error during aligning

[safisher]

I received the following error when aligning. I tried to rerun the RUM job and RUM tells me that my config file has the output director set to ".". However, the config file clearly has the output directory properly set. The config file is also included below.

---

Thu Jan 3 18:34:25 2013 59706 FATAL RUM::Death - Can't close(GLOB(0x491268b8)) filehandle: '' at /home/fisher/local/src/RUM-Pipeline-v2.0.3_04/bin/../lib/RUM/Script/SortRumByLocation.pm line 271
Thu Jan 3 18:34:32 2013 46723 FATAL RUM::Death -
Error running "perl /home/fisher/local/src/RUM-Pipeline-v2.0.3_04/bin/../bin/sort_RUM_by_location.pl --ram 6 /data12/fisher/Sample_H0D11/rum.trim/chunks/RUM_NU.16 -o /data12/fisher/Sample_H0D11/rum.trim/chunks/RUM_NU.sorted.16.tmp.Dm_CmqHW >> /data12/fisher/Sample_H0D11/rum.trim/chunks/chr_counts_nu.16.tmp._IJnR6PX"

The stderr from that command is

Can't close(GLOB(0x491268b8)) filehandle: '' at /home/fisher/local/src/RUM-Pipeline-v2.0.3_04/bin/../lib/RUM/Script/SortRumByLocation.pm line 271

The error log file Sample_H0D11/rum.trim/log/rum_errors_16.log may have more details.

---

$VAR1 = bless( {
'version' => 'v2.0.3_04',
'name' => 'Sample_H0D11',
'reverse_reads' => 'Sample_H0D11/trimAT/unaligned_2.fq',
'output_dir' => '/data12/fisher/Sample_H0D11/rum.trim',
'chunks' => '48',
'paired_end' => 1,
'variable_length_reads' => 1,
'forward_reads' => 'Sample_H0D11/trimAT/unaligned_1.fq',
'index_dir' => '/lab/repo/resources/rum2/drosophila',
'_default' => bless( {
'bowtie_nu_limit' => 100,
'blat_rep_match' => 256,
'blat_max_intron' => 500000,
'max_insertions' => 1,
'blat_tile_size' => 12,
'blat_min_identity' => 93,
'platform' => 'Local',
'blat_step_size' => 6
}, 'RUM::Config' ),
'ram_ok' => 1,
'read_length' => 'v',
'ram' => 6
}, 'RUM::Config' );