nservant
mergeSAM.log error
Dear HiC-Pro Authors,
Thank you for your software. However, I encountered an error while running my own data:
Pairing of R1 and R2 tags ... Logs: logs/Fuji/mergeSAM.log Makefile:144: bowtie_pairing] Error 1
Upon further investigation, I found the following error in the mergeSAM.log file.
I have tried many solutions, including installing the HiC-Pro Singularity image, but I still haven't been able to resolve this issue.
Could you kindly assist me with this problem? I greatly appreciate your help.
Best regards, Haochen Sun
Could you check the read names in R1/R2 files. They should be identical, and it seems that recently some sequencers add /1, /2 at the end of the read names .... which make HiC-Pro crashing
Could you check the read names in R1/R2 files. They should be identical, and it seems that recently some sequencers add
/1,/2at the end of the read names .... which make HiC-Pro crashing
Excuse me，I have a same error when I running HiC-pro process. My error like this: Run HiC-Pro 3.1.0
Bowtie2 alignment step1 ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_step1.log
Bowtie2 alignment step2 ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_step2.log
Combine R1/R2 alignment files ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_combine.log
Mapping statistics for R1 and R2 tags ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_stats.log
Pairing of R1 and R2 tags ... Logs: logs/iPSC_P13_Hi-C_R1r1/mergeSAM.log make: *** [path../../HiC-Pro_3.1.0/bin/../scripts//Makefile:144: bowtie_pairing] Error 1
And this is my mergeSAMlog: python_path/../bin/python /../HiC-Pro_3.1.0/scripts/mergeSAM.py -q 0 -t -v -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam -r bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_hg38.bwt2pairs.bam [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam' [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam'
mergeBAM.py
forward= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam
reverse= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam
output= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_hg38.bwt2pairs.bam
min mapq= 0
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.
And my mapping_conbine.log is : ../bin/samtools merge -@ 144 -n -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam bowtie_results/bwt2_global/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2glob.bam bowtie_results/bwt2_local/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2glob.unmap_bwt2loc.bam ../bin/samtools merge -@ 144 -n -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam bowtie_results/bwt2_global/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2glob.bam bowtie_results/bwt2_local/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2glob.unmap_bwt2loc.bam ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_1_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_2_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam ../bin/HiC-Pro_3.1.0/scripts/hic.inc.sh: Line 86: 2519760 Killed ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_1_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam [bam_sort_core] merging from 288 files and 144 in-memory blocks... mv bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam
With your answer for hcsun1, I while try your solvement, but how can I check the read names in my files? Like that: iPSC_P13_Hi-C_R1r1_1.fq.gz iPSC_P13_Hi-C_R1r1_2.fq.gz If you need the config-hicpro.txt ,I while support it.Thanks a lot
I also encountered the same problem during the run（mapping）. I have checked my bam file in bwt2. Some of the content is as follows：(hicpro) iy1702@iyun17:~$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R1.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.2 SRR12062646.3 SRR12062646.4 SRR12062646.5 SRR12062646.6 SRR12062646.7 SRR12062646.8 SRR12062646.9 SRR12062646.10 (hicpro) iy1702@iyun17:~$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R2.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.1 SRR12062646.2 SRR12062646.2 SRR12062646.3 SRR12062646.3 SRR12062646.4 SRR12062646.4 SRR12062646.5 SRR12062646.5 ，Indeed, as you said, how should I specifically solve this problem? Thank you!
Hello, the problem I encountered before, I think it should be caused by insufficient computer memory. After I added memory, there was no similar error report. However, I have not encountered your problem before. If I can help you with anything, we can discuss it via email.
At 2024-11-29 16:06:37, "lilongjuan" @.***> wrote:
I also encountered the same problem during the run（mapping）. I have checked my bam file in bwt2. Some of the content is as follows：(hicpro) @.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R1.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.2 SRR12062646.3 SRR12062646.4 SRR12062646.5 SRR12062646.6 SRR12062646.7 SRR12062646.8 SRR12062646.9 SRR12062646.10 (hicpro) @.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R2.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.1 SRR12062646.2 SRR12062646.2 SRR12062646.3 SRR12062646.3 SRR12062646.4 SRR12062646.4 SRR12062646.5 SRR12062646.5 ，Indeed, as you said, how should I specifically solve this problem? Thank you!
