Tool: bedtools intersect (aka intersectBed) Version: v2.27.1 Summary: Report overlaps between two feature files. Usage: bedtools intersect [OPTIONS] -a -b Note: -b may be followed with multiple databases and/or wildcard (*) character(s). Options: -wa Write the original entry in A for each overlap. -wb Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r. -loj Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B. -wo Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. Only A features with overlap are reported. -wao Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. -u Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r. -c For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r. -v Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v" (an homage). -ubam Write uncompressed BAM output. Default writes compressed BAM. -s Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand. -S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand. -f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -F Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -r Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. -e Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. -split Treat "split" BAM or BED12 entries as distinct BED intervals. -g Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option. -nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01". -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input. -names When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record. -filenames When using multiple databases, show each complete filename instead of a fileId when also printing the DB record. -sortout When using multiple databases, sort the output DB hits for each record. -bed If using BAM input, write output as BED. -header Print the header from the A file prior to results. -nobuf Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time. -iobuf Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files. Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and excluded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps. ***** ERROR: -b option given, but no database file specified. ***** ============================================= vcfanno version 0.3.0 [built with go1.11] see: https://github.com/brentp/vcfanno ============================================= vcfanno.go:115: found 4 sources from 1 files vcfanno.go:241: annotated 0 variants in 0.00 seconds (0.0 / second) Traceback (most recent call last): File "./ClinVar/CV_Individual.py", line 8, in if (os.stat(fileName).st_size == 0 or ('OMIM:' not in open(fileName).read())): OSError: [Errno 2] No such file or directory: './ClinVar/Annotat_./ClinVar/CV_Individual.py_noHeader.vcf' Tool: bedtools intersect (aka intersectBed) Version: v2.27.1 Summary: Report overlaps between two feature files. Usage: bedtools intersect [OPTIONS] -a -b Note: -b may be followed with multiple databases and/or wildcard (*) character(s). Options: -wa Write the original entry in A for each overlap. -wb Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r. -loj Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B. -wo Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. Only A features with overlap are reported. -wao Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. -u Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r. -c For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r. -v Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v" (an homage). -ubam Write uncompressed BAM output. Default writes compressed BAM. -s Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand. -S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand. -f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -F Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -r Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. -e Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. -split Treat "split" BAM or BED12 entries as distinct BED intervals. -g Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option. -nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01". -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input. -names When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record. -filenames When using multiple databases, show each complete filename instead of a fileId when also printing the DB record. -sortout When using multiple databases, sort the output DB hits for each record. -bed If using BAM input, write output as BED. -header Print the header from the A file prior to results. -nobuf Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time. -iobuf Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files. Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and excluded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps. ***** ERROR: -b option given, but no database file specified. ***** Traceback (most recent call last): File "./GWAS/GWAS_Individual.py", line 9, in if (os.stat(fileName).st_size == 0): OSError: [Errno 2] No such file or directory: './GWAS/gwas_Data_./GWAS/GWAS_Individual.py' Tool: bedtools intersect (aka intersectBed) Version: v2.27.1 Summary: Report overlaps between two feature files. Usage: bedtools intersect [OPTIONS] -a -b Note: -b may be followed with multiple databases and/or wildcard (*) character(s). Options: -wa Write the original entry in A for each overlap. -wb Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r. -loj Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B. -wo Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. Only A features with overlap are reported. -wao Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. -u Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r. -c For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r. -v Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v" (an homage). -ubam Write uncompressed BAM output. Default writes compressed BAM. -s Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand. -S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand. -f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -F Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -r Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. -e Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. -split Treat "split" BAM or BED12 entries as distinct BED intervals. -g Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option. -nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01". -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input. -names When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record. -filenames When using multiple databases, show each complete filename instead of a fileId when also printing the DB record. -sortout When using multiple databases, sort the output DB hits for each record. -bed If using BAM input, write output as BED. -header Print the header from the A file prior to results. -nobuf Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time. -iobuf Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files. Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and excluded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps. ***** ERROR: -b option given, but no database file specified. ***** Traceback (most recent call last): File "./PharmGKB/PharmGKB_Individual.py", line 8, in if (os.stat(fileName).st_size == 0): OSError: [Errno 2] No such file or directory: './PharmGKB/PhG_./PharmGKB/PharmGKB_Individual.py' Tool: bedtools intersect (aka intersectBed) Version: v2.27.1 Summary: Report overlaps between two feature files. Usage: bedtools intersect [OPTIONS] -a -b Note: -b may be followed with multiple databases and/or wildcard (*) character(s). Options: -wa Write the original entry in A for each overlap. -wb Write the original entry in B for each overlap. - Useful for knowing _what_ A overlaps. Restricted by -f and -r. -loj Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B. -wo Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlaps restricted by -f and -r. Only A features with overlap are reported. -wao Write the original A and B entries plus the number of base pairs of overlap between the two features. - Overlapping features restricted by -f and -r. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. -u Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found. - Overlaps restricted by -f and -r. -c For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -f and -r. -v Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v" (an homage). -ubam Write uncompressed BAM output. Default writes compressed BAM. -s Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand. -S Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand. -f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -F Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) -r Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. -e Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. -split Treat "split" BAM or BED12 entries as distinct BED intervals. -g Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option. -nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01". -sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input. -names When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record. -filenames When using multiple databases, show each complete filename instead of a fileId when also printing the DB record. -sortout When using multiple databases, sort the output DB hits for each record. -bed If using BAM input, write output as BED. -header Print the header from the A file prior to results. -nobuf Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time. -iobuf Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files. Notes: (1) When a BAM file is used for the A file, the alignment is retained if overlaps exist, and excluded if an overlap cannot be found. If multiple overlaps exist, they are not reported, as we are only testing for one or more overlaps. ***** ERROR: -b option given, but no database file specified. ***** Traceback (most recent call last): File "./DIDA/DIDA_Individual.py", line 8, in if (os.stat(fileName).st_size == 0): OSError: [Errno 2] No such file or directory: './DIDA/Di_./DIDA/DIDA_Individual.py' Syntax error Usage: table_annovar.pl [arguments] Optional arguments: -h, --help print help message -m, --man print complete documentation -v, --verbose use verbose output --protocol comma-delimited string specifying database protocol --operation comma-delimited string specifying type of operation --outfile output file name prefix --buildver genome build version (default: hg18) --remove remove all temporary files --(no)checkfile check if database file exists (default: ON) --genericdbfile specify comma-delimited generic db files --gff3dbfile specify comma-delimited GFF3 files --bedfile specify comma-delimited BED files --vcfdbfile specify comma-delimited VCF files --otherinfo print out otherinfo (infomration after fifth column in queryfile) --onetranscript print out only one transcript for exonic variants (default: all transcripts) --nastring string to display when a score is not available (default: null) --csvout generate comma-delimited CSV file (default: tab-delimited txt file) --argument comma-delimited strings as optional argument for each operation (use & for comma inside string) --convertarg argument to convert2annovar.pl --codingarg argument to coding_change.pl --tempdir directory to store temporary files (default: --outfile) --vcfinput specify that input is in VCF format and output will be in VCF format --dot2underline change dot in field name to underline (eg, Func.refGene to Func_refGene) --thread specify the number of threads to be used in annotation --maxgenethread specify the maximum number of threads allowed in gene annotation (default: 6) --polish polish the protein notation for indels (such as p.G12Vfs*2) --xreffile specify a cross-reference file for gene-based annotation Function: automatically run a pipeline on a list of variants and summarize their functional effects in a comma-delimited file, or to an annotated VCF file if the original input is a VCF file Example: table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -csvout -polish -xreffile example/gene_fullxref.txt table_annovar.pl example/ex2.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -vcfinput Version: $Date: 2018-04-16 00:47:49 -0400 (Mon, 16 Apr 2018) $ rm: cannot remove 'MCAP_.avinput': No such file or directory rm: cannot remove 'MCAP_.hg19_multianno.txt': No such file or directory cannot open the input file at MCAP_filter.pl line 9. rm: cannot remove 'MCAP_.hg19_multianno.vcf': No such file or directory Traceback (most recent call last): File "./IndvResults/MCAPRes.py", line 8, in if (os.stat(fileName).st_size == 0): OSError: [Errno 2] No such file or directory: './IndvResults/FilterMCAP_./IndvResults/MCAPRes.py' Traceback (most recent call last): File "./IndvResults/CombineAllInfo.py", line 49, in Combine.to_csv("./VisFiles/Final_"+str(fileName), index = False, sep="\t") File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line 1524, in to_csv formatter.save() File "/usr/lib/python2.7/dist-packages/pandas/io/formats/format.py", line 1637, in save compression=self.compression) File "/usr/lib/python2.7/dist-packages/pandas/io/common.py", line 387, in _get_handle f = open(path_or_buf, mode) IOError: [Errno 2] No such file or directory: './VisFiles/Final_./IndvResults/CombineAllInfo.py' Traceback (most recent call last): File "./VisFiles/PrepareJForJson.py", line 6, in f = open("./VisFiles/Final_"+str(fileName),'r').read() IOError: [Errno 2] No such file or directory: './VisFiles/Final_./VisFiles/PrepareJForJson.py' Traceback (most recent call last): File "./VisFiles/JsonIndv.py", line 10, in AllData = pd.read_table("./VisFiles/ToJson_"+str(fileName)+".txt", sep=" ") File "/usr/lib/python2.7/dist-packages/pandas/io/parsers.py", line 709, in parser_f return _read(filepath_or_buffer, kwds) File "/usr/lib/python2.7/dist-packages/pandas/io/parsers.py", line 449, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/usr/lib/python2.7/dist-packages/pandas/io/parsers.py", line 818, in __init__ self._make_engine(self.engine) File "/usr/lib/python2.7/dist-packages/pandas/io/parsers.py", line 1049, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/usr/lib/python2.7/dist-packages/pandas/io/parsers.py", line 1695, in __init__ self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 402, in pandas._libs.parsers.TextReader.__cinit__ File "pandas/_libs/parsers.pyx", line 718, in pandas._libs.parsers.TextReader._setup_parser_source IOError: File ./VisFiles/ToJson_./VisFiles/JsonIndv.py.txt does not exist