SRA Toolkit update for prefork and fastq-dump

[wesleyemason]

Please update the SRA Toolkit packages (prefork and fastq-dump) in the dep folder to the latest 3.0.2 version. They no longer download data from NCBI due to an invalid SSL certificate. For example:

$ ./Finder/dep/fastq-dump --version

./Finder/dep/fastq-dump : 2.9.6

$ ./Finder/dep/fastq-dump --stdout -X 2 SRR390728
2023-01-23T18:48:27 fastq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-01-23T18:48:27 fastq-dump.2.9.6 sys: mbedtls_ssl_get_verify_result returned 0x4008 ( !! The certificate is not correctly signed by the trusted CA !! The certificate is signed with an unacceptable hash. )
2023-01-23T18:48:27 fastq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.29.113' from '10.123.131.29'
2023-01-23T18:48:27 fastq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'trace.ncbi.nlm.nih.gov' (130.14.29.113) from '10.123.131.29'
2023-01-23T18:48:27 fastq-dump.2.9.6 err: item not found while constructing within virtual database module - the path 'SRR390728' cannot be opened as database or table

$ ./fastq-dump --version

./fastq-dump : 3.0.2

$ ./fastq-dump --stdout -X 2 SRR390728
Read 2 spots for SRR390728
Written 2 spots for SRR390728
@SRR390728.1 1 length=72
CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCGATGGAGAATGACTTTGACAAGCTGAGAGAAGNTNC
+SRR390728.1 1 length=72
;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142;;;;;;;;;;;;;;;;;;;;;;;;;;;;;96&&&&(
@SRR390728.2 2 length=72
AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGTTCCAGCTGACCCACTCCCTGGGTGGGGGGACTGGGT
+SRR390728.2 2 length=72
;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&&;;;;;;;;;;;;;;;;;;;;;<9;<;;;;;464262

In addition, the downloadAndDumpFastqFromSRA.py script in the utils directory needs to be updated for the new prefetch version. The "-O" option for prefetch will now download each fastq file into a separate directory. The downloadAndDumpFastqFromSRA.py script currently expects the fastq files to all download into the same parent folder. If the script is modified to use the "-o" option and specify the filename then it will execute properly. For example:

$ diff -u downloadAndDumpFastqFromSRA.py.orig downloadAndDumpFastqFromSRA.py
--- downloadAndDumpFastqFromSRA.py.orig 2023-01-20 10:47:53.318973000 -0600
+++ downloadAndDumpFastqFromSRA.py 2023-01-20 10:48:06.832207000 -0600
@@ -36,7 +36,7 @@

def downloadSRAFile( allinput ):
sra, default_path_to_download, output_directory = allinput

• os.system( "prefetch -X 104857600 -O " + output_directory + "/" + " " + sra + " 2> " + output_directory + "/" + sra + ".error" )

• os.system( "prefetch -X 104857600 -o " + output_directory + "/" + sra + ".sra" + " " + sra + " 2> " + output_directory + "/" + sra + ".error" )
  cmd = "fastq-dump -X 1 -Z --split-spot " + output_directory + "/" + sra + ".sra|wc -l > " + output_directory + "/" + sra + ".temp"
  os.system( cmd )
  if int( open( output_directory + "/" + sra + ".temp" ).read() ) == 4:

[sagnikbanerjee15]

Hello @wesleyemason,

Thank you very much for your interest in finder. We are working to provide an alternative framework for executing FINDER. All the software will be made available through docker images.

Thank you.