YaqiangCao
commented
5 years ago Dear User, The run.sh has been updated, and please use the new first command line as following: cLoops -f GSM1872886_GM12878_CTCF_ChIA-PET_chr21_hg38.bedpe.gz -o chiapet -w -j -s -m 1 -m 1 is added as in latest version. Sorry for the trouble.
On Fri, May 3, 2019 at 12:44 PM simjbaum notifications@github.com wrote:
I get the following error after isntallation and running the test script:
[seb@pc examples]$ sh run.sh 2019-05-03 18:39:59,823 INFO Command line: cLoops -f GSM1872886_GM12878_CTCF_ChIA-PET_chr21_hg38.bedpe.gz -o chiapet -m 0 -eps 0 -minPts 0 -p 1 -w True -j True -s True -c -hic False -cut 0 -plot False -max_cut False 2019-05-03 18:39:59,824 ERROR minPts not assigned! Converting to .hic file which could be loaded in juicebox juicer_tools pre -n -r 1000,5000,10000,20000 -d 0.951037801484 CTCF_chr21_juice.hic hg38 0.951037801484 does not exist or does not contain any reads. rm 0.951037801484 Converting CTCF_chr21_juice.hic to juicer's hic file finished. Converting to washU track. bedtools sort -i 0.139065929601 > CTCF_chr21_PETs_washU.txt rm 0.139065929601 bgzip CTCF_chr21_PETs_washU.txt tabix -p bed CTCF_chr21_PETs_washU.txt.gz Converting CTCF_chr21_PETs_washU.txt to washU random accessed track finished. 2019-05-03 18:40:02,585 INFO Getting finger print for chiapet Traceback (most recent call last): File "/pc/home/seb/no_backup/python/bin/jd2fingerprint", line 4, in import('pkg_resources').run_script('cLoops==0.93', 'jd2fingerprint') File "/pc/home/seb/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/pc/home/seb/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 1453, in run_script exec(script_code, namespace, namespace) File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 118, in
File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 94, in getFingerPrint
File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 70, in jds2FingerPrint
ValueError: need at least one array to concatenate
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I get the following error after isntallation and running the test script:
[seb@pc examples]$ sh run.sh 2019-05-03 18:39:59,823 INFO Command line: cLoops -f GSM1872886_GM12878_CTCF_ChIA-PET_chr21_hg38.bedpe.gz -o chiapet -m 0 -eps 0 -minPts 0 -p 1 -w True -j True -s True -c -hic False -cut 0 -plot False -max_cut False 2019-05-03 18:39:59,824 ERROR minPts not assigned! Converting to .hic file which could be loaded in juicebox juicer_tools pre -n -r 1000,5000,10000,20000 -d 0.951037801484 CTCF_chr21_juice.hic hg38 0.951037801484 does not exist or does not contain any reads. rm 0.951037801484 Converting CTCF_chr21_juice.hic to juicer's hic file finished. Converting to washU track. bedtools sort -i 0.139065929601 > CTCF_chr21_PETs_washU.txt rm 0.139065929601 bgzip CTCF_chr21_PETs_washU.txt tabix -p bed CTCF_chr21_PETs_washU.txt.gz Converting CTCF_chr21_PETs_washU.txt to washU random accessed track finished. 2019-05-03 18:40:02,585 INFO Getting finger print for chiapet Traceback (most recent call last): File "/pc/home/seb/no_backup/python/bin/jd2fingerprint", line 4, in
import('pkg_resources').run_script('cLoops==0.93', 'jd2fingerprint')
File "/pc/home/seb/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/pc/home/seb/.local/lib/python2.7/site-packages/pkg_resources/init.py", line 1453, in run_script
exec(script_code, namespace, namespace)
File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 118, in
File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 94, in getFingerPrint
File "/pc/home/seb/no_backup/python/lib/python2.7/site-packages/cLoops-0.93-py2.7.egg/EGG-INFO/scripts/jd2fingerprint", line 70, in jds2FingerPrint
ValueError: need at least one array to concatenate