Minimap2: [WARNING] For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.

[dangchenyuan]

when I used the nanopore data to map the Illunima raw data (150bp), the minimap2 was warnning as blow:
[WARNING] For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.
My code is :
minimap2 -ax sr all_nanopore_0-10reads.racon.consensus.fasta ../4-h-0-10_R1.fastq ../4-h-0-10_R2.fastq > Nano_NGS_aln.sam

[lh3]

As the warning message said – apply option --split-index.

[dangchenyuan]

Thank you!
But I find another question that the different potsion of "--split-prefix" can make different results.
for example,
If I used the code:
minimap2 -ax sr --split-prefix 4pf_0-10.clean.fasta 4PF-0-10_R1_prinseq_good_4pFy.fastq 4PF-0-10_R2_prinseq_good_M_b_.fastq > Nano4pfclean_NGS_aln.sam
I can get a 53G sam file.

But if I used the code:
minimap2 -ax sr 4pf_0-10.clean.fasta --split-prefix 4PF-0-10_R1_prinseq_good_4pFy.fastq 4PF-0-10_R2_prinseq_good_M_b_.fastq > Nano4pfclean_NGS_aln_smp.sam
I just can get a 41G sam file.

The two codes are just different in "--split-prefix " positions, why did I get different results?

[lh3]

Read the manual. --split-prefix requires an argument.

[hasindu2008]

@dangchenyuan

eg :

minimap2 -ax sr --split-prefix temp_name 4pf_0-10.clean.fasta 4PF-0-10_R1_prinseq_good_4pFy.fastq 4PF-0-10_R2_prinseq_good_M_b_.fastq > Nano4pfclean_NGS_aln_smp.sam

This will create temporary files in the current directory under the prefix _temp_name._
To use the _/tmp_ as the location for temporary files you can give --split-prefix /tmp/temp_name instead.

The problem in your ocmmands are as follows :

minimap2 -ax sr --split-prefix 4pf_0-10.clean.fasta 4PF-0-10_R1_prinseq_good_4pFy.fastq 4PF-0-10_R2_prinseq_good_M_b_.fastq > Nano4pfclean_NGS_aln.sam : 4pf_0-10.clean.fast is taken as the temporary file prefix and 4PF-0-10_R2_prinseq_good_M_b_.fastq will be mapped against 4PF-0-10_R1_prinseq_good_4pFy.fastq

minimap2 -ax sr 4pf_0-10.clean.fasta --split-prefix 4PF-0-10_R1_prinseq_good_4pFy.fastq 4PF-0-10_R2_prinseq_good_M_b_.fastq > Nano4pfclean_NGS_aln_smp.sam : 4PF-0-10_R1_prinseq_good_4pFy.fastq will be the temporary file prefix and 4PF-0-10_R2_prinseq_good_M_b_.fastq will be mapped against 4pf_0-10.clean.fasta.

[dangchenyuan]

@hasindu2008 @lh3 thank you very much