#1010110 ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception'

Package:
ncbi-blast+
Source:
ncbi-blast+
Description:
next generation suite of BLAST sequence search tools
Submitter:
Patrice DUROUX
Date:
2022-05-17 17:48:03 UTC
Severity:
normal
Tags:
#1010110#5
Date:
2022-04-24 17:41:46 UTC
From:
To:
Dear Maintainer,

Using the same command line with different versions of the package,
here are the results:

2.10.1+ds-1 (using snapshot.d.o) ok

2.11.0+ds-1 (Bullseye) ko (exitcode=134)
terminate called after throwing an instance of 'ncbi::CIO_Exception'
  what():  NCBI C++ Exception:
    T3 "c++/include/corelib/ncbidiag.hpp", line 445: Error: (CIO_Exception::eIO_InvalidArg) ncbi::s_HttpConnectorBuilder() - CConn_HttpStream::CConn_HttpStream():  Bad URL

Aborted

2.12.0+ds-3+b1 (Sid) ok

Moreover, I also tried a local installation of the new upstream 2.13.0+ [1,2]
and it is ok.

Regards,
Patrice

[1] https://www.ncbi.nlm.nih.gov/books/NBK131777/
[2] https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

#1010110#10
Date:
2022-04-24 20:11:38 UTC
From:
To:
Patrice DUROUX <patrice.duroux@gmail.com> writes:

Can you please give an example of a command line that reproduces the error?

Thanks!

