I attempted to open the indexed bam file [E::hts_hopen] Failed to open file SC5314_2_sorted.bam.bai [E::hts_open_format] Failed to open file SC5314_2_sorted.bam.bai samtools view: failed to open "SC5314_2_sorted.bam.bai" for reading: Exec format error Nnadi Nnaemeka Emmanuel,Ph...
sub exec_command { my $sCmd = shift;if ((!(defined $sCmd)) || ($sCmd eq "")) { die "\nSubroutine::exec_command : ERROR! Incorrect command!\n"; }my $nExitCode;print STDERR "$sCmd\n"; $nExitCode = system("$sCmd");...
Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. Samtools is designed to work on a stream. It regards...
Samtools is designed to work on a stream. It regards an input file `-' as the standard input (stdin) and an output file `-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error ou...
REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) $${TEST_OPTS:-} test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init @@ -278,18 +273,18 @@ misc/md5fa: misc/md5fa.o $(HTSLIB) misc/md5sum-lite: misc/md5sum...
PLUGINPATH='$(libexecdir)/bcftools' PLUGIN_EXT='.so' SHELL='/bin/sh' USE_GPL='' ac_ct_CC='gcc' bcf_plugindir='$(libexecdir)/bcftools' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' ...
I get these errors with the first file in the list, [E::hts_hopen] Failed to open file filename.bcf.csi and [E::hts_open_format] Failed to open file filename.bcf.csi and Failed to open filename.bcf.csi Exec format error... I take .bcf files and index them with bcftools index...
[i]\n" " exec('def xfit(x): return '+pfit[5])\n" " istart = int(pfit[3])\n" " iend = int(pfit[4])+1\n" " vals = dat[chr][istart:iend]\n" " args = {}\n" " if i==0: args = {'label':'Target to Fit'}\n" " ax.plot([x[2] for x in vals],[x[3...
{REF_GENOME} \ --annotate FORMAT/AD,FORMAT/DP,INFO/AD \ --max-depth 100000 \ --max-idepth 100000 \ ${SC_BAM} | \ ${BCFTOOLS_EXEC} call \ --keep-alts \ -C alleles \ -T ${CANDIDATE_ALLELE} \ --multiallelic-caller \ -Ou | \ ${BCFTOOLS_EXEC} norm \ -Oz \ -o ${SC_...
(*str); str++; } } static int perl_exec(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack) { #if ENABLE_PERL_FILTERS PerlInterpreter *perl = flt->perl; if ( !perl ) error("Error: perl expression without a perl script name\n"); dSP; ENTER; SAVE...