If the specified SnpEff database version has not yet been downloaded, the parallelized SnpEff instances called by the bash script will cause three simultaneous download attempts into the same /tmp/ subdirectory (because SnpEff automatically downloads databases if they are not already downloaded, and the /tmp/ subdirectory used to cache the download is hard-coded), probably setting up some race condition, and causing all the downloads to fail:
java.lang.RuntimeException: java.io.FileNotFoundException: /tmp/snpEff_v5_0_GRCh37.87.zip (No such file or directory)
at org.snpeff.util.Download.unzip(Download.java:395)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:33)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1227)
at org.snpeff.SnpEff.loadDb(SnpEff.java:514)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:940)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923)
at org.snpeff.SnpEff.run(SnpEff.java:1188)
at org.snpeff.SnpEff.main(SnpEff.java:168)
Caused by: java.io.FileNotFoundException: /tmp/snpEff_v5_0_GRCh37.87.zip (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:112)
at org.snpeff.util.Download.unzip(Download.java:330)
... 9 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:940)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923)
at org.snpeff.SnpEff.run(SnpEff.java:1188)
at org.snpeff.SnpEff.main(SnpEff.java:168)
I do not think there is an easy fix to this, so I would propose adding a disclaimer for this in the README.
If the specified SnpEff database version has not yet been downloaded, the parallelized SnpEff instances called by the bash script will cause three simultaneous download attempts into the same
/tmp/subdirectory (because SnpEff automatically downloads databases if they are not already downloaded, and the/tmp/subdirectory used to cache the download is hard-coded), probably setting up some race condition, and causing all the downloads to fail:I do not think there is an easy fix to this, so I would propose adding a disclaimer for this in the README.