make: *** [/HiC-Pro_3.0.0/bin/../scripts//Makefile:144: bowtie_pairing] Error 1

[ld9866]

Hello! l am using the docker version hic-pro, but l find it is hard for me because the step "Pairing of R1 and R2 tags ..." is always wrong, can you tell me how to solve this problem? Thank you！

Run HiC-Pro 3.0.0

Mon Aug 16 14:31:19 UTC 2021 Bowtie2 alignment step1 ... Logs: logs/rawdata/mapping_step1.log

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Tue Aug 17 09:46:26 UTC 2021 Bowtie2 alignment step2 ... Logs: logs/rawdata/mapping_step2.log

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Tue Aug 17 15:22:47 UTC 2021 Combine R1/R2 alignment files ... Logs: logs/rawdata/mapping_combine.log

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Tue Aug 17 17:33:15 UTC 2021 Mapping statistics for R1 and R2 tags ... Logs: logs/rawdata/mapping_stats.log

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Tue Aug 17 18:26:20 UTC 2021 Pairing of R1 and R2 tags ... Logs: logs/rawdata/mergeSAM.log make: *** [/HiC-Pro_3.0.0/bin/../scripts//Makefile:144: bowtie_pairing] Error 1

[nservant]

Hi, Could you please check the logs/rawdata/mergeSAM.log file ? and tell me which files you have in the mapping output folder (and if they are not empty) ? Thanks

[ld9866]

Hello! I found that this is mainly due to the mismatch between the data of my two chains. I am now trying a new one. Thank you for your help!

[jacomegutierrez]

Hello, I have the same error, in the mergeSAM.log file says "Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted." How can I fix it? apparently my fastq files are ok.

[ld9866]

Dear jacomegutierrez: Did you test on the original data? Please remember that due to double-stranded sequencing, the quality control of the two strands needs to be performed at the same time. If this does not work, try another software, such as juicer, etc. Best wishes!

[KurotakiDaisuke]

Hello, I am using conda HiC-pro 3.1.0. I have the same error. I prefer to use the HiC-pro instead of other software. Is there any solution to this problem? Thanks!

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Pairing of R1 and R2 tags ... Logs: logs/sample1/mergeSAM.log make: *** [/root/HiC-Pro/bin/../scripts//Makefile:144: bowtie_pairing] Error 1

/HiC-Pro_3.1.0/scripts/mergeSAM.py -q 10 -t -v -f bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam -r bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam -o bowtie_results/bwt2/sample1/SKK1_combined_q_genome.bwt2pairs.bam [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam' [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam'

mergeBAM.py

forward= bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam

reverse= bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam

output= bowtie_results/bwt2/sample1/SKK1_combined_q_genome.bwt2pairs.bam

min mapq= 10

report_single= False

report_multi= False

verbose= True

Merging forward and reverse tags ...

Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted.

[ld9866]

您好， 我正在使用 conda HiC-pro 3.1.0。我遇到了同样的错误。 我更喜欢使用 HiC-pro 而不是其他软件。 这个问题有解决办法吗？ 谢谢！

R1 和 R2 标签配对... 日志：logs/sample1/mergeSAM.log make：*** [/root/HiC-Pro/bin/../scripts//Makefile:144: bowtie_pairing] 错误 1

/HiC-Pro_3.1.0/scripts/mergeSAM.py -q 10 -t -v -f bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam -r bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam -o bowtie_results/bwt2/sample1/SKK1_combined_q_genome.bwt2pairs.bam [E::idx_find_and_load] 无法检索“bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam”的索引文件 [E::idx_find_and_load] 无法检索'bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam'

合并BAM.py

转发= bowtie_results/bwt2/sample1/SKK1_combined_q_R1_genome.bwt2merged.bam

反向= bowtie_results/bwt2/sample1/SKK1_combined_q_R2_genome.bwt2merged.bam

输出 = bowtie_results/bwt2/sample1/SKK1_combined_q_genome.bwt2pairs.bam

最小 mapq= 10

report_single=False

report_multi = False

详细=真

合并正向和反向标签...

正向和反向读取不成对。请检查 BAM 文件是否具有相同的读取名称并且已排序。

You could try juicer first, or use some example data to try to know whether the data is ok

[KurotakiDaisuke]

Thanks! I have already analyzed the same fastq files using Juicer and successfully obtained output files such as .hic files.

[ld9866]

OK

[KurotakiDaisuke]

Can I convert Juicer .hic files to validPairs files? Thanks for your help!