#1010110#15
Date:
2022-04-25 06:30:38 UTC
From:
To:
Hi,

Sure it is in the following test case isolated from a larger process that
was facing the problem:
---------------- #!/bin/sh ulimit -n 8192 export BLASTDB=databases blastn -db "IGH_V_F_CAAT_SIGNAL IGH_V_F_OCTAMER IGH_V_F_N1-REGION IGH_V_F_HEPTANUCLEOTIDE IGH_V_F_L-REGION IGH_V_F_FR1-IMGT IGH_V_F_FR2-IMGT IGH_V_F_D- REGION IGH_V_F_L-PART2 IGH_V_F_L-PART1 IGH_V_F_V-NONAMER IGH_V_F_N2-REGION IGH_V_F_FR4-IMGT IGH_V_F_CDR1-IMGT IGH_V_F_V-HEPTAMER IGH_V_F_JUNCTION IGH_V _F_V-RS IGH_V_F_INTERNAL-HEPTAMER IGH_V_F_CDR2-IMGT IGH_V_F_J-REGION IGH_V_F_FR3-IMGT IGH_V_F_CDR3-IMGT IGH_V_F_TATA_BOX IGH_V_F_PYR-RICH IGH_V_F_P-REG ION IGH_V_F_V-REGION IGH_V_F_V-SPACER IGH_V_P_CDR3-IMGT IGH_V_P_V-NONAMER IGH_V_P_L-REGION IGH_V_P_FR2-IMGT IGH_V_P_FR3-IMGT IGH_V_P_PYR-RICH IGH_V_P_V -SPACER IGH_V_P_L-PART2 IGH_V_P_L-PART1 IGH_V_P_CDR1-IMGT IGH_V_P_V-HEPTAMER IGH_V_P_HEPTANUCLEOTIDE IGH_V_P_V-REGION IGH_V_P_TATA_BOX IGH_V_P_CDR2-IMG T IGH_V_P_FR1-IMGT IGH_V_P_OCTAMER IGH_V_P_V-RS IGH_V_ORF_V-REGION IGH_V_ORF_V-HEPTAMER IGH_V_ORF_FR1-IMGT IGH_V_ORF_CDR2-IMGT IGH_V_ORF_L-PART1 IGH_V_ ORF_L-PART2 IGH_V_ORF_FR3-IMGT IGH_V_ORF_V-RS IGH_V_ORF_CDR1-IMGT IGH_V_ORF_V-SPACER IGH_V_ORF_V-NONAMER IGH_V_ORF_FR2-IMGT IGH_V_ORF_L-REGION IGH_V_OR F_CDR3-IMGT IGH_J_F_V-SPACER IGH_J_F_J-NONAMER IGH_J_F_J-REGION IGH_J_F_J-RS IGH_J_F_FR3-IMGT IGH_J_F_J-HEPTAMER IGH_J_F_OCTAMER IGH_J_F_FR4-IMGT IGH_J _F_CDR2-IMGT IGH_J_P_J-HEPTAMER IGH_J_P_J-RS IGH_J_P_J-REGION IGH_J_P_J-NONAMER IGH_D_F_N1-REGION IGH_D_F_M2 IGH_D_F_M1 IGH_D_F_3D-SPACER IGH_D_F_CH9 I GH_D_F_CH6 IGH_D_F_CH7 IGH_D_F_JUNCTION IGH_D_F_CH4 IGH_D_F_CH5 IGH_D_F_CH2 IGH_D_F_CH3 IGH_D_F_CH1 IGH_D_F_D-GENE-UNIT IGH_D_F_CH2D2 IGH_D_F_D1-REGION IGH_D_F_CH3D2 IGH_D_F_5D-NONAMER IGH_D_F_CH4D IGH_D_F_5D-HEPTAMER IGH_D_F_CHS IGH_D_F_3D-NONAMER IGH_D_F_L-PART1 IGH_D_F_L-PART2 IGH_D_F_D2-REGION IGH _D_F_CH3-CHS IGH_D_F_CH10 IGH_D_F_CH3D IGH_D_F_CH2D IGH_D_F_CH1D IGH_D_F_CH4D2 IGH_D_F_M IGH_D_F_5D-SPACER IGH_D_F_P-REGION IGH_D_F_CONNECTING-REGION I GH_D_F_3D-HEPTAMER IGH_D_F_CDR3-IMGT IGH_D_F_H1 IGH_D_F_H2 IGH_D_F_D-REGION IGH_D_F_H 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TRD_J_P_J-REGION TRD_J_P_J-HEPTAMER TRD_J_P_J-RS TRD_D_F_N-REGION TRD_D_F_3D-SPACER TRD_D_F_D3-REGI ON TRD_D_F_D1-REGION TRD_D_F_D-GENE-UNIT TRD_D_F_5D-NONAMER TRD_D_F_N1-REGION TRD_D_F_5D-SPACER TRD_D_F_D2-REGION TRD_D_F_D-REGION TRD_D_F_5D-HEPTAMER TRD_D_F_N3-REGION TRD_D_F_3D-NONAMER TRD_D_F_3D-HEPTAMER TRD_C_F_EX3 TRD_C_F_EX4 TRD_C_F_EX1 TRD_C_F_EX2 TRG_V_F_V-RS TRG_V_F_V-SPACER TRG_V_F_CDR2-IMG T TRG_V_F_CDR3-IMGT TRG_V_F_V-HEPTAMER