[E::sam_parse1] incomplete aux field

[a-pallav]

Hi,

I am encountering "incomplete aux field" when I am looking to execute pipel subcommand. please see detailed error log here.

[MM] /production/BatMeth2-master/bin/memalign c2t -1 Bis-AG876_S3_R1_001.fastq.clean.gz -2 Bis-AG876_S3_R2_001.fastq.clean.gz -o Bis-AG876.type2 | /production/BatMeth2-master/bin/bwame mem -t 8 -C -p -Y /production/References/ViralIndexes/batMeth/type2/EBV_type_2_complete_genome_FASTA_GenBank_NC_009334.1.fa.batmeth2.fa - | samtools sort -@ 8 -o ./Bis-AG876.type2.sort.bam - Process paired-end reads! Process input file: Bis-AG876_S3_R1_001.fastq.clean.gz, Bis-AG876_S3_R2_001.fastq.clean.gz [M::mem_align] read 0 ALT contigs [M::process] read 91692 sequences (10874058 bp)... [M::process] 0 single-end sequences; 91692 paired-end sequences [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 38061, 1, 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: (104, 129, 164) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 284) [M::mem_pestat] mean and std.dev: (137.14, 44.39) [M::mem_pestat] low and high boundaries for proper pairs: (1, 344) [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 91692 reads in 6.221 CPU sec, 0.785 real sec [E::sam_parse1] incomplete aux field samtools sort: truncated file. Aborting

[ZhouQiangwei]

Hi, could u please run the command below and check whether the sam file 'Bis-AG876.type2.sam' is correct?

/production/BatMeth2-master/bin/memalign c2t -1 Bis-AG876_S3_R1_001.fastq.clean.gz -2 Bis-AG876_S3_R2_001.fastq.clean.gz -o Bis-AG876.type2 | /production/BatMeth2-master/bin/bwame mem -t 8 -C -p -Y /production/References/ViralIndexes/batMeth/type2/EBV_type_2_complete_genome_FASTA_GenBank_NC_009334.1.fa.batmeth2.fa - > Bis-AG876.type2.sam

[a-pallav]

Hi, could u please run the command below and check whether the sam file 'Bis-AG876.type2.sam' is correct?

/production/BatMeth2-master/bin/memalign c2t -1 Bis-AG876_S3_R1_001.fastq.clean.gz -2 Bis-AG876_S3_R2_001.fastq.clean.gz -o Bis-AG876.type2 | /production/BatMeth2-master/bin/bwame mem -t 8 -C -p -Y /production/References/ViralIndexes/batMeth/type2/EBV_type_2_complete_genome_FASTA_GenBank_NC_009334.1.fa.batmeth2.fa - > Bis-AG876.type2.sam

Hi, Yes, above command works like a charm. with 35MB sam file.

[a-pallav]

Even this is working: /production/BatMeth2-master/bin/memalign c2t -1 Bis-AG876_S3_R1_001.fastq.clean.gz -2 Bis-AG876_S3_R2_001.fastq.clean.gz -o Bis-AG876.type2 | /production/BatMeth2-master/bin/bwame mem -t 8 -C -p -Y /production/References/ViralIndexes/batMeth/type2/EBV_type_2_complete_genome_FASTA_GenBank_NC_009334.1.fa.batmeth2.fa - | samtools sort -o ./Bis-AG876.type2.batmeth2.sorted.bam

I think there is an issue with samtools threads usage using -@ flag.

[ZhouQiangwei]

Great. Maybe you can check the version of samtools on your server?

[ZhouQiangwei]

http://www.htslib.org/doc/samtools-sort.html the new version of samtools is support -@ threads paramater, could you please update the samtools in your server

[a-pallav]

I see. it is using system / usr/local/bin samtools. Commands are working after I updated system samtools. Thank you very much.

I have another question. Our sequences have good stretch of repeat elements. Do you have recommendations to set the thresholds for viral data?

[ZhouQiangwei]

In fact, the mapping and analysis of repeat regions has always been very difficult, especially for DNA methylation data. At present, there are no separate parameters for this part in mapping and methylation level calculation. You can also do some processing according to the situation. For example, merge repeat regions. I hope you can successfully perform the analysis.

[a-pallav]

Hi Guoliang,

Thank you very much for getting back. I have one more question. How do I run pipel command but with using bwa-meth as the aligner of choice? I figured the pipel command requires parmeter1/2 files that it creates automatically if I use bat-meth2 internal aligner.

Please advise,

aparna

From: momocoding @.> Date: Sunday, May 1, 2022 at 2:40 AM To: GuoliangLi-HZAU/BatMeth2 @.> Cc: Aparna Pallavajjala @.>, Author @.> Subject: Re: [GuoliangLi-HZAU/BatMeth2] [E::sam_parse1] incomplete aux field (Issue #29)

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In fact, the mapping and analysis of repeat regions has always been very difficult, especially for DNA methylation data. At present, there are no separate parameters for this part in mapping and methylation level calculation. You can also do some processing according to the situation. For example, merge repeat regions. I hope you can successfully perform the analysis.

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[ZhouQiangwei]

hi, In the new version, we have removed the parameters of select aligner, and the BWA MEM align algorithm is used for alignment by default, so you can run bt2 directly. mo