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Error with Quiver polishing of unzipped haplotypes on test data
I have been trying to get your bioconda falcon/falcon-unzip install to work on CentOS and had partial success with the Example test case. Following the instructions in the Readme, I can get falcon to run to completion and falcon-unzip to generate the expected alternate haplotypes. However, I consistently get an error at the quiver step. I have tried several clean installs of the conda environment and the test data repositories on 2 different machines, one using Centos 6 on a directly attached disk and one on Centos 7 using a lustre filesystem. The behavior is identical on both systems. No 4-quiver/cns-output directory is generated.
The results of my test run are as follows:
(FALCON) [cbergman@genome] $ ls -lrt 3-unzip/
total 480
drwxr-xr-x. 8 cbergman bergmanlab 4096 Sep 6 15:41 reads
drwxr-xr-x. 6 cbergman bergmanlab 4096 Sep 6 15:41 0-phasing
drwxr-xr-x. 3 cbergman bergmanlab 4096 Sep 6 15:41 1-hasm
drwxr-xr-x. 6 cbergman bergmanlab 4096 Sep 6 15:41 2-htigs
-rw-r--r--. 1 cbergman bergmanlab 1394 Sep 6 15:41 template.sh
-rw-r--r--. 1 cbergman bergmanlab 581 Sep 6 15:41 task.sh
-rw-r--r--. 1 cbergman bergmanlab 593 Sep 6 15:41 task.json
-rw-r--r--. 1 cbergman bergmanlab 207 Sep 6 15:41 run.sh
-rwxr-xr-x. 1 cbergman bergmanlab 254 Sep 6 15:41 run-Pa16d27079404fc.bash
-rw-r--r--. 1 cbergman bergmanlab 1671 Sep 6 15:41 user_script.sh
-rw-r--r--. 1 cbergman bergmanlab 188573 Sep 6 15:41 all_h_ctg.fa
-rw-r--r--. 1 cbergman bergmanlab 0 Sep 6 15:41 hasm_done
-rw-r--r--. 1 cbergman bergmanlab 203182 Sep 6 15:41 all_p_ctg.fa
-rw-r--r--. 1 cbergman bergmanlab 7709 Sep 6 15:41 all_p_ctg_edges
-rw-r--r--. 1 cbergman bergmanlab 79 Sep 6 15:41 all_h_ctg.paf
-rw-r--r--. 1 cbergman bergmanlab 17 Sep 6 15:41 all_h_ctg_ids
-rw-r--r--. 1 cbergman bergmanlab 8190 Sep 6 15:41 all_h_ctg_edges
-rw-r--r--. 1 cbergman bergmanlab 16329 Sep 6 15:41 all_phased_reads
-rw-r--r--. 1 cbergman bergmanlab 0 Sep 6 15:41 run.sh.done
-rw-r--r--. 1 cbergman bergmanlab 3419 Sep 6 15:41 run-Pa16d27079404fc.bash.stdout
-rw-r--r--. 1 cbergman bergmanlab 7451 Sep 6 15:41 run-Pa16d27079404fc.bash.stderr
(FALCON) [cbergman@genome] $ ls -lrt 4-quiver/
total 48
drwxr-xr-x. 2 cbergman bergmanlab 4096 Sep 6 15:41 track-reads
drwxr-xr-x. 2 cbergman bergmanlab 4096 Sep 6 15:41 select-reads
drwxr-xr-x. 4 cbergman bergmanlab 4096 Sep 6 15:41 merge-reads
drwxr-xr-x. 2 cbergman bergmanlab 4096 Sep 6 15:41 segregate-split
drwxr-xr-x. 4 cbergman bergmanlab 4096 Sep 6 15:41 segregate-chunks
drwxr-xr-x. 4 cbergman bergmanlab 4096 Sep 6 15:41 segregate-run
drwxr-xr-x. 2 cbergman bergmanlab 4096 Sep 6 15:42 segregate-gathered
drwxr-xr-x. 2 cbergman bergmanlab 4096 Sep 6 15:42 segregated-bam
drwxr-xr-x. 3 cbergman bergmanlab 4096 Sep 6 15:42 quiver-split
drwxr-xr-x. 3 cbergman bergmanlab 4096 Sep 6 15:42 cns-gather
drwxr-xr-x. 4 cbergman bergmanlab 4096 Sep 6 15:42 quiver-chunks
drwxr-xr-x. 4 cbergman bergmanlab 4096 Sep 6 15:42 quiver-run
- the errors output to the terminal are as follows:
[INFO](slept for another 0.4s -- another 3 loop iterations)
[INFO](slept for another 1.4s -- another 4 loop iterations)
[INFO](slept for another 4.0s -- another 5 loop iterations)
[ERROR]Task Node(4-quiver/quiver-run/000000Fp01_00001) failed with exit-code=1
[ERROR]Task Node(4-quiver/quiver-run/000000Fp01) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])