TRG_V_F_CDR1-IMGT TRG_V_F_TATA_BOX TRG_V_F_V-NONAMER TRG_V_F_FR1-IMGT TRG_V_F_N-REGION TRG_V_F_JUNCTION TRG_V_F_ FR3-IMGT TRG_V_F_DECAMER TRG_V_F_FR2-IMGT TRG_V_F_L-REGION TRG_V_F_CAAT_SIGNAL TRG_V_F_L-PART1 TRG_V_F_L-PART2 TRG_V_F_V-REGION TRG_V_P_CDR1-IMGT TRG_V _P_FR2-IMGT TRG_V_P_L-REGION TRG_V_P_V-SPACER TRG_V_P_CDR3-IMGT TRG_V_P_V-RS TRG_V_P_V-NONAMER TRG_V_P_V-REGION TRG_V_P_FR3-IMGT TRG_V_P_FR1-IMGT TRG_V _P_L-PART2 TRG_V_P_L-PART1 TRG_V_P_V-HEPTAMER TRG_V_P_CDR2-IMGT TRG_V_ORF_FR3-IMGT TRG_V_ORF_V-RS TRG_V_ORF_CDR3-IMGT TRG_V_ORF_V-REGION TRG_V_ORF_CDR2 -IMGT TRG_V_ORF_V-SPACER TRG_V_ORF_L-PART2 TRG_V_ORF_L-PART1 TRG_V_ORF_V-HEPTAMER TRG_V_ORF_FR1-IMGT TRG_V_ORF_FR2-IMGT TRG_V_ORF_L-REGION TRG_V_ORF_CD R1-IMGT TRG_V_ORF_V-NONAMER TRG_J_F_J-RS TRG_J_F_J-REGION TRG_J_F_J-NONAMER TRG_J_F_J-HEPTAMER TRG_J_F_FR4-IMGT TRG_J_F_EX1 TRG_J_P_J-NONAMER TRG_J_P_J -HEPTAMER TRG_J_P_J-RS TRG_J_P_J-REGION TRG_C_F_CONNECTING-REGION TRG_C_F_EX4 TRG_C_F_EX3 TRG_C_F_EX2 TRG_C_F_EX1 TRG_C_F_EX2T TRG_C_F_EX2R TRG_C_F_EX2 A TRG_C_F_EX2B TRG_C_F_EX2C TRG_C_P_EX1 TRG_C_P_EX2 TRG_C_P_EX3 TRG_C_P_CONNECTING-REGION TRG_C_P_EX2B TRG_C_P_EX2C TRG_C_P_EX2A" -outfmt 15 -out test_ out.json -query test_seq.fa -perc_identity 85 -task blastn -word_size 11 -gapopen 4 -gapextend 2 -penalty -3 -reward 2 -evalue 0.1 -max_target_seqs 500 000 -best_hit_overhang 0.1 -best_hit_score_edge 0.1 -num_threads 2 echo "exitcode="$? ---------------- Note that the ulimit is needed to avoid another trouble: Error memory mapping:/home/patrice/tmp/ligmotif/databases/TRA_V_F_J-REGION.nsq openedFilesCount=1019 threadID=0 Error: NCBI C++ Exception: T0 "c++/include/corelib/ncbidiag.hpp", line 980: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. Stack trace: /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xA6 addr=0x7f9c456b9f76 /usr/lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0xAE7 addr=0x7f9c46bd8f77 /usr/lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CLocalBlast::Run() offset=0x537 addr=0x7f9c46b82ce7 blastn ???:0 CBlastnApp::Run() offset=0xF2A addr=0x5617458408fa /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x193 addr=0x7f9c45605dd3 /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) offset=0x61D addr=0x7f9c4560732d blastn ???:0 main offset=0x6B addr=0x56174583ee5b /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xEA addr=0x7f9c4514ad0a blastn ???:0 _start offset=0x2A addr=0x56174583f76a exitcode=255 Many thanks! Le dim. 24 avr. 2022 à 22:11, Aaron M. Ucko <ucko@debian.org> a écrit :
#1010110#20
Date:
2022-04-25 07:47:38 UTC
From:
To:
sorry for the wrapped lines in my previous message:

