the command line can not be run with "nohup"

[cnxiaobo94]

[laixl@L001 MSMC2]$ nohup bcftools mpileup -Ou -r CM035273.1 -f ../../../refgenomes/xbinewg/GCA_020226075.1_Hydropotes_inermis_genomic.fa AS_N1.bam --threads 16 | bcftools call -c --threads 16 -V indels | ../../../MSMC2/msmc-tools/bamCaller.py 12 AS_N1_chr5_mask.bed.gz > AS_N1_chr5.vcf &
[3] 100129
[laixl@L001 MSMC2]$ nohup: ignoring input and redirecting stderr to stdout
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[E::hts_hopen] Failed to open file -
[E::hts_open_format] Failed to open file "-" : Exec format error
Failed to read from standard input: Exec format error

Hi, could you help me with this? The "bcftools mpileup -Ou -r CM035273.1 -f ../../../refgenomes/xbinewg/GCA_020226075.1_Hydropotes_inermis_genomic.fa AS_N1.bam --threads 16 | bcftools call -c --threads 16 -V indels | ../../../MSMC2/msmc-tools/bamCaller.py 12 AS_N1_chr5_mask.bed.gz > AS_N1_chr5.vcf" can be run in a window and generate the two requested files. When I add a nohup task, it got an error.

[stschiff]

No idea. I'm afraid I can't support nohup, nor how to run bcftools. If it helps, you can split up the pipeline and first generate the pileup-output into a separate file and then feed that to bamCaller.