, 1719, 4473) 9644 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12393) 9645 [M::mem_pestat] mean and std.dev: (2777.48, 2737.17) 9646 [M::mem_pestat] low and high boundaries for proper pairs: (1, 16353) 9647 [M::mem_pestat] analyzing insert size distribution for orientation RR... 9648 [M::mem_pestat] (25, 50, 75) percentile: (800, 2377, 5061) 9649 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13583) 9650 [M::mem_pestat] mean and std.dev: (3207.29, 2823.76) 9651 [M::mem_pestat] low and high boundaries for proper pairs: (1, 17844) 9652 [M::mem_pestat] skip orientation FF 9653 [M::mem_pestat] skip orientation RF 9654 [M::mem_pestat] skip orientation RR 9655 [M::mem_process_seqs] Processed 1044668 reads in 780.379 CPU sec, 49.587 real sec 9656 [fsync] Input/output error 9657 ***! Alignment of /ME4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi.fa/splits/SY1-F2-3_R1.fastq.gz /ME4 012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi.fa/splits/SY1-F2-3_R2.fastq.gz failed.

9646 [M::mem_pestat] mean and std.dev: (2750.11, 2680.78) 9647 [M::mem_pestat] low and high boundaries for proper pairs: (1, 16062) 9648 [M::mem_pestat] analyzing insert size distribution for orientation RR... 9649 [M::mem_pestat] (25, 50, 75) percentile: (742, 2423, 5081) 9650 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13759) 9651 [M::mem_pestat] mean and std.dev: (3196.86, 2815.57) 9652 [M::mem_pestat] low and high boundaries for proper pairs: (1, 18098) 9653 [M::mem_pestat] skip orientation FF 9654 [M::mem_pestat] skip orientation RF 9655 [M::mem_pestat] skip orientation RR 9656 [M::mem_process_seqs] Processed 796818 reads in 575.975 CPU sec, 26.110 real sec 9657 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0) 9658 [M::mem_pestat] skip orientation FF as there are not enough pairs 9659 [M::mem_pestat] skip orientation FR as there are not enough pairs 9660 [M::mem_pestat] skip orientation RF as there are not enough pairs 9661 [M::mem_pestat] skip orientation RR as there are not enough pairs 9662 [mem_sam_pe] paired reads have different names: "@EEFFFGFFFFEFCBDGEFFFFAEFFFFFFG=F", "E100051117L1C007R0231643190" 9663 9664 ***! Alignment of /ME4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi2.fa/splits/SY1-F2-3_R1.fastq.gz /ME 4012_Vol0002/dengaiping/genome_analysis/三亚基因组分析/hic数据辅助组装/hifi2.fa/splits/SY1-F2-3_R2.fastq.gz failed.

Before, I cloned juicer2 directly, and juicer-tools was an old version, but I couldn't generate .hic in one step at the end, so I downloaded the latest juicer-tools and ran it again, but an error was reported earlier. Please help me, what is the possible problem?

[moshe-olshansky]

Hi there,

The problem is found here:

9662 [mem_sam_pe] paired reads have different names: "@EEFFFGFFFFEFCBDGEFFFFAEFFFFFFG=F", "E100051117L1C007R0231643190"

Your fastq files (at least one of them) seem to be corrupted.

[cherryDAP]

thanks for your answer, do you know what is the reason for the other error

[liuchanchan0317]

have you solved the issues?