blastn -db "IGH_V_F_CAAT_SIGNAL IGH_V_F_OCTAMER IGH_V_F_N1-REGION
IGH_V_F_HEPTANUCLEOTIDE IGH_V_F_L-REGION IGH_V_F_FR1-IMGT IGH_V_F_FR2-IMGT
IGH_V_F_D-REGION IGH_V_F_L-PART2 IGH_V_F_L-PART1 IGH_V_F_V-NONAMER
IGH_V_F_N2-REGION IGH_V_F_FR4-IMGT IGH_V_F_CDR1-IMGT IGH_V_F_V-HEPTAMER
IGH_V_F_JUNCTION IGH_V_F_V-RS IGH_V_F_INTERNAL-HEPTAMER IGH_V_F_CDR2-IMGT
IGH_V_F_J-REGION IGH_V_F_FR3-IMGT IGH_V_F_CDR3-IMGT IGH_V_F_TATA_BOX
IGH_V_F_PYR-RICH IGH_V_F_P-REGION IGH_V_F_V-REGION IGH_V_F_V-SPACER
IGH_V_P_CDR3-IMGT IGH_V_P_V-NONAMER IGH_V_P_L-REGION IGH_V_P_FR2-IMGT
IGH_V_P_FR3-IMGT IGH_V_P_PYR-RICH IGH_V_P_V-SPACER IGH_V_P_L-PART2
IGH_V_P_L-PART1 IGH_V_P_CDR1-IMGT IGH_V_P_V-HEPTAMER
IGH_V_P_HEPTANUCLEOTIDE IGH_V_P_V-REGION IGH_V_P_TATA_BOX IGH_V_P_CDR2-IMGT
IGH_V_P_FR1-IMGT IGH_V_P_OCTAMER IGH_V_P_V-RS IGH_V_ORF_V-REGION
IGH_V_ORF_V-HEPTAMER IGH_V_ORF_FR1-IMGT IGH_V_ORF_CDR2-IMGT
IGH_V_ORF_L-PART1 IGH_V_ORF_L-PART2 IGH_V_ORF_FR3-IMGT IGH_V_ORF_V-RS
IGH_V_ORF_CDR1-IMGT IGH_V_ORF_V-SPACER IGH_V_ORF_V-NONAMER
IGH_V_ORF_FR2-IMGT IGH_V_ORF_L-REGION IGH_V_ORF_CDR3-IMGT IGH_J_F_V-SPACER
IGH_J_F_J-NONAMER IGH_J_F_J-REGION IGH_J_F_J-RS IGH_J_F_FR3-IMGT
IGH_J_F_J-HEPTAMER IGH_J_F_OCTAMER IGH_J_F_FR4-IMGT IGH_J_F_CDR2-IMGT
IGH_J_P_J-HEPTAMER IGH_J_P_J-RS IGH_J_P_J-REGION IGH_J_P_J-NONAMER
IGH_D_F_N1-REGION IGH_D_F_M2 IGH_D_F_M1 IGH_D_F_3D-SPACER IGH_D_F_CH9
IGH_D_F_CH6 IGH_D_F_CH7 IGH_D_F_JUNCTION IGH_D_F_CH4 IGH_D_F_CH5
IGH_D_F_CH2 IGH_D_F_CH3 IGH_D_F_CH1 IGH_D_F_D-GENE-UNIT IGH_D_F_CH2D2
IGH_D_F_D1-REGION IGH_D_F_CH3D2 IGH_D_F_5D-NONAMER IGH_D_F_CH4D
IGH_D_F_5D-HEPTAMER IGH_D_F_CHS IGH_D_F_3D-NONAMER IGH_D_F_L-PART1
IGH_D_F_L-PART2 IGH_D_F_D2-REGION IGH_D_F_CH3-CHS IGH_D_F_CH10 IGH_D_F_CH3D
IGH_D_F_CH2D IGH_D_F_CH1D IGH_D_F_CH4D2 IGH_D_F_M IGH_D_F_5D-SPACER
IGH_D_F_P-REGION IGH_D_F_CONNECTING-REGION IGH_D_F_3D-HEPTAMER
IGH_D_F_CDR3-IMGT IGH_D_F_H1 IGH_D_F_H2 IGH_D_F_D-REGION IGH_D_F_H
IGH_D_F_N2-REGION IGH_D_P_D-GENE-UNIT IGH_D_P_5D-SPACER IGH_D_P_3D-NONAMER
IGH_D_P_3D-HEPTAMER IGH_D_P_D-REGION IGH_D_P_3D-SPACER IGH_D_P_5D-HEPTAMER
IGH_D_P_5D-NONAMER IGH_C_F_CH4-CHS IGH_C_F_CH4D3 IGH_C_F_CH4D2 IGH_C_F_H1
IGH_C_F_H3 IGH_C_F_H2 IGH_C_F_H4 IGH_C_F_CH3-CHS IGH_C_F_OCTAMER
IGH_C_F_CH3D3 IGH_C_F_CH3D2 IGH_C_F_CONNECTING-REGION IGH_C_F_CH2D3
IGH_C_F_CH2D2 IGH_C_F_M2 IGH_C_F_M1 IGH_C_F_CHS IGH_C_F_CH2D IGH_C_F_CH7