[ERROR]ready: set([])
submitted: set([])
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
Traceback (most recent call last):
File "/home/cbergman/miniconda3/envs/FALCON/bin/fc_unzip.py", line 11, in <module>
load_entry_point('falcon-unzip==1.1.2', 'console_scripts', 'fc_unzip.py')()
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/mains/start_unzip.py", line 29, in main
unzip.run(**vars(args))
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 126, in run
unzip_all(config)
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/unzip.py", line 28, in unzip_all
tasks_unzip.run_workflow(wf, config, rule_writer)
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_unzip/tasks/unzip.py", line 708, in run_workflow
job_dict=config['job.step.unzip.quiver'],
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/falcon_kit/pype.py", line 192, in gen_parallel_tasks
wf.refreshTargets()
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 277, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/home/cbergman/miniconda3/envs/FALCON/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 361, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])
- the errors in the all.log file are as follows:
(FALCON) [cbergman@genome] $ tail -n 20 all.log
2018-09-06 19:55:34,598 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)
2018-09-06 19:55:34,599 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)
2018-09-06 19:55:36,099 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)
2018-09-06 19:55:36,100 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)
2018-09-06 19:55:36,540 - pwatcher.blocking:235 - DEBUG - rc: 1
2018-09-06 19:55:36,540 - pwatcher.blocking:87 - DEBUG - Thread notify_exited(P1f23d83c72cc91->1).
2018-09-06 19:55:37,495 - pwatcher.blocking:235 - DEBUG - rc: 1
2018-09-06 19:55:37,495 - pwatcher.blocking:87 - DEBUG - Thread notify_exited(P2f4330e72933ab->1).
2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:324 - DEBUG - N in queue: 2 (max_jobs=8)
2018-09-06 19:55:37,702 - pwatcher.blocking:463 - DEBUG - query(which='list', jobids=<2>)
2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-quiver/quiver-run/000000Fp01_00001) failed with exit-code=1
2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:94 - ERROR - Task Node(4-quiver/quiver-run/000000Fp01) failed with exit-code=1
2018-09-06 19:55:37,702 - pypeflow.simple_pwatcher_bridge:342 - DEBUG - recently_done: [(Node(4-quiver/quiver-run/000000Fp01), False), (Node(4-quiver/quiver-run/000000Fp01_00001), False)]
2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:343 - DEBUG - Num done in this iteration: 2
2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:357 - ERROR - Some tasks are recently_done but not satisfied: set([Node(4-quiver/quiver-run/000000Fp01), Node(4-quiver/quiver-run/000000Fp01_00001)])
2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:358 - ERROR - ready: set([])
submitted: set([])
2018-09-06 19:55:37,703 - pwatcher.blocking:467 - DEBUG - delete(which='known', jobids=<0>)
2018-09-06 19:55:37,703 - pwatcher.blocking:431 - ERROR - Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
2018-09-06 19:55:37,703 - pypeflow.simple_pwatcher_bridge:189 - DEBUG - In notifyTerminate(), result of delete:None
Any ideas what might be causing this?
Thanks in advance!
Problem of Python version on cluster ?
Hello,
I installed pb-assembly suite on a cluster using conda (python2.7 and 3).
