继续获取错误：[E::fai_build3_core]未能打开我一直在使用的脚本的文件区域

Question

我一直在使用下面的脚本，然而，我不断地得到一个错误的输出。知道为什么吗？

#!/bin/bash

set - eu

bam_input=$3

geome=/storage1/DISK1/TCGA_scripts/ref_genome/GRCh38.ref.fa
export genome




function bam_chromosomes {
        samtools idxstats $bam_input | cut -f 1 | grep -v '*'
}

export -f bam_chromosomes




function parallel_call {
    bcftools mpileup \
        --fasta-ref ${genome} \
        --regions $2 \
        --output-type u \
        $1 | \
    bcftools call --multiallelic-caller \
                  --variants-only \
                  --output-type u - > ${1/.bam/}.$2.bcf
}

export -f parallel_call


chrom_set=`bam_chromosomes test.bam`
parallel --verbose -j 90% parallel_call sample_A.bam ::: ${chrom_set}

上面的脚本是并行化流程mpil发的第一步，它应该计算.bam文件中的变体。以下错误一直处于锁定状态：

parallel_call sample_A.bam 'Usage:'
parallel_call sample_A.bam samtools
parallel_call sample_A.bam idxstats
parallel_call sample_A.bam '[options]'
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are     diploid
[E::fai_build3_core] Failed to open the file --regions
Failed to open -: unknown file type
parallel_call sample_A.bam '<in.bam>'
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are   diploid
[E::fai_build3_core] Failed to open the file --regions
Failed to open -: unknown file type
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are   diploid
[E::fai_build3_core] Failed to open the file --regions
Failed to open -: unknown file type
parallel_call sample_A.bam --input-fmt-option
parallel_call sample_A.bam 'OPT[=VAL]'
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are  diploid
[E::fai_build3_core] Failed to open the file --regions
Failed to open -: unknown file type
parallel_call sample_A.bam Specify
parallel_call sample_A.bam a
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[E::fai_build3_core] Failed to open the file --regions

理论上，上面的脚本应该使用变量替换${1/..bam/}.$2.bcf创建许多文件，从而避免了文件名冲突。我很难上传任何一个文件，因为它们很大，而且我的互联网速度非常慢。谢谢你的帮助。

Answer 1

建议替换线：

 geome=/storage1/DISK1/TCGA_scripts/ref_genome/GRCh38.ref.fa

一行：

 genome=/storage1/DISK1/TCGA_scripts/ref_genome/GRCh38.ref.fa