IGH_C_F_CH9 IGH_C_F_CH1 IGH_C_F_CH2 IGH_C_F_CH3 IGH_C_F_CH4 IGH_C_F_CH5
IGH_C_F_CH3D IGH_C_F_CH6 IGH_C_F_CH4D IGH_C_F_TATA_BOX IGH_C_F_M IGH_C_F_H
IGH_C_F_CH10 IGH_C_F_CH1D IGH_C_P_CH3-CHS IGH_C_P_CH3D2 IGH_C_P_CH3D3
IGH_C_P_CH2D3 IGH_C_P_CH2D2 IGH_C_P_CH4-CHS IGH_C_P_CHS IGH_C_P_H5
IGH_C_P_H4 IGH_C_P_H1 IGH_C_P_H3 IGH_C_P_H2 IGH_C_P_CH4D3 IGH_C_P_CH4D2
IGH_C_P_CH6 IGH_C_P_CH5 IGH_C_P_CH7 IGH_C_P_CH2 IGH_C_P_CH1 IGH_C_P_CH4
IGH_C_P_CH3 IGH_C_P_M2 IGH_C_P_M1 IGH_C_P_H IGH_C_P_M IGH_C_P_CH3D
IGH_C_P_CH4D IGH_C_P_CH2D IGH_C_P_CONNECTING-REGION IGK_V_F_CAAT_SIGNAL
IGK_V_F_OCTAMER IGK_V_F_TATA_BOX IGK_V_F_CDR2-IMGT IGK_V_F_V-REGION
IGK_V_F_N-REGION IGK_V_F_FR1-IMGT IGK_V_F_PENTADECAMER IGK_V_F_J-REGION
IGK_V_F_P-REGION IGK_V_F_CDR1-IMGT IGK_V_F_V-SPACER IGK_V_F_FR3-IMGT
IGK_V_F_CDR3-IMGT IGK_V_F_V-NONAMER IGK_V_F_L-REGION IGK_V_F_JUNCTION
IGK_V_F_FR2-IMGT IGK_V_F_V-RS IGK_V_F_L-PART1 IGK_V_F_L-PART2
IGK_V_F_DECAMER IGK_V_F_V-HEPTAMER IGK_V_P_V-SPACER IGK_V_P_CDR1-IMGT
IGK_V_P_DECAMER IGK_V_P_FR1-IMGT IGK_V_P_L-REGION IGK_V_P_V-HEPTAMER
IGK_V_P_OCTAMER IGK_V_P_FR2-IMGT IGK_V_P_FR3-IMGT IGK_V_P_V-RS
IGK_V_P_CDR2-IMGT IGK_V_P_L-PART2 IGK_V_P_L-PART1 IGK_V_P_PENTADECAMER
IGK_V_P_V-REGION IGK_V_P_V-NONAMER IGK_V_P_CDR3-IMGT IGK_V_P_TATA_BOX
IGK_V_ORF_DECAMER IGK_V_ORF_V-SPACER IGK_V_ORF_V-HEPTAMER
IGK_V_ORF_CDR2-IMGT IGK_V_ORF_FR2-IMGT IGK_V_ORF_V-REGION
IGK_V_ORF_L-REGION IGK_V_ORF_CDR1-IMGT IGK_V_ORF_L-PART1 IGK_V_ORF_L-PART2
IGK_V_ORF_FR3-IMGT IGK_V_ORF_V-RS IGK_V_ORF_PENTADECAMER
IGK_V_ORF_V-NONAMER IGK_V_ORF_TATA_BOX IGK_V_ORF_FR1-IMGT IGK_V_ORF_OCTAMER
IGK_V_ORF_CDR3-IMGT IGK_J_F_FR4-IMGT IGK_J_F_J-HEPTAMER IGK_J_F_J-RS
IGK_J_F_J-REGION IGK_J_F_CH2D IGK_J_F_V-HEPTAMER IGK_J_F_J-NONAMER
IGK_J_P_J-REGION IGK_J_P_J-NONAMER IGK_J_ORF_J-REGION IGK_J_ORF_J-NONAMER
IGK_J_ORF_J-HEPTAMER IGK_J_ORF_J-RS IGK_C_F_CL IGL_V_F_OCTAMER
IGL_V_F_CDR2-IMGT IGL_V_F_FR4-IMGT IGL_V_F_FR1-IMGT IGL_V_F_L-PART2
IGL_V_F_L-PART1 IGL_V_F_J-REGION IGL_V_F_TATA_BOX IGL_V_F_CDR1-IMGT
IGL_V_F_P-REGION IGL_V_F_V-RS IGL_V_F_V-SPACER IGL_V_F_V-REGION
IGL_V_F_FR2-IMGT IGL_V_F_FR3-IMGT IGL_V_F_L-REGION IGL_V_F_DECAMER
IGL_V_F_V-NONAMER IGL_V_F_JUNCTION IGL_V_F_CDR3-IMGT IGL_V_F_PENTADECAMER
IGL_V_F_V-HEPTAMER IGL_V_F_N-REGION IGL_V_P_FR1-IMGT IGL_V_P_CDR1-IMGT
IGL_V_P_TATA_BOX IGL_V_P_PENTADECAMER IGL_V_P_L-PART2 IGL_V_P_L-PART1
IGL_V_P_DECAMER IGL_V_P_V-HEPTAMER IGL_V_P_FR3-IMGT IGL_V_P_CDR2-IMGT