I have the following problem ;
[ERROR]Task Node(0-rawreads/build) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
[ERROR]ready: set([])
submitted: set([])
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
Traceback (most recent call last):
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/bin/fc_run", line 11, in
load_entry_point('falcon-kit==1.2.4', 'console_scripts', 'fc_run')()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 726, in main
main1(argv[0], args.config, args.logger)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 76, in main1
input_fofn_fn=input_fofn_fn,
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 242, in run
dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']),
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/pype.py", line 106, in gen_parallel_tasks
wf.refreshTargets()
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 278, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/media/vol2/home/lcornet/anaconda2/envs/denovo_asm/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 362, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
##0-rawreads/build/run-Pae771765a0c133.bash.stderr
executable=${PYPEFLOW_JOB_START_SCRIPT}
- executable=/media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build/run-Pae771765a0c133.bash
timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default - timeout=60
Wait up to timeout seconds for the executable to become "executable",
then exec.
#timeleft = int(timeout)
while [[ ! -x "${executable}" ]]; do
if [[ "${timeout}" == "0" ]]; then
echo "timed out waiting for (${executable})"
exit 77
fi
echo "not executable: '${executable}', waiting ${timeout}s"
sleep 1
timeout=$((timeout-1))
done
- [[ ! -x /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build/run-Pae771765a0c133.bash ]]
/bin/bash ${executable}
- /bin/bash /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build/run-Pae771765a0c133.bash
- '[' '!' -d /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build ']'
- cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
- eval '/bin/bash run.sh'
++ /bin/bash run.sh
export PATH=$PATH:/bin - export PATH=/media/vol2/home/lcornet/anaconda2/bin:/media/vol1/apps/perlbrew/bin:/media/vol1/apps/perlbrew/perls/perl-5.22.0-thread-multi/bin:/media/vol1/gridengine/bin/linux-x64:/tmp/973061.1.smallnodes.q:/media/vol2/home/lcornet/miniconda2/bin:/usr/lib64/openmpi/bin:/media/vol1/gridengine/bin/linux-x64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/opt/ibutils/bin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/bin
- PATH=/media/vol2/home/lcornet/anaconda2/bin:/media/vol1/apps/perlbrew/bin:/media/vol1/apps/perlbrew/perls/perl-5.22.0-thread-multi/bin:/media/vol1/gridengine/bin/linux-x64:/tmp/973061.1.smallnodes.q:/media/vol2/home/lcornet/miniconda2/bin:/usr/lib64/openmpi/bin:/media/vol1/gridengine/bin/linux-x64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/opt/ibutils/bin:/media/vol1/apps/bin:/media/vol1/apps/mustexe:/media/vol1/apps/get_homologues-x86_64-20160331/:/bin
cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build - cd /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build
/bin/bash task.sh - /bin/bash task.sh
/media/vol2/home/lcornet/anaconda2/bin/python2.7: No module named pypeflow
+++ pwd
++ echo 'FAILURE. Running top in /media/vol2/scratch/lcornet/cassava/falcon-test/0-rawreads/build (If you see -terminal database is inaccessible- you are using the python bin-wrapper, so you will not get diagnostic info. No big deal. This process is crashing anyway.)'
++ rm -f top.txt
++ which python
++ which top
++ env -u LD_LIBRARY_PATH top -b -n 1
++ env -u LD_LIBRARY_PATH top -b -n 1
++ pstree -apl
real 0m0.685s
user 0m0.034s
sys 0m0.082s
- finish
- echo 'finish code: 1'
Can you help me ?
Luc
FALCON doesn't work on test data (CENTOS)
Hi all,
I installed the latest version of FALCON with your instructions, on my CENTOS server. I created a new conda environment and I used this conda to install FALCON with the command : conda install pb-assembly. This installation worked perfectly.
Then, I recovered the test data, and launched Falcon with your instructions :
git clone https://github.com/cdunn2001/git-sym.git
git clone https://github.com/pb-cdunn/FALCON-examples.git
cd FALCON-examples
../git-sym/git-sym update run/greg200k-sv2
cd run/greg200k-sv2
fc_run fc_run.cfg
And I got the following error :
falcon-kit 1.2.2
pypeflow 2.0.4
[INFO]Setup logging from file "None".
