针对conda环境中，trinity调用align_and_estimate_abundance.pl脚本时samtools报错！

首先时报错的内容：

(base) [root@localhost samtools]# samtools 
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

可以按如下命令解决

conda install -c bioconda samtools openssl=1.0

可是最近由于清华源的镜像用不了了，所以以上方法行不通。
所以旧的换个方法了，查看一下运行trinity调用脚本align_and_estimate_abundance.pl进行表达量估计的时候的报错：

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open  shared object file: No such file or directory
(ERR): bowtie2-align died with signal 13 (PIPE)
Error, cmd: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000  --end-to-end -k 200  -q -X 800 -x  /data1/spider/ytbiosoft/data/SF.fq.gz/trinity_out_dir_all.Trinity.fasta.bowtie2 -1  <(gunzip -c /data1/spider/ytbiosoft/data/SF.fq.gz/J2_1.fq.gz) -2 <(gunzip -c  /data1/spider/ytbiosoft/data/SF.fq.gz/J2_2.fq.gz) -p 20 | samtools view -F 4 -S -b  -o bowtie2.bam - died with ret: 32512 at  /data1/spider/miniconda3/envs/bioinforspace/bin/align_and_estimate_abundance.pl  line 766.

发现第脚本的766行报错，其实就是samtools包错，应该是conda环境里少了一个东西，那咋门就不用conda环境中的samtools，用自己在外面安装的samtools.
具体解决办法就是吧align_and_estimate_abundance.pl这个脚本类调用conda环境的samtools的全换成自己再外面安装的samtools:

改之前

改之后

再看看与报错哪里有何不同：

CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000  --end-to-end -k 200  -q -X 800 -x  /data1/spider/ytbiosoft/data/SF.fq.gz/trinity_out_dir_all.Trinity.fasta.bowtie2 -1  <(gunzip -c /data1/spider/ytbiosoft/data/SF.fq.gz/J2_1.fq.gz) -2 <(gunzip -c  /data1/spider/ytbiosoft/data/SF.fq.gz/J2_2.fq.gz) -p 20 | samtools view -F 4 -S -b  -o bowtie2.bam -
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open  shared object file: No such file or directory
(ERR): bowtie2-align died with signal 13 (PIPE)
Error, cmd: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000  --end-to-end -k 200  -q -X 800 -x  /data1/spider/ytbiosoft/data/SF.fq.gz/trinity_out_dir_all.Trinity.fasta.bowtie2 -1  <(gunzip -c /data1/spider/ytbiosoft/data/SF.fq.gz/J2_1.fq.gz) -2 <(gunzip -c  /data1/spider/ytbiosoft/data/SF.fq.gz/J2_2.fq.gz) -p 20 | samtools view -F 4 -S -b  -o bowtie2.bam - died with ret: 32512 at  /data1/spider/miniconda3/envs/bioinforspace/bin/align_and_estimate_abundance.pl  line 766.

CMD: set -o pipefail && bowtie2 --no-mixed --no-discordant --gbar 1000  --end-to-end -k 200  -q -X 800 -x  /data1/spider/ytbiosoft/data/SF.fq.gz/cd-hit.out.bowtie2 -1 <(gunzip -c  /data1/spider/ytbiosoft/data/SF.fq.gz/J2_1.fq.gz) -2 <(gunzip -c  /data1/spider/ytbiosoft/data/SF.fq.gz/J2_2.fq.gz) -p 20 |  /data/zhaoqingyuan/biosoft/samtools-1.3.1/samtools view -F 4 -S -b -o bowtie2.bam  -
35301153 reads; of these:
  35301153 (100.00%) were paired; of these:
    12049295 (34.13%) aligned concordantly 0 times
    17229355 (48.81%) aligned concordantly exactly 1 time
    6022503 (17.06%) aligned concordantly >1 times
65.87% overall alignment rate
CMD: touch bowtie2.bam.ok

我们发现这个脚本不在调用conda环境内的samtools了，而是调用我在外面安装的samtools了，问题就解决了.

具体在哪改可以吧脚本考到Notepad++中去改，可以Ctrl+F搜索。