Hongchang-Gu
commented
5 years ago i will appreciate it if someone can help me solve this problem！
Closed Hongchang-Gu closed 5 years ago
Hongchang-Gu
commented
5 years ago i will appreciate it if someone can help me solve this problem！
gconcepcion
commented
5 years ago Hi,
Can you please share the contents of your fc_run.cfg.
This is the line in particular that i'm interested in:
pa_HPCTANmask_option =
Hongchang-Gu
commented
5 years ago I am sorry to reply you two days later after your response.
I did not set pa_HPCTANmask_option = in my fc_run.cfg
and this is my fc_run.cfg:
[General]
input_fofn = input.fofn
input_type = raw
job_type=local
length_cutoff = 10000
genome_size = 1200000000
length_cutoff_pr = 10000
sge_option_da = -pe smp 4 -q bigmem
sge_option_la = -pe smp 20 -q bigmem
sge_option_pda = -pe smp 6 -q bigmem
sge_option_pla = -pe smp 16 -q bigmem
sge_option_fc = -pe smp 24 -q bigmem
sge_option_cns = -pe smp 8 -q bigmem
pa_concurrent_jobs = 64
cns_concurrent_jobs = 64
ovlp_concurrent_jobs = 64
pa_HPCdaligner_option = -v -B128 -M24
ovlp_HPCdaligner_option = -v -B128 -M24
pa_daligner_option = -e.75 -l3200 -k18 -h480 -w8 -s100
ovlp_daligner_option = -e.96 -l2500 -k24 -h1024 -w6 -s100
pa_DBsplit_option = -a -x500 -s200
ovlp_DBsplit_option = -s200
falcon_sense_option = --output_multi --output_dformat --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 8
falcon_sense_skip_contained = True
overlap_filtering_setting = --max_diff 120 --max_cov 120 --min_cov 2 --n_core 6thank you!
Hongchang-Gu
commented
5 years ago hello, the information of my fc_run.cfg had already shown in github. I hope you can take a look at this issue at your convenience. thx!
在2018-12-08 03:06:26，Gregnotifications@github.com写道：
Hi,
Can you please the contents of your fc_run.cfg.
This is the line in particular that i'm interested in: pa_HPCTANmask_option =
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.
suvi93
commented
5 years ago Any update as to how to go about this error? I'm getting the same error as well.
2019-02-19 08:11:58,284 - pwatcher.fs_based:600 - ERROR - Failed to kill job for heartbeat 'heartbeat-Pd905dffe513485' (which might mean it was already gone): IOError(2, 'No such file or directory') Traceback (most recent call last): File "/home/ssubha/software/falcon/falcon-2018.31.08-03.06/lib/python2.7/site-packages/pwatcher/fs_based.py", line 597, in delete_heartbeat bjob.kill(state, heartbeat) File "/home/ssubha/software/falcon/falcon-2018.31.08-03.06/lib/python2.7/site-packages/pwatcher/fs_based.py", line 272, in kill with open(heartbeat_fn) as ifs: IOError: [Errno 2] No such file or directory: '/home/ssubha/Suvratha/mosquito/pacbiodata/falcon/mypwatcher/heartbeats/heartbeat-Pd905dffe513485' 2019-02-19 08:11:58,285 - pwatcher.fs_based:607 - DEBUG - Cannot remove heartbeat '/home/ssubha/Suvratha/mosquito/pacbiodata/falcon/mypwatcher/heartbeats/heartbeat-Pd905dffe513485': OSError(2, 'No such file or directory')
Hongchang-Gu
commented
5 years ago Sorry, I have not solved this problem so far. At present, because of other data processing, this error is temporarily put on hold. I hope that if you can solve the problem, you can notify me. THANKS A LOT!
在2019-02-19 16:33:57，suvi93notifications@github.com写道：
Any update as to how to go about this error? I'm getting the same error as well.
2019-02-19 08:11:58,284 - pwatcher.fs_based:600 - ERROR - Failed to kill job for heartbeat 'heartbeat-Pd905dffe513485' (which might mean it was already gone): IOError(2, 'No such file or directory') Traceback (most recent call last): File "/home/ssubha/software/falcon/falcon-2018.31.08-03.06/lib/python2.7/site-packages/pwatcher/fs_based.py", line 597, in delete_heartbeat bjob.kill(state, heartbeat) File "/home/ssubha/software/falcon/falcon-2018.31.08-03.06/lib/python2.7/site-packages/pwatcher/fs_based.py", line 272, in kill with open(heartbeat_fn) as ifs: IOError: [Errno 2] No such file or directory: '/home/ssubha/Suvratha/mosquito/pacbiodata/falcon/mypwatcher/heartbeats/heartbeat-Pd905dffe513485' 2019-02-19 08:11:58,285 - pwatcher.fs_based:607 - DEBUG - Cannot remove heartbeat '/home/ssubha/Suvratha/mosquito/pacbiodata/falcon/mypwatcher/heartbeats/heartbeat-Pd905dffe513485': OSError(2, 'No such file or directory')
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.
pb-cdunn
commented
5 years ago First, DEBUG is not an error. Might be fine. If it crashes for a specific task, look for a stderr file in the run-dir for that task.
Also, please switch to pwatcher_type = block. It is very difficult to support fs_based.
https://github.com/PacificBiosciences/pypeFLOW/wiki/configuration
hello, recently I recently encountered a tricky problem when running falcon.I checked all the issue lists and found no similar problems like the following： firstly，I found the error in all.log file, and the error was
These errors has been repeated many times.
AND then i try find the reason in stdrr ,and we can see these contents：
Now I don't know how to solve it，I hope to get help from everyone！ THANKS A LOT!