Do not have an answer for you, but this also happens to me. Sometimes if I re-convert the files (even if I know there is nothing wrong with the file based on viewing in SeeMS), or use less threads, I do not have the issue.
Thank you for your reply. I have tried doing same as suggested by you and also changing the sequence of samples in the list for processing but still got stuck at same place (screenshot attached).
@Hiroshi Tsugawa and @MS DIAL TEAM I believe that, a skip button to go to next step bypassing those unprocessed sample will be helpful in such case. Looking forward to get this feature in coming updates.
Besides, GCMS library is not suitable for LCMS data as GCMS uses hard ionization while LCMS uses soft one and the fragments of a given substance in these two systems could vary a lot. For annotating LCMS data, Hiroshi's team has compiled publicly available libraries in both positive and negative modes. You can download libraries here http://prime.psc.riken.jp/compms/msdial/main.html#MSP.
In GC-MS, first, you should choose the msp library that contains retention index (RI) by the same column as you use. The RI value should be reliable. (but hopefully, if you do TMS-derivative metabolite profiling, analyzing standards of sugar compounds like glucose and galactose is needed to validate the results because they have very similar RI/RT values.
Then, you may use the library like "All records with Kovats RI" that contains experimental/predicted RI values. Not all of RI values should be compatible with your experimental data, but the annotation using this wider coverage library will be helpful for your annotation pipeline.
what could be the possible reason for skipping the sample processing as shown in attached image. I repeated it with different set of samples, found the same result. Also, what to do next when its stuck at this level?