IGL_V_P_V-NONAMER IGL_V_P_V-RS IGL_V_P_FR2-IMGT IGL_V_P_L-REGION
IGL_V_P_V-REGION IGL_V_P_OCTAMER IGL_V_P_CDR3-IMGT IGL_V_P_V-SPACER
IGL_J_F_FR4-IMGT IGL_J_F_J-REGION IGL_J_F_J-HEPTAMER IGL_J_F_L-REGION
IGL_J_F_J-NONAMER IGL_J_F_EX1 IGL_J_F_J-RS IGL_J_P_J-HEPTAMER
IGL_J_P_J-REGION IGL_J_P_J-RS IGL_J_P_J-NONAMER IGL_J_ORF_J-REGION
IGL_C_F_CL IGL_C_F_EX3 IGL_C_P_CL IGI_V_F_V-SPACER IGI_V_F_CDR1-IMGT
IGI_V_F_FR4-IMGT IGI_V_F_V-RS IGI_V_F_L-PART1 IGI_V_F_L-PART2
IGI_V_F_FR1-IMGT IGI_V_F_FR3-IMGT IGI_V_F_JUNCTION IGI_V_F_V-NONAMER
IGI_V_F_V-HEPTAMER IGI_V_F_CDR3-IMGT IGI_V_F_CDR2-IMGT IGI_V_F_L-REGION
IGI_V_F_FR2-IMGT IGI_V_F_V-REGION IGI_V_P_CDR3-IMGT IGI_V_P_L-REGION
IGI_V_P_FR2-IMGT IGI_V_P_V-SPACER IGI_V_P_V-RS IGI_V_P_V-NONAMER
IGI_V_P_V-REGION IGI_V_P_FR3-IMGT IGI_V_P_CDR1-IMGT IGI_V_P_CDR2-IMGT
IGI_V_P_L-PART2 IGI_V_P_L-PART1 IGI_V_P_V-HEPTAMER IGI_V_P_FR1-IMGT
IGI_V_ORF_V-REGION IGI_V_ORF_FR1-IMGT IGI_V_ORF_FR3-IMGT
IGI_V_ORF_CDR3-IMGT IGI_V_ORF_CDR1-IMGT IGI_V_ORF_CDR2-IMGT
IGI_V_ORF_FR2-IMGT IGI_J_F_J-HEPTAMER IGI_J_F_J-REGION IGI_J_F_J-NONAMER
IGI_J_F_FR4-IMGT IGI_J_F_J-RS IGI_J_P_J-RS IGI_J_P_J-HEPTAMER
IGI_J_P_J-REGION IGI_J_P_J-NONAMER TRA_V_F_CDR3-IMGT TRA_V_F_V-NONAMER
TRA_V_F_V-RS TRA_V_F_L-PART1 TRA_V_F_EX3 TRA_V_F_L-PART2 TRA_V_F_FR3-IMGT
TRA_V_F_J-REGION TRA_V_F_FR1-IMGT TRA_V_F_V-SPACER TRA_V_F_CDR2-IMGT
TRA_V_F_N-REGION TRA_V_F_V-REGION TRA_V_F_CDR1-IMGT TRA_V_F_JUNCTION
TRA_V_F_V-HEPTAMER TRA_V_F_FR2-IMGT TRA_V_F_L-REGION TRA_V_P_V-HEPTAMER
TRA_V_P_CDR2-IMGT TRA_V_P_V-RS TRA_V_P_V-REGION TRA_V_P_V-NONAMER
TRA_V_P_L-REGION TRA_V_P_FR2-IMGT TRA_V_P_CDR3-IMGT TRA_V_P_L-PART2
TRA_V_P_L-PART1 TRA_V_P_FR1-IMGT TRA_V_P_V-SPACER TRA_V_P_CDR1-IMGT
TRA_V_P_FR3-IMGT TRA_J_F_J-HEPTAMER TRA_J_F_J-NONAMER TRA_J_F_V-NONAMER
TRA_J_F_V-RS TRA_J_F_J-REGION TRA_J_F_J-RS TRA_J_F_FR4-IMGT
TRA_J_P_J-NONAMER TRA_J_P_J-REGION TRA_J_P_J-HEPTAMER TRA_J_P_J-RS
TRA_J_ORF_J-REGION TRA_D_F_CDR3-IMGT TRA_D_F_CDR1-IMGT TRA_D_F_JUNCTION
TRA_D_F_FR1-IMGT TRA_D_F_N-REGION TRA_D_F_CDR2-IMGT TRA_D_F_FR3-IMGT
TRA_D_F_FR2-IMGT TRA_D_F_L-PART2 TRA_C_F_EX1 TRA_C_F_EX3 TRA_C_F_EX2
TRA_C_F_EX4 TRB_V_F_V-RS TRB_V_F_N2-REGION TRB_V_F_FR3-IMGT
TRB_V_F_D-REGION TRB_V_F_FR2-IMGT TRB_V_F_V-NONAMER TRB_V_F_L-REGION
TRB_V_F_DECAMER TRB_V_F_CDR3-IMGT TRB_V_F_J-REGION TRB_V_F_V-REGION