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hello, the problem I encountered before, I think it should be caused by insufficient computer memory. After I added memory, there was no similar error report. However, I have not encountered your problem before. If I can help you with anything, we can discuss it via email. At 2024-11-29 16:06:37, "lilongjuan" @.> wrote: I also encountered the same problem during the run（mapping）. I have checked my bam file in bwt2. Some of the content is as follows：(hicpro) @.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R1.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.2 SRR12062646.3 SRR12062646.4 SRR12062646.5 SRR12062646.6 SRR12062646.7 SRR12062646.8 SRR12062646.9 SRR12062646.10 (hicpro) @.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R2.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.1 SRR12062646.2 SRR12062646.2 SRR12062646.3 SRR12062646.3 SRR12062646.4 SRR12062646.4 SRR12062646.5 SRR12062646.5 ，Indeed, as you said, how should I specifically solve this problem? Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.>
Hello, thank you very much for your reply, but I don't particularly understand which problem you encountered before. Can you tell me more about it? I am very eager to get your help to solve the problem I am currently encountering. Thank you again.
Hello, the problem I encountered before, I think it should be caused by insufficient computer memory. After I added memory, there was no similar error report. However, I have not encountered your problem before. If I can help you with anything, we can discuss it via email. At 2024-11-29 16:06:37, "lilongjuan" @.> wrote: I also encountered the same problem during the run（mapping）. I have checked my bam file in bwt2. Some of the content is as follows：(hicpro) _@**._:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R1.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.2 SRR12062646.3 SRR12062646.4 SRR12062646.5 SRR12062646.6 SRR12062646.7 SRR12062646.8 SRR12062646.9 SRR12062646.10 (hicpro) _@.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R2.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.1 SRR12062646.2 SRR12062646.2 SRR12062646.3 SRR12062646.3 SRR12062646.4 SRR12062646.4 SRR12062646.5 SRR12062646.5 ，Indeed, as you said, how should I specifically solve this problem? Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.**_>
Hello, thank you very much for your reply, but I don't particularly understand which problem you encountered before. Can you tell me more about it? I am very eager to get your help to solve the problem I am currently encountering. Thank you again.
Hello，the problem I encountered before was that the operation stopped before the mergesam stage, and there would be a log file (there would be a log in the commit step, but I deleted it before, sorry), but then I speculated that it was a memory overflow, and the relationship between threads and memory is still worth considering in hicpro, so I think if you check the logs file and find that there is a similar problem, you can adjust the threads and memory in the config file, which may help you.
Hello, thank you very much for your patient answer. I do have the problem you mentioned, but I also made some modifications before I encountered this problem as you said. thank you very much for your reply!
---- Replied Message ---- | From | @.> | | Date | 12/8/2024 18:31 | | To | @.> | | Cc | @.>, @.> | | Subject | Re: [nservant/HiC-Pro] mergeSAM.log error (Issue #649) |
Hello, the problem I encountered before, I think it should be caused by insufficient computer memory. After I added memory, there was no similar error report. However, I have not encountered your problem before. If I can help you with anything, we can discuss it via email. At 2024-11-29 16:06:37, "lilongjuan" @.> wrote: I also encountered the same problem during the run（mapping）. I have checked my bam file in bwt2. Some of the content is as follows：(hicpro) @**.:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R1.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.2 SRR12062646.3 SRR12062646.4 SRR12062646.5 SRR12062646.6 SRR12062646.7 SRR12062646.8 SRR12062646.9 SRR12062646.10 (hicpro) @.*:$ samtools view /media/desk15/iy1702/newstools/HiC-Pro_3.1.0/output_data/bowtie_results/bwt2/sample1/sample1_R2.bam | head -n 10 | cut -f1 SRR12062646.1 SRR12062646.1 SRR12062646.2 SRR12062646.2 SRR12062646.3 SRR12062646.3 SRR12062646.4 SRR12062646.4 SRR12062646.5 SRR12062646.5 ，Indeed, as you said, how should I specifically solve this problem? Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @._>
Hello, thank you very much for your reply, but I don't particularly understand which problem you encountered before. Can you tell me more about it? I am very eager to get your help to solve the problem I am currently encountering. Thank you again.
Hello，the problem I encountered before was that the operation stopped before the mergesam stage, and there would be a log file (there would be a log in the commit step, but I deleted it before, sorry), but then I speculated that it was a memory overflow, and the relationship between threads and memory is still worth considering in hicpro, so I think if you check the logs file and find that there is a similar problem, you can adjust the threads and memory in the config file, which may help you.
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>