[INFO]$ lfs setstripe -c 12 /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2 >
[INFO]Apparently '/cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2' is not in lustre filesystem, which is fine.
[INFO]fc_run started with configuration fc_run.cfg
[WARNING]Unexpected keys in input config: set(['ovlp_HPCTANmask_option'])
[WARNING]Please supply a default for "njobs" (aka concurrency) in section [job.defaults]. For now, we will use 8
[INFO]cfg=
{
"General": {
"LA4Falcon_preload": false,
"avoid_text_file_busy": true,
"bestn": 12,
"dazcon": false,
"falcon_sense_greedy": false,
"falcon_sense_option": "--output-multi --min-cov-aln 4 --min-idt 0.70 --min-cov 4 --max-n-read 200 --n-core 8",
"falcon_sense_skip_contained": false,
"fc_ovlp_to_graph_option": " --min_len 1",
"genome_size": "200000",
"input_fofn": "input.fofn",
"input_type": "raw",
"length_cutoff": "1000",
"length_cutoff_pr": "1",
"overlap_filtering_setting": "--max-diff 120 --max-cov 120 --min-cov 2 --n-core 8",
"ovlp_DBsplit_option": "-s100",
"ovlp_HPCTANmask_option": "-l500",
"ovlp_HPCdaligner_option": "-v -B128 -M24",
"ovlp_daligner_option": "-e.9 -l2500 -k24 -h1024 -w6 -s100",
"pa_DBdust_option": "",
"pa_DBsplit_option": "-a -x500 -s4",
"pa_HPCTANmask_option": "-l500",
"pa_HPCdaligner_option": "-v -B128 -M24",
"pa_REPmask_code": "0,300;0,300;0,300",
"pa_daligner_option": "-e.8 -l3200 -k18 -h480 -w8 -s100",
"pa_dazcon_option": "-j 4 -x -l 500",
"pa_fasta_filter_option": "streamed-median",
"seed_coverage": 20,
"skip_checks": false,
"target": "assembly"
},
"job.defaults": {
"NPROC": "4",
"job_type": "string",
"njobs": 8,
"pwatcher_type": "blocking",
"submit": "bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}",
"use_tmpdir": false
},
"job.step.asm": {
"NPROC": "32"
},
"job.step.cns": {
"NPROC": "8"
},
"job.step.da": {},
"job.step.la": {},
"job.step.pda": {},
"job.step.pla": {}
}
[INFO]In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.blocking' from '/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pwatcher/blocking.pyc'>
[INFO]job_type='string', (default)job_defaults={'pwatcher_type': 'blocking', 'use_tmpdir': False, 'job_type': 'string', 'submit': 'bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}', 'NPROC': '4', 'njobs': 8}, use_tmpdir=False, squash=True, job_name_style=0
[INFO]Setting max_jobs to 8; was None
[INFO]Num unsatisfied: 2, graph: 2
[INFO]About to submit: Node(0-rawreads/build)
[INFO]Popen: 'bash -C /cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pwatcher/mains/job_start.sh >| /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P47d6213d776274.bash.stdout 2>| /cm/shared/apps/FALCON_10-09-2018/FALCON-examples/run/greg200k-sv2/0-rawreads/build/run-P47d6213d776274.bash.stderr'
[INFO](slept for another 0.0s -- another 1 loop iterations)
[INFO](slept for another 0.3s -- another 2 loop iterations)
[ERROR]Task Node(0-rawreads/build) failed with exit-code=1
[ERROR]Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
[ERROR]ready: set([])
submitted: set([])
[ERROR]Noop. We cannot kill blocked threads. Hopefully, everything will die on SIGTERM.
Traceback (most recent call last):
File "/cm/shared/apps/FALCON_10-09-2018/bin/fc_run", line 11, in
load_entry_point('falcon-kit==1.2.2', 'console_scripts', 'fc_run')()
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 724, in main
main1(argv[0], args.config, args.logger)
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 76, in main1
input_fofn_fn=input_fofn_fn,
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/mains/run1.py", line 242, in run
dist=Dist(NPROC=4, MB=4000, job_dict=config['job.step.da']),
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/falcon_kit/pype.py", line 106, in gen_parallel_tasks
wf.refreshTargets()
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 277, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/cm/shared/apps/FALCON_10-09-2018/lib/python2.7/site-packages/pypeflow/simple_pwatcher_bridge.py", line 361, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/build)])
Have you an idea about that ?
