Empty wig file

[YichaoOU]

Hello,

After running MCC_analysis.pl, I basically got no results. But looking at the report.txt, it seems fine?

what is wrong here?

Script version: /home/yli11/Programs/Micro-Capture-C/MCC_analyser.pl
Input parameters
Input path/file: R_H2_10_HBG2.sam
Public folder: 
Public URL: 
Full URL: 
Bigwig Foler: 
Genome hg19
Sample name: MCC
Oligo file: H2_10_HBG2_HBG2_bait.bed_split_800bp.fa
#### Script started at: 8/1/122 15:5:26                              ####
#### If you don't see a time stamp for the script finishing it has crashed somewhere! ####
From the filename - processing HBG2_R   chr11   oligo start     5276754 oligo_end       5277554

#### If you don't see a this time stamp for the script finishing it has crashed!      ####
#### Script finished at: 8/1/122 15:5:                                 ####

Run Statistics
01 DNA sequences in oligo file qq       2
01 Number of oligos loaded      2
01a Duplicate reads Total:      7,581
01a Lines in sam file headder:  86
01a Number of non-duplicated reads Total:       4,549
01a Total number of reads:      12,170
01b Total lines in sam file:    12,778
01c Aligning sequences: 12,645
01c Non aligning sequences:     47
01c Normalisation factor        1
02 Wobble duplicates excluded:  40
02 readname reporters defined   582
02 readno reporters defined     582
02!Blat vs oligo mismatches     12,063
02_fragments_without_oligo_map_and_reporter     4,833
06b Number of non-duplicated reads n=1  4,269
06b Number of non-duplicated reads n=2  276
06b Number of non-duplicated reads n=3  4
06c Duplicate reads n=1:        7,438
06c Duplicate reads n=2:        143
10 Gene: R      12,645
10_input_oligo_size:    800     2
11 Non PCR duplicate filtered reads types reporter v oligo N v N:       11,695
11 Non PCR duplicate filtered reads types reporter v oligo Y v N:       475
11 PCR duplicate filtered reads types reporter v oligo N v N:   4,291
11 PCR duplicate filtered reads types reporter v oligo Y v N:   258
21d readtype: C1.0      12,083
21d readtype: C1.1      103
21d readtype: C1.4      1
21d readtype: C2.0      52
21d readtype: C2.1      3
21d readtype: C2.2      1
21d readtype: R 402
22a_fragments_without_oligo_map_and_reporter_oligo_match_E:     4,544
22a_fragments_without_oligo_map_and_reporter_oligo_match_R:     289
22b_fragments_without_oligo_map_and_reporter_blat_match_C1.0:   4,520
22b_fragments_without_oligo_map_and_reporter_blat_match_C1.1:   35
22b_fragments_without_oligo_map_and_reporter_blat_match_C1.4:   1
22b_fragments_without_oligo_map_and_reporter_blat_match_C2.0:   36
22b_fragments_without_oligo_map_and_reporter_blat_match_C2.1:   2
22b_fragments_without_oligo_map_and_reporter_blat_match_C2.2:   1
22b_fragments_without_oligo_map_and_reporter_blat_match_R:      238
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v C1.0:       8,972
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v C1.1:       48
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v C2.0:       54
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v C2.1:       2
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v C2.2:       2
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_E v R:  10
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v C1.0:       68
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v C1.1:       22
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v C1.4:       2
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v C2.0:       18
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v C2.1:       2
22c_fragments_without_oligo_map_and_reporter_oligo_v_blat_match_R v R:  466
22d_fragments_without_oligo_map_and_reporter_reporter_v_oligo_readtype_N v N:   4,327
22d_fragments_without_oligo_map_and_reporter_reporter_v_oligo_readtype_Y v N:   506
26!Blat vs oligo mismatches HBG2_L      15
26!Blat vs oligo mismatches HBG2_R      12,048