bcl2fastq ZlibError software error

Question

[sw]

hey guys, I'm running bcl2fastq version 2.17.1.14 to process bcl files. But after several minutes before it was about to open s_6_1121.bcl.gz, it crashed down and gave the error message as followed:

2018-08-31 12:08:10 [7f90b8352700] INFO: Opened BCL file '/home/Data/Intensities/BaseCalls/L006/C310.1/s_6_1120.bcl.gz' with 6470949 clusters
2018-08-31 12:08:10 [7f90960d1700] WARNING: Rethrowing a thread exception 
2018-08-31 12:08:10 [7f90960d1700] ERROR: Thread: 0 caught an exception first: /home/tools/bcl2fastq/src/cxx/lib/data/BclFile.cpp(234): Throw in function virtual std::streamsize bcl2fastq::data::BclFile::read(char*, std::streamsize)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::io::ZlibError>
std::exception::what: invalid stored block lengths
z_stream(  next_in: 0x1d6cc40, avail_in: 36256, total_in: 29280, next_out: 0x7f8db5ef09b3, avail_out: 6382994, total_out: 87959, msg: 'invalid stored block lengths', state: 0x7f90b4606198, zalloc: 1, zfree: 1, opaque: 0x7f90b4606198, data_type: 96, adler: 3009181836, reserved: 0 )

2018-08-31 12:08:10 [7f90bcb4b780] WARNING: Rethrowing a thread exception 
2018-08-31 12:08:16 [7f90bcb4b780] ERROR: bcl2fastq::common::Exception: 2018-Aug-31 12:08:16: Unknown error -3 (-3): /home/tools/bcl2fastq/src/cxx/lib/data/BclFile.cpp(234): Throw in function virtual std::streamsize bcl2fastq::data::BclFile::read(char*, std::streamsize)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::io::ZlibError>
std::exception::what: invalid stored block lengths
z_stream(  next_in: 0x1d6cc40, avail_in: 36256, total_in: 29280, next_out: 0x7f8db5ef09b3, avail_out: 6382994, total_out: 87959, msg: 'invalid stored block lengths', state: 0x7f90b4606198, zalloc: 1, zfree: 1, opaque: 0x7f90b4606198, data_type: 96, adler: 3009181836, reserved: 0 )

I highly doubt that something went wrong with s_6_1121.bcl.gz files so that they could not be processed by bcl2fastq, but I'm not sure. Does anyone have any idea? Thanks a lot in advance.

Answer 1

[GenoMax]

Does that file exist? Are you able to get around the problem using --ignore-missing-bclsoption? A specific reason you are still using v. 2.17? bcl2fastq is currently in v.2.20.

[sw]

thanks for your reply. Yes, all the s_6_1121.bcl.gz files exist. I think this option may cause missing of reads in those bcls files. Does it matter?

[GenoMax]

Do you have a different copy of the data? You could try replacing that bcl file with a new copy in case current one is corrupt. If that does not work then you will have to live with a few reads with N's.

[sw]

I have tried once to replace the data. But the same error occurred. It was a progress because the option you showed me did help the software to work, but gave 230 warnings like this:

2018-08-31 21:22:48 [7f3723e5a700] WARNING: Ignoring read failure for bcl file '/home/Data/Intensities/BaseCalls/L006/C162.1/s_6_1120.bcl.gz'.
2018-08-31 21:22:48 [7f3723e5a700] WARNING: BCL file '"/home/Data/Intensities/BaseCalls/L006/C162.1/s_6_1120.bcl.gz"' truncated: bytes_read=-1 bytes_expected=6470949:Success (0)
2018-08-31 21:23:04 [7f3722e58700] WARNING: Ignoring read failure for bcl file '/home/Data/Intensities/BaseCalls/L006/C162.1/s_6_1121.bcl.gz'.
2018-08-31 21:23:04 [7f3722e58700] WARNING: Unable to read header of 'BCL' file '/home/Data/Intensities/BaseCalls/L006/C162.1/s_6_1121.bcl.gz' : bytes_read=-1 bytes_expected=4:Success (0)
2018-08-31 21:23:09 [7f37023da700] WARNING: Mismatching cluster count in BCL file: Cycle #162: bytes_real=0 bytes_expected=6470949

All warnings happened in C162.1, even though all the bcl files in cycle 162 seem to be the same in structure as other files in other cycles. Maybe the cycle 162 went wrong?

[GenoMax]

That is certainly possible.

[sw]

Your answer helps me a lot. Thanks