Best,
Amandine
FALCOn very slow.
Hi,
I have a new question about the new version of Falcon, pb-assembly.
The first step of reads correction is much faster, I don't know if the configuration that I recovered allows me to accelerate this step. On the other hand, it's been 4 days since the unzip stage runs and I feel that it's an infinite loop, here are the last lines of the log. Do you find it normal?
It's weird because my log is still updated an hour ago, with the last sentence and I don't know how many iterations it will still have to do to reach a result.
Best,
Amandine
set([Node(3-unzip/0-phasing/phasing-chunks/002449F)])
[INFO]Num satisfied in this iteration: 1
[INFO]Num still unsatisfied: 5151
[INFO]About to submit: Node(3-unzip/0-phasing/000309F)
[INFO]Popen: 'bash -C /cm/shared/apps/FALCON_12_09_2018/lib/python2.7/site-packages/pwatcher/mains/job_start.sh >| /data2/avelt/Assembly_amurensis/3-unzip/0-phasing/000309F/run-P5ed16ea251015d.bash.stdout 2>| /data2/avelt/Assembly_amurensis/3-unzip/0-phasing/000309F/run-P5ed16ea251015d.bash.stderr'
[INFO](slept for another 55.3s -- another 90 loop iterations)
[INFO](slept for another 527.3s -- another 91 loop iterations)
[INFO](slept for another 920.0s -- another 92 loop iterations)
[INFO](slept for another 930.0s -- another 93 loop iterations)
[INFO](slept for another 940.0s -- another 94 loop iterations)
[INFO](slept for another 950.0s -- another 95 loop iterations)
[INFO](slept for another 960.0s -- another 96 loop iterations)
[INFO](slept for another 970.0s -- another 97 loop iterations)
[INFO](slept for another 980.0s -- another 98 loop iterations)
[INFO](slept for another 990.0s -- another 99 loop iterations)
[INFO](slept for another 1000.0s -- another 100 loop iterations)
[INFO](slept for another 1010.0s -- another 101 loop iterations)
[INFO](slept for another 1020.0s -- another 102 loop iterations)
[INFO](slept for another 1030.0s -- another 103 loop iterations)
[INFO](slept for another 1040.0s -- another 104 loop iterations)
[INFO](slept for another 1050.0s -- another 105 loop iterations)
[INFO](slept for another 1060.0s -- another 106 loop iterations)
[INFO](slept for another 1070.0s -- another 107 loop iterations)
[INFO](slept for another 1080.0s -- another 108 loop iterations)
[INFO](slept for another 1090.0s -- another 109 loop iterations)
[INFO](slept for another 1100.0s -- another 110 loop iterations)
[INFO](slept for another 1110.0s -- another 111 loop iterations)
[INFO](slept for another 1120.0s -- another 112 loop iterations)
[INFO](slept for another 1130.0s -- another 113 loop iterations)
[INFO](slept for another 1140.0s -- another 114 loop iterations)
[INFO](slept for another 1150.0s -- another 115 loop iterations)
[INFO](slept for another 1160.0s -- another 116 loop iterations)
[INFO](slept for another 1170.0s -- another 117 loop iterations)
[INFO](slept for another 1180.0s -- another 118 loop iterations)
[INFO](slept for another 1190.0s -- another 119 loop iterations)
[INFO](slept for another 1200.0s -- another 120 loop iterations)
[INFO](slept for another 1210.0s -- another 121 loop iterations)
[INFO](slept for another 1220.0s -- another 122 loop iterations)
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running falcon and falcon_unzip with HiFi reads
To whom it may concern,
I am attempting to run falcon and falcon_unzip through pb-assembly. The fasta header of CCS/HiFi reads does not seem to be compatible with the daligner that is installed together with pb-assembly. I was wondering when PacBio might push an update for pb-assembly that would run with the HiFI reads.
Regards,
Sangjin Lee
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