TRB_V_F_V-SPACER TRB_V_F_CAAT_SIGNAL TRB_V_F_TATA_BOX TRB_V_F_FR1-IMGT
TRB_V_F_L-PART1 TRB_V_F_L-PART2 TRB_V_F_CDR2-IMGT TRB_V_F_CDR1-IMGT
TRB_V_F_N-REGION TRB_V_F_V-HEPTAMER TRB_V_F_N1-REGION TRB_V_F_JUNCTION
TRB_V_P_V-HEPTAMER TRB_V_P_FR3-IMGT TRB_V_P_V-NONAMER TRB_V_P_L-REGION
TRB_V_P_FR2-IMGT TRB_V_P_JUNCTION TRB_V_P_CDR3-IMGT TRB_V_P_FR1-IMGT
TRB_V_P_CAAT_SIGNAL TRB_V_P_DECAMER TRB_V_P_TATA_BOX TRB_V_P_V-RS
TRB_V_P_CDR1-IMGT TRB_V_P_D-REGION TRB_V_P_J-REGION TRB_V_P_L-PART1
TRB_V_P_L-PART2 TRB_V_P_CDR2-IMGT TRB_V_P_V-REGION TRB_V_P_V-SPACER
TRB_V_ORF_DECAMER TRB_J_F_V-RS TRB_J_F_J-NONAMER TRB_J_F_J-HEPTAMER
TRB_J_F_J-RS TRB_J_F_TATA_BOX TRB_J_F_J-REGION TRB_J_F_FR4-IMGT
TRB_J_P_J-REGION TRB_J_P_J-RS TRB_J_P_J-NONAMER TRB_J_P_J-HEPTAMER
TRB_J_ORF_J-NONAMER TRB_J_ORF_J-REGION TRB_J_ORF_J-HEPTAMER TRB_J_ORF_J-RS
TRB_D_F_3D-NONAMER TRB_D_F_3D-HEPTAMER TRB_D_F_3D-SPACER TRB_D_F_5D-SPACER
TRB_D_F_D-REGION TRB_D_F_5D-HEPTAMER TRB_D_F_5D-NONAMER TRB_D_F_D-GENE-UNIT
TRB_D_P_5D-SPACER TRB_D_P_5D-NONAMER TRB_D_P_5D-HEPTAMER TRB_C_F_EX2
TRB_C_F_EX1 TRB_C_F_EX4 TRB_C_F_EX3 TRB_C_P_EX3 TRB_C_P_EX4 TRB_C_P_EX1
TRB_C_P_EX2 TRD_V_F_CDR1-IMGT TRD_V_F_V-HEPTAMER TRD_V_F_OCTAMER
TRD_V_F_FR2-IMGT TRD_V_F_L-REGION TRD_V_F_TATA_BOX TRD_V_F_CDR3-IMGT
TRD_V_F_V-RS TRD_V_F_V-REGION TRD_V_F_N-REGION TRD_V_F_V-NONAMER
TRD_V_F_L-PART1 TRD_V_F_L-PART2 TRD_V_F_JUNCTION TRD_V_F_V-SPACER
TRD_V_F_FR3-IMGT TRD_V_F_CDR2-IMGT TRD_V_F_DECAMER TRD_V_F_FR1-IMGT
TRD_V_P_V-NONAMER TRD_V_P_V-RS TRD_V_P_V-HEPTAMER TRD_V_P_FR3-IMGT
TRD_V_P_L-PART1 TRD_V_P_L-PART2 TRD_V_P_FR1-IMGT TRD_V_P_CDR3-IMGT
TRD_V_P_V-REGION TRD_V_P_CDR1-IMGT TRD_V_P_V-SPACER TRD_V_P_CDR2-IMGT
TRD_V_P_FR2-IMGT TRD_V_P_L-REGION TRD_J_F_J-NONAMER TRD_J_F_FR4-IMGT
TRD_J_F_J-REGION TRD_J_F_J-RS TRD_J_F_J-HEPTAMER TRD_J_P_J-NONAMER
TRD_J_P_J-REGION TRD_J_P_J-HEPTAMER TRD_J_P_J-RS TRD_D_F_N-REGION
TRD_D_F_3D-SPACER TRD_D_F_D3-REGION TRD_D_F_D1-REGION TRD_D_F_D-GENE-UNIT
TRD_D_F_5D-NONAMER TRD_D_F_N1-REGION TRD_D_F_5D-SPACER TRD_D_F_D2-REGION
TRD_D_F_D-REGION TRD_D_F_5D-HEPTAMER TRD_D_F_N3-REGION TRD_D_F_3D-NONAMER
TRD_D_F_3D-HEPTAMER TRD_C_F_EX3 TRD_C_F_EX4 TRD_C_F_EX1 TRD_C_F_EX2
TRG_V_F_V-RS TRG_V_F_V-SPACER TRG_V_F_CDR2-IMGT TRG_V_F_CDR3-IMGT
TRG_V_F_V-HEPTAMER TRG_V_F_CDR1-IMGT TRG_V_F_TATA_BOX TRG_V_F_V-NONAMER
TRG_V_F_FR1-IMGT TRG_V_F_N-REGION TRG_V_F_JUNCTION TRG_V_F_FR3-IMGT
