In the process of running run_gx.py, the following error is reported. Can you help me to solve it? thanks!!!
Here are my commands and error..
/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py
--fasta /mnt/z/lcb/genoms/bharal/0300.purge/purged.fa
--tax-id 1204301
--gx-db /mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/database/gxdb/all
--out-dir /mnt/z/lcb/genoms/bharal/0301.fcs-gx
--bin-dir /mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release
Fatal error: index.cpp:484 in from_stream(...): Unrecognized file content.
Warning: missing header '##[["GX hits",2,1]]'
Fatal error: taxify.cpp:350 in make_run_info_json(...): Assertion failed: agg_cvg <= 1
Error: Process failed with retcode 1: ['nice', '-n19', '/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/gx', 'align', '--gx-db=/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/database/gxdb/all.gxi', '--repeats-basis-fa=/dev/fd/6'])
Traceback (most recent call last):
File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 1114, in
main()
File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 1089, in main
run_gx_pipeline(args)
File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 732, in run_gx_pipeline
with ProcessPipeline() as p_main:
File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 312, in exit
self.wait()
File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 302, in wait
assert num_errors == 0, "Had errors."
^^^^^^^^^^^^^^^
AssertionError: Had errors.
I've verify the database. I ran my code with the Integrated database. But still the same error was reported. Should I extract the two .gz files from the database before running?
The command run in the tutorial is ". /dist/run_gx". When I run this command, the program fails to run and displays the content of "--help". So I run the command ". /scripts/run_gx.py" and got the aforementioned error. Is this the cause of my reported errors? How should I modify it?
In the process of running run_gx.py, the following error is reported. Can you help me to solve it? thanks!!!
Here are my commands and error.. /mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py --fasta /mnt/z/lcb/genoms/bharal/0300.purge/purged.fa --tax-id 1204301 --gx-db /mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/database/gxdb/all --out-dir /mnt/z/lcb/genoms/bharal/0301.fcs-gx --bin-dir /mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release
Fatal error: index.cpp:484 in from_stream(...): Unrecognized file content. Warning: missing header '##[["GX hits",2,1]]' Fatal error: taxify.cpp:350 in make_run_info_json(...): Assertion failed: agg_cvg <= 1 Error: Process failed with retcode 1: ['nice', '-n19', '/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/gx', 'align', '--gx-db=/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/database/gxdb/all.gxi', '--repeats-basis-fa=/dev/fd/6'])
Traceback (most recent call last): File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 1114, in main() File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 1089, in main run_gx_pipeline(args) File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 732, in run_gx_pipeline with ProcessPipeline() as p_main: File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 312, in exit self.wait() File "/mnt/z/lcb/fcs-gx/fcs-gx-release/fcs-gx-release/scripts/run_gx.py", line 302, in wait assert num_errors == 0, "Had errors." ^^^^^^^^^^^^^^^ AssertionError: Had errors.
I've verify the database. I ran my code with the Integrated database. But still the same error was reported. Should I extract the two .gz files from the database before running?
The command run in the tutorial is ". /dist/run_gx". When I run this command, the program fails to run and displays the content of "--help". So I run the command ". /scripts/run_gx.py" and got the aforementioned error. Is this the cause of my reported errors? How should I modify it?