Hi, I hope this message finds you well. I am seeking your expertise regarding an issue I encountered during the alignment of my data with lambda. The process yielded the following log:
Read files are in compressed FASTQ format...
Successfully opened /database/lambda_bs_index/genome.index!
Beginning to load hash table.
refGenLength = 48502
Successfully opened /database/lambda_bs_index/genome.index.bs.pac!
Total Time: 4066.55
No. of Reads: 731395647
No. of Unique Mapped Reads: 99374694 (13.59%)
No. of Ambiguous Mapped Reads: 13881 (0.00%)
No. of Unmapped Reads: 632007072 (86.41%)
Mismatch and Indel Rate: 0.55%
During this process, I encountered several instances of the message 'error best_score' with varying values, such as 'error best_score: -200, scoreMax: -128' and 'error best_score: -178, scoreMax: -112' repeatedly.
May I kindly ask for your interpretation of the 'error best_score: -178, scoreMax: -112'? Does this suggest there may be an issue with my dataset? Additionally, the alignment rate was calculated to be 13.59%, which intuitively seems somewhat elevated. Could this be indicative of an underlying problem or an anomaly in the data?
Hi, I hope this message finds you well. I am seeking your expertise regarding an issue I encountered during the alignment of my data with lambda. The process yielded the following log:
High_occ_table_length=4 Start alignment in default fast mode. error best_score: -200, scoreMax: -128 error best_score: -182, scoreMax: -112 error best_score: -178, scoreMax: -112 ....... thread 0 completed! thread 5 completed! thread 6 completed! thread 2 completed! thread 3 completed! thread 1 completed! thread 7 completed! thread 4 completed!
Total Time: 4066.55 No. of Reads: 731395647 No. of Unique Mapped Reads: 99374694 (13.59%) No. of Ambiguous Mapped Reads: 13881 (0.00%) No. of Unmapped Reads: 632007072 (86.41%) Mismatch and Indel Rate: 0.55%
During this process, I encountered several instances of the message 'error best_score' with varying values, such as 'error best_score: -200, scoreMax: -128' and 'error best_score: -178, scoreMax: -112' repeatedly.
May I kindly ask for your interpretation of the 'error best_score: -178, scoreMax: -112'? Does this suggest there may be an issue with my dataset? Additionally, the alignment rate was calculated to be 13.59%, which intuitively seems somewhat elevated. Could this be indicative of an underlying problem or an anomaly in the data?