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HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data
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1.mpileup.R: Warning messages #12

Closed SRHilz closed 7 years ago

SRHilz commented 7 years ago

When running 1.mpileup.R, get the following warning message:

= warnings() ================================================================== Warning messages: 1: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai 2: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 3: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai 4: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 5: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai 6: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 7: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai 8: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00047.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 9: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai 10: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 11: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai 12: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 13: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai 14: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' 15: In getIndexFile.BamDataFile(this, create = FALSE) : Detected outdated index file and recreated it: bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai 16: In file.remove(pathnameIDX) : cannot remove file 'bamData/CostelloP_2015-Exome,bwa,realigned,rmDups,recal/Homo_sapiens/Patient68/Z00048.bwa.realigned.rmDups.recal.bam.bai', reason 'Permission denied' Rscript_203901-20170627.o882206.txt

SRHilz commented 7 years ago 
[14:16:42] [n6 Patient68]$ ls -la --time-style=full-iso .
total 53504640
drwxr-xr-x   2 jocostello costellolab        4096 2014-11-25 13:48:53.540399257 -0800 .
drwxr-xr-x 211 jocostello costellolab        8192 2017-06-20 12:29:11.758754894 -0700 ..
-rw-r--r--   1 jocostello costellolab        1292 2014-11-25 13:46:27.725399528 -0800 Patient68.merged.realigned.mateFixed.metrics
-rw-r--r--   1 jocostello costellolab        1665 2014-11-25 13:47:13.970399455 -0800 Z00047.bwa.realigned.rmDups.recal.alignment_summary_metrics
-rw-r--r--   1 jocostello costellolab 13216691443 2014-11-25 13:48:53.329399295 -0800 Z00047.bwa.realigned.rmDups.recal.bam
-rw-r--r--   1 jocostello costellolab     6193576 2014-11-25 13:46:27.713399528 -0800 Z00047.bwa.realigned.rmDups.recal.bam.bai
-rw-r--r--   1 jocostello costellolab         407 2014-11-25 13:47:13.954399455 -0800 Z00047.bwa.realigned.rmDups.recal.flagstat
-rw-r--r--   1 jocostello costellolab        1742 2014-11-25 13:47:13.963399455 -0800 Z00047.bwa.realigned.rmDups.recal.hybrid_selection_metrics
-rw-r--r--   1 jocostello costellolab       11713 2014-11-25 13:47:14.036399453 -0800 Z00047.bwa.realigned.rmDups.recal.insert_size_histogram.pdf
-rw-r--r--   1 jocostello costellolab        9125 2014-11-25 13:47:14.019399455 -0800 Z00047.bwa.realigned.rmDups.recal.insert_size_metrics
-rw-r--r--   1 jocostello costellolab        8417 2014-11-25 13:47:13.990399455 -0800 Z00047.bwa.realigned.rmDups.recal.quality_by_cycle.pdf
-rw-r--r--   1 jocostello costellolab        5442 2014-11-25 13:47:13.981399455 -0800 Z00047.bwa.realigned.rmDups.recal.quality_by_cycle_metrics
-rw-r--r--   1 jocostello costellolab        5468 2014-11-25 13:47:14.010399455 -0800 Z00047.bwa.realigned.rmDups.recal.quality_distribution.pdf
-rw-r--r--   1 jocostello costellolab        1598 2014-11-25 13:47:14.001399455 -0800 Z00047.bwa.realigned.rmDups.recal.quality_distribution_metrics
-rw-r--r--   1 jocostello costellolab        1674 2014-11-25 13:47:14.084399454 -0800 Z00048.bwa.realigned.rmDups.recal.alignment_summary_metrics
-rw-r--r--   1 jocostello costellolab 17187671600 2014-11-25 13:49:52.435399201 -0800 Z00048.bwa.realigned.rmDups.recal.bam
-rw-r--r--   1 jocostello costellolab     6262856 2014-11-25 13:47:13.812399455 -0800 Z00048.bwa.realigned.rmDups.recal.bam.bai

First warning due to .bai files being generated at an earlier time than .bam, which makes them untrustworthy. Second due to not having write privileges to directory where .bai files are, in order to regenerate them from the newer .bam files. Script will still complete, using the existing .bai files.