find_circ
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fix missing redirect in test_data/Makefile
When running make
in test_data
to check the installation of find_circ
I did, I ran into this:
>>> building bowtie2 index
bowtie2-build CDR1as_locus.fa bt2_cdr1as_locus > bt2_build.log 2>&1;
>>> aligning example reads
bowtie2 -p8 --very-sensitive --score-min=C,-15,0 --reorder --mm \
-f -U cdr1as_reads.fa -x bt2_cdr1as_locus \
2> bt2_firstpass.log | samtools view -hbuS - | samtools sort - cdr1as_test
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
[E::bgzf_close] File write failed
samtools view: error closing standard output: -1
make: *** [cdr1as_test.bam] Error 1
It seems like this is just a missing redirect cdr1as_test.bam
Makefile
target.
Not sure if it matters at all, but I was using SAMtools 1.6, maybe there was a change to recent SAMtools versions that requires this?