extract unmapped reads from the paired end samples using hisat2

Hi AlI,
I am trying to get the unmapped reads for paired end samples using hisat2 and command is :

hisat2  
-S {output.sam} 
-x {params.index} 
-1 {input.fq1} 
-2 {input.fq2} 
--un-conc {output.fq}
--threads {threads}

I am getting an error of

Waiting at most 60 seconds for missing files. Removing output files of failed job remove_host_reads since they might be corrupted: p21005_ht2.sam

But when I ran the same sample without --un-conc option, it worked (and gave me both mapped + unmapped reads which are crazy big files).If I omitted ".sam" in the output as I am interested in unmapped reads, I got the error of "missing files". Any help would be appreciated.Thanks


unmappedreads


pairedends


hisat2

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