Thanks, So I have try the first option and it wasn’t successful 
this is the output:
bash-4.2$ eval (cryosparcm env)
bash-4.2 mongod --dbpath ./ --repair
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] MongoDB starting : pid=38942 port=27017 dbpath=./ 64-bit host=cryogpu2.csb.vanderbilt.edu
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] modules: none
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] build environment:
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] distarch: x86_64
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] target_arch: x86_64
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] options: { repair: true, storage: { dbPath: “./” } }
2020-01-07T09:40:51.595-0600 W - [initandlisten] Detected unclean shutdown - ./mongod.lock is not empty.
2020-01-07T09:40:51.630-0600 I - [initandlisten] Detected data files in ./ created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2020-01-07T09:40:51.631-0600 W STORAGE [initandlisten] Recovering data from the last clean checkpoint.
2020-01-07T09:40:51.632-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=257430M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2020-01-07T09:40:51.651-0600 E STORAGE [initandlisten] WiredTiger error (0) [1578411651:651363][38942:0x2b680d844e00], file:WiredTiger.wt, connection: WiredTiger.turtle: encountered an illegal file format or internal value
2020-01-07T09:40:51.651-0600 E STORAGE [initandlisten] WiredTiger error (-31804) [1578411651:651445][38942:0x2b680d844e00], file:WiredTiger.wt, connection: the process must exit and restart: WT_PANIC: WiredTiger library panic
2020-01-07T09:40:51.651-0600 I - [initandlisten] Fatal Assertion 28558 at src/mongo/db/storage/wiredtiger/wiredtiger_util.cpp 361
2020-01-07T09:40:51.651-0600 I - [initandlisten]
***aborting after fassert() failure
2020-01-07T09:40:51.660-0600 F - [initandlisten] Got signal: 6 (Aborted).
0x55cd815a6d6b 0x55cd815a5fe6 0x55cd815a64c3 0x2b680e7b95e0 0x2b680e9fb1f7 0x2b680e9fc8e8 0x55cd807c5887 0x55cd8129d597 0x55cd807cfe75 0x55cd807d008c 0x55cd807d02f5 0x55cd81f9d9d7 0x55cd81f9c1d9 0x55cd81f51893 0x55cd81fdc974 0x55cd81fdcf1f 0x55cd81fdd1cc 0x55cd81f5f8a9 0x55cd81fd2618 0x55cd81f9b8fe 0x55cd81f9b9eb 0x55cd81f4de6a 0x55cd81282685 0x55cd8127a9ca 0x55cd8116050a 0x55cd807d1bab 0x2b680e9e7c05 0x55cd80835cff
----- BEGIN BACKTRACE -----
{“backtrace”:[{“b”:“55CD80186000”,“o”:“1420D6B”,“s”:“_ZN5mongo15printStackTraceERSo”},{“b”:“55CD80186000”,“o”:“141FFE6”},{“b”:“55CD80186000”,“o”:“14204C3”},{“b”:“2B680E7AA000”,“o”:“F5E0”},{“b”:“2B680E9C6000”,“o”:“351F7”,“s”:“gsignal”},{“b”:“2B680E9C6000”,“o”:“368E8”,“s”:“abort”},{“b”:“55CD80186000”,“o”:“63F887”,“s”:“_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj”},{“b”:“55CD80186000”,“o”:“1117597”},{“b”:“55CD80186000”,“o”:“649E75”,“s”:“__wt_eventv”},{“b”:“55CD80186000”,“o”:“64A08C”,“s”:“__wt_err”},{“b”:“55CD80186000”,“o”:“64A2F5”,“s”:“__wt_panic”},{“b”:“55CD80186000”,“o”:“1E179D7”,“s”:“__wt_turtle_read”},{“b”:“55CD80186000”,“o”:“1E161D9”,“s”:“__wt_metadata_search”},{“b”:“55CD80186000”,“o”:“1DCB893”,“s”:“__wt_conn_btree_open”},{“b”:“55CD80186000”,“o”:“1E56974”,“s”:“__wt_session_get_btree”},{“b”:“55CD80186000”,“o”:“1E56F1F”,“s”:“__wt_session_get_btree”},{“b”:“55CD80186000”,“o”:“1E571CC”,“s”:“__wt_session_get_btree_ckpt”},{“b”:“55CD80186000”,“o”:“1DD98A9”,“s”:“__wt_curfile_open”},{“b”:“55CD80186000”,“o”:“1E4C618”},{“b”:“55CD80186000”,“o”:“1E158FE”,“s”:“__wt_metadata_cursor_open”},{“b”:“55CD80186000”,“o”:“1E159EB”,“s”:“__wt_metadata_cursor”},{“b”:“55CD80186000”,“o”:“1DC7E6A”,“s”:“wiredtiger_open”},{“b”:“55CD80186000”,“o”:“10FC685”,“s”:“_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb”},{“b”:“55CD80186000”,“o”:“10F49CA”},{“b”:“55CD80186000”,“o”:“FDA50A”,“s”:“_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv”},{“b”:“55CD80186000”,“o”:“64BBAB”,“s”:“main”},{“b”:“2B680E9C6000”,“o”:“21C05”,“s”:“__libc_start_main”},{“b”:“55CD80186000”,“o”:“6AFCFF”}],“processInfo”:{ “mongodbVersion” : “3.4.10-4-g67ee356c6b”, “gitVersion” : “67ee356c6be377cda547d16423daef5beb4e8377”, “compiledModules” : , “uname” : { “sysname” : “Linux”, “release” : “3.10.0-957.27.2.el7.x86_64”, “version” : “#1 SMP Mon Jul 29 17:46:05 UTC 2019”, “machine” : “x86_64” }, “somap” : [ { “b” : “55CD80186000”, “elfType” : 3, “buildId” : “A14732EAAA95508462633A5030B501E08B1B106F” }, { “b” : “7FFC34CA6000”, “elfType” : 3, “buildId” : “88212B24946DE81A7B05A4F4422F5A8B37CBD908” }, { “b” : “2B680D64B000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0”, “elfType” : 3 }, { “b” : “2B680D84D000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libssl.so.1.0.0”, “elfType” : 3 }, { “b” : “2B680DAC3000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libcrypto.so.1.0.0”, “elfType” : 3 }, { “b” : “2B680DF28000”, “path” : “/lib64/librt.so.1”, “elfType” : 3, “buildId” : “6D322588B36D2617C03C0F3B93677E62FCFFDA81” }, { “b” : “2B680E130000”, “path” : “/lib64/libdl.so.2”, “elfType” : 3, “buildId” : “1E42EBFB272D37B726F457D6FE3C33D2B094BB69” }, { “b” : “2B680E334000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libstdc++.so.6”, “elfType” : 3 }, { “b” : “2B680E4A8000”, “path” : “/lib64/libm.so.6”, “elfType” : 3, “buildId” : “808BD35686C193F218A5AAAC6194C49214CFF379” }, { “b” : “2B680D82E000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libgcc_s.so.1”, “elfType” : 3 }, { “b” : “2B680E7AA000”, “path” : “/lib64/libpthread.so.0”, “elfType” : 3, “buildId” : “A48D21B2578A8381FBD8857802EAA660504248DC” }, { “b” : “2B680E9C6000”, “path” : “/lib64/libc.so.6”, “elfType” : 3, “buildId” : “95FF02A4BEBABC573C7827A66D447F7BABDDAA44” }, { “b” : “2B680ED89000”, “path” : “/lib64/libutil.so.1”, “elfType” : 3, “buildId” : “C1CAEB92FAB92F5D9AFBA13867535EFD4BB55055” }, { “b” : “2B680D629000”, “path” : “/lib64/ld-linux-x86-64.so.2”, “elfType” : 3, “buildId” : “22FA66DA7D14C88BF36C69454A357E5F1DEFAE4E” } ] }}
mongod(_ZN5mongo15printStackTraceERSo+0x3B) [0x55cd815a6d6b]
mongod(+0x141FFE6) [0x55cd815a5fe6]
mongod(+0x14204C3) [0x55cd815a64c3]
libpthread.so.0(+0xF5E0) [0x2b680e7b95e0]
libc.so.6(gsignal+0x37) [0x2b680e9fb1f7]
libc.so.6(abort+0x148) [0x2b680e9fc8e8]
mongod(_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj+0x0) [0x55cd807c5887]
mongod(+0x1117597) [0x55cd8129d597]
mongod(__wt_eventv+0x3E4) [0x55cd807cfe75]
mongod(__wt_err+0xA0) [0x55cd807d008c]
mongod(__wt_panic+0x2F) [0x55cd807d02f5]
mongod(__wt_turtle_read+0x227) [0x55cd81f9d9d7]
mongod(__wt_metadata_search+0x99) [0x55cd81f9c1d9]
mongod(__wt_conn_btree_open+0x73) [0x55cd81f51893]
mongod(__wt_session_get_btree+0xE4) [0x55cd81fdc974]
mongod(__wt_session_get_btree+0x68F) [0x55cd81fdcf1f]
mongod(__wt_session_get_btree_ckpt+0x14C) [0x55cd81fdd1cc]
mongod(__wt_curfile_open+0x169) [0x55cd81f5f8a9]
mongod(+0x1E4C618) [0x55cd81fd2618]
mongod(__wt_metadata_cursor_open+0x6E) [0x55cd81f9b8fe]
mongod(__wt_metadata_cursor+0x4B) [0x55cd81f9b9eb]
mongod(wiredtiger_open+0x183A) [0x55cd81f4de6a]
mongod(_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb+0x815) [0x55cd81282685]
mongod(+0x10F49CA) [0x55cd8127a9ca]
mongod(_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv+0x69A) [0x55cd8116050a]
mongod(main+0xE9B) [0x55cd807d1bab]
libc.so.6(__libc_start_main+0xF5) [0x2b680e9e7c05]
mongod(+0x6AFCFF) [0x55cd80835cff]
----- END BACKTRACE -----
Aborted (core dumped)
I’ll try the plan B.
Thanks,