TRG_V_F_DECAMER TRG_V_F_FR2-IMGT TRG_V_F_L-REGION TRG_V_F_CAAT_SIGNAL
TRG_V_F_L-PART1 TRG_V_F_L-PART2 TRG_V_F_V-REGION TRG_V_P_CDR1-IMGT
TRG_V_P_FR2-IMGT TRG_V_P_L-REGION TRG_V_P_V-SPACER TRG_V_P_CDR3-IMGT
TRG_V_P_V-RS TRG_V_P_V-NONAMER TRG_V_P_V-REGION TRG_V_P_FR3-IMGT
TRG_V_P_FR1-IMGT TRG_V_P_L-PART2 TRG_V_P_L-PART1 TRG_V_P_V-HEPTAMER
TRG_V_P_CDR2-IMGT TRG_V_ORF_FR3-IMGT TRG_V_ORF_V-RS TRG_V_ORF_CDR3-IMGT
TRG_V_ORF_V-REGION TRG_V_ORF_CDR2-IMGT TRG_V_ORF_V-SPACER TRG_V_ORF_L-PART2
TRG_V_ORF_L-PART1 TRG_V_ORF_V-HEPTAMER TRG_V_ORF_FR1-IMGT
TRG_V_ORF_FR2-IMGT TRG_V_ORF_L-REGION TRG_V_ORF_CDR1-IMGT
TRG_V_ORF_V-NONAMER TRG_J_F_J-RS TRG_J_F_J-REGION TRG_J_F_J-NONAMER
TRG_J_F_J-HEPTAMER TRG_J_F_FR4-IMGT TRG_J_F_EX1 TRG_J_P_J-NONAMER
TRG_J_P_J-HEPTAMER TRG_J_P_J-RS TRG_J_P_J-REGION TRG_C_F_CONNECTING-REGION
TRG_C_F_EX4 TRG_C_F_EX3 TRG_C_F_EX2 TRG_C_F_EX1 TRG_C_F_EX2T TRG_C_F_EX2R
TRG_C_F_EX2A TRG_C_F_EX2B TRG_C_F_EX2C TRG_C_P_EX1 TRG_C_P_EX2 TRG_C_P_EX3
TRG_C_P_CONNECTING-REGION TRG_C_P_EX2B TRG_C_P_EX2C TRG_C_P_EX2A" -outfmt
15 -out test_out.json -query test_seq.fa -perc_identity 85 -task blastn
-word_size 11 -gapopen 4 -gapextend 2 -penalty -3 -reward 2 -evalue 0.1
-max_target_seqs 500000 -best_hit_overhang 0.1 -best_hit_score_edge 0.1
-num_threads 2

#1010110#25
Date:
2022-04-28 18:28:11 UTC
From:
To:
Finally I also checked with the x64-linux binary package available here:
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.11.0/

and got the same problem that confirms that this is an upstream
issue with this version.
A not so stable version for the current Debian stable then. ;-)

Thanks!

#1010110#30
Date:
2022-04-29 05:29:58 UTC
From:
To:
Am Thu, Apr 28, 2022 at 08:28:11PM +0200 schrieb Patrice Duroux:

Would it be helpful for you if we would provide version 2.12.0+ds-3 in
stable-backports?

Kind regards

      Andreas.

#1010110#35
Date:
2022-04-30 07:33:22 UTC
From:
To:
That would be very nice!
Thanks,
Patrice

#1010110#40
Date:
2022-05-13 06:18:28 UTC
From:
To:
Am Sat, Apr 30, 2022 at 09:33:22AM +0200 schrieb patrice.duroux@gmail.com:

There is a backport to stable available now.

I've tagged the bug wontfix since there is no good way to fix it in
official stable but users can read about the issue and learn about
the fix in backports.

Kind regards

     Andreas.

#1010110#47
Date:
2022-05-17 17:44:46 UTC
From:
To:
Thanks a lot!