Minimap2: the .sam file generated from minimap2 can not convert to .bam file

[dangchenyuan]

when I used minimap2 to map Illunima paired reads to assemebled contigs, the header of the sam file seems to be wrong.
my minimap2 code is : minimap2 -ax sr ../contigs.longer500.fasta ../../4PF-0-10_1_R1.fq ../../4PF-0-10_1_R2.fq > 4PF_mapping_aln.sam
the header of sam is:
[M::mm_idx_gen::4.2701.41] collected minimizers
[M::mm_idx_gen::4.8921.60] sorted minimizers
@SQ SN:NODE_1_length_85864_cov_10.921310 LN:85864
@SQ SN:NODE_2_length_74117_cov_12.025521 LN:74117
@SQ SN:NODE_3_length_71198_cov_10.602147 LN:71198
.......

after that, I convert .sam file to .bam file using samtools, there is an error like this:
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

[wdecoster]

Did you use nohup with this alignment? Your stderr is mixed with your stdout (the sam file).

[jmarshall]

This is another example of why it is good for tools to have a -o FILE option to do built-in output redirection, rather than depending on shell redirections to do the simple expected thing in less simple circumstances like nohup.

Happily minimap2 has acquired such an option in 8b05880f73c76ccc00d2d1aa62eb3c999ca1c130.

[lh3]

As @wdecoster and @jmarshall said. Another solution is to use -v1 to disable messages and warnings. Nonetheless, it is still recommended to get familiar with piping. That way you can directly generate a BAM file, saving both disk space and wall-clock time.

[dangchenyuan]

@wdecoster @jmarshall @lh3 thanks a lot. But how can I generate a BAM file using minimap2 directly ?

[wdecoster]

By piping the output of minimap2 into samtools:

minimap2 -ax sr ../contigs.longer500.fasta ../../4PF-0-10_1_R1.fq ../../4PF-0-10_1_R2.fq | samtools sort -o 4PF_mapping_aln.bam

Note that this may not solve your issue if you use nohup.