Dataset 18: Wig/BedGraph-to-bigWig on data 12
Tool execution generated the following error message:
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe
..put: Broken pipe
grep: writing output: Broken pipe
grep: writing output: Broken pipe..
grep: writing output: Broken pipe
grep: write error
Error running wigToBigWig.
The tool produced the following additional output:
hashMustFindVal: '1' not found
I searched and found this link:
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10745&S=2a335135e76cf9b7160c0e9d41353767
which says that there is a naming convention difference.
I followed what he did and replaced chrom=1 to chrom=chr1 etc, now it goes further, but
still dies with error:
line 18020168 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276760
line 18020169 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276770
line 18020170 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276780
line 18020171 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276790
line 18020172 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276800
line 18020173 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276810
line 18020174 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276820
line 18020175 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276830
line 18020176 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276840
line 18020177 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276850
line 18020178 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276860
line 18020179 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276870
line 18020180 of /tmp/t3: chromosome chr1 has 195276750 bases, but item ends at 195276880
Unrecognized line 18020181 of /tmp/t3:
variableStep chr10 span=10
Error running wigToBigWig.
The command line is: wigToBigWig /tmp/t3 /home/bioinfoadmin/app/galaxy-dist/tool-data/shared/ucsc/chrom/ucsc_gg4.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_769.dat -clip 2>&1 || echo "Error running wigToBigWig." >&2
Quite puzzled...wondering if anyone has seen it before and could give me a hand. :-) I'll really appreciate!
Thanks,
Rui