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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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from: can't read /var/mail/falcon_unzip.ovlp_filter_with_phase #46

Closed danshu closed 7 years ago

danshu commented 7 years ago

Hi,

I'm running falcon_unzip and I have the following error when running fc_ovlp_filter_with_phase.py --fofn ../../2-asm-falcon/las.fofn --max_diff 120 --max_cov 120 --min_cov 1 --n_core 12 --min_len 2500 --db ../../1-preads_ovl/preads.db --rid_phase_map ./rid_to_phase.all > preads.p_ovl" in "hasm.sh"

from: can't read /var/mail/falcon_unzip.ovlp_filter_with_phase
PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
import: unable to open X server `localhost:10.0' @ error/import.c/ImportImageCommand/364.
/tools/assembler/FALCON_unzip-master/src/py_scripts/fc_ovlp_filter_with_phase.py: 4: /tools/assembler/FALCON_unzip-master/src/py_scripts/fc_ovlp_filter_with_phase.py: Syntax error: word unexpected (expecting ")")"

Best, Quan

danshu commented 7 years ago

When I run using MobaXterm, the only message is from: can't read /var/mail/falcon_unzip.ovlp_filter_with_phase and fc_ovlp_filter_with_phase.py keeps running without exit.

danshu commented 7 years ago

I solved this problem by source env.sh because I installed falcon_unzip unter "fc_env". So I want to know that do I need to source again everytime I run falcon or falcon_unzip?

I deleted 1-hasm directory under 3-unzip and rerun fc_unzip.py again. Can falcon_unzip identify those already finished jobs (track_reads and fetch_reads) and then work properly?

danshu commented 7 years ago

Then here is another error: fc_graphs_to_h_tigs.py --fc_asm_path ../../2-asm-falcon/ --fc_hasm_path ./ --ctg_id all --rid_phase_map ./rid_to_phase.all --fasta ../../1-preads_ovl/preads4falcon.fasta

IOError: [Errno 2] No such file or directory: '../../1-preads_ovl/preads4falcon.fasta'

It seems that falcon_unzip expects there preads to be in the 1-preads_ovl directory, while actually these preads are under 1-preads_ovl/db2falcon. Is this a bug or a confict of the version of falcon and falcon_unzip I used? I'm using FALCON-integrate 0.7+git.4ef2433d41140c2a232fa7f0ea3db4f6b39ed84f and Falcon_unzip version 0.1.0.

danshu commented 7 years ago

I copied preads4falcon.fasta to "1-preads_ovl" directory. Can this solve the problem?

pb-jchin commented 7 years ago

@pb-cdunn might have changed where the pread4falcon.fasta location, you can just make a symlink to the1-pread_ovl for now.

pb-cdunn commented 7 years ago

I'll push a quick fix tonight. Expect a proper fix soon.

pb-cdunn commented 7 years ago

Try the tip of the master branch. Not tested yet.