cicero公开提供了一个软件系统，可以更好地检测基因融合。这个名为西塞罗（CICERO）的系统为癌症研究提供了新的视角，也为药物治疗提供了新的靶点。网址https://github.com/stjude/CICERO

cicero仅支持GRCh37-lite or GRCh38_no_alt这个两个库，GRCh38_no_alt已经下载在/TJPROJ6/RNA_SH/software/CICERO-master/database

软件下载路径：

  /TJPROJ6/RNA_SH/software/CICERO-master

使用/TJPROJ6/RNA_SH/software/CICERO-master/src/scripts/Cicero.sh 做测试，需要star比对bam，通过github中需要使用docker或者singularity得到*.junctions.tab.shifted.tab，具体命名如下：

docker run -v <outdir>:/results ghcr.io/stjude/rnapeg:latest -b bamfile -f fasta -r refflat
· fasta reference genome; i.e. "Homo_sapiens/GRCh38_no_alt/FASTA/GRCh38_no_alt.fa" or "Homo_sapiens/GRCh37-lite/FASTA/GRCh37-lite.fa" from Reference Files.
· refflat i.e. "Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt" or "Homo_sapiens/GRCh37-lite/mRNA/Combined/all_refFlats.txt" from Reference Files.

或者

singularity run --containall --bind <outdir>:/results docker://ghcr.io/stjude/rnapeg:latest -b bamfile -f fasta -r refflat

测试到以上步骤卡住，报错如下：

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:a0d0a0d46f8b52473982a3c466318f479767577551a53ffc9074c9fa7035982e
Copying blob sha256:29dd7c3b051f400bc4d6ec2107095a9d2d56f552efdb161863babc3c939778ed
Copying blob sha256:1df097a71bdca139e8f6afe9f2ef1dc0bd0102eccee737a971b4747d16033376
Copying blob sha256:ec672de6e236a393821e56a33c510b07d6f249426b4dcf87f3965218c6c117f9
Copying blob sha256:057bfa539d0c5d1558c5b6d8bc61ae47b27aa1a5aa718fc915af2a6bd4bfaa3d
Copying blob sha256:4b87f6fe92569ca11522e34876b3cab94d1a6f2bb0d390de599206d621527e50
Copying blob sha256:d4e6e3873ebe0d92a006253ac8909dbb3bfa420327c374fe0637fc4eed2d9e54
Copying blob sha256:68bf93fc04e21d478db9b18e0ee77a110a75832082119890855bc37639b21a6d
Copying blob sha256:59b30f0d0533ef51fb78209eedbe98928cac625984421754be28c9aba03cc121
Copying blob sha256:68030b3155a8e0ec3154d38e6f44db435cdee02b4cd359005c2f2ee092b90708
Copying blob sha256:b92ee98f5e739d99d6991bf2546ba5046e49687f0210ca71dc5b4b3f0a70881b
Copying blob sha256:7ede5b957ee8c6357f6c4ca114de03d3ee88487e9e109d88da8da2b10c38b9f8
Copying blob sha256:40496b4038082007c4289a07844d71033975987ab55f452aedb12628a9ef6012
Copying blob sha256:30e59702c3f97a7ca42c290dca2a82f33f32a306ea3901d04422033307ae9bb4
Copying blob sha256:c0dd8c286a9290612ba1b23785071be1e14c5b33f551884d43a4d1f8d9e9746e
Copying blob sha256:16f83a6fb2e10147af4d0d963cf5afebcd5ed7205f8fbcbd1006c9b213b708c7
Copying blob sha256:d1acad9f4e6932cb86403531f3464a7fcfba2c2443a02dba16f422f575cc5dbd
Copying blob sha256:2529ea849bf3678f30d316d1da910d030c5359c482d31c780dd8179b3c511cf3
Copying blob sha256:ce010ed65131be1d98d42ff8a87391c3b32c9ed39ccf404892e12880d64cdf41
Copying blob sha256:81b25b25bbf9245503b97038c0f4617876d40b6e1e1a9a7e59f4845fa1f49cb5
Copying blob sha256:ff509268ec568ad51c6df24f8dda65255fbbf3ed936ed499c9feff1d5d2cb5f8
Copying blob sha256:272f361ce2c11d4d7ece24528e041b8c5fbcba1a4fd3389fc3b5e90d07be2c14
Copying blob sha256:0f049d4e65405ad78df10d7f297c1f2430c11dda877354e52cadf97489019b1e
Copying blob sha256:b1928f4b4c2a88585053f396b69b2b2f4ea75764869b214634b2a09c84fd3fad
Copying blob sha256:2b7bae88c86f6b228ae4bc4be17b504276d7284c7aba66b2ab4c06a29af31237
Copying blob sha256:f9221ec50a32010ab52a05c01c525764ccbe10958a922924a93bffce2bbd6fb0
FATAL:   Unable to handle docker://ghcr.io/stjude/rnapeg:latest uri: while building SIF from layers: conveyor 
failed to get: initializing source 
oci:/home/zhangxin/.singularity/cache/blob:43ead3c309652700081f9c2362b09788d13f434f24aa405bc7bf5958c922191d: 
writing blob: happened during read: read tcp 10.64.1.137:36706->185.199.108.154:443: read: connection reset by peer