HuangYicheng-Bio
commented
2 days ago Hi,
Thank you for developing this excellent tool! I am using the DEGAP script with the GapFiller mode, but I encountered an issue while analyzing the log files. My command was:
python ./bin/DEGAP.py --mode gapfiller --seqleft ~/Dsuz/genome/Y_Dsuz/left.fa --seqright ~/Dsuz/genome/Y_Dsuz/right.fa -t 40 --reads ~/Dsuz/data/hifi/Dsuz_male_all.hifi.fa -o ./Output --flag leftand the error isThe log file contains the following errors:
[E::idx_find_and_load] Could not retrieve index file for './Output/process/round1/potentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round1/minimumThresholdReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round1/minimumThresholdExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round1/selectPotentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round2/potentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round2/minimumThresholdReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round2/minimumThresholdExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round2/selectPotentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round3/potentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round3/minimumThresholdReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round3/minimumThresholdExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round3/selectPotentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round4/potentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round4/minimumThresholdReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round4/minimumThresholdExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round4/selectPotentialExtensionReads.left.bam' [E::idx_find_and_load] Could not retrieve index file for './Output/process/round5/potentialExtensionReads.left.bam'Although these errors appeared, the program did not terminate, and it continued running. I would like to clarify:
Will these missing index files affect the final results of the gap-filling process? Is this a bug, or could my version of the software be outdated or misconfigured? How can I resolve this issue to ensure that the necessary .bam index files are generated or loaded correctly? Thank you for your assistance!
Best regards, Shuangxiong
Hi Shuangxiong,
This warning you're seeing is caused by pysam attempting to open a BAM file that has not been indexed. While pysam allows for sequential reading of BAM files without an index file, this does not affect the results or the analysis.
Best, Yicheng
Hi,
Thank you for developing this excellent tool! I am using the DEGAP script with the GapFiller mode, but I encountered an issue while analyzing the log files. My command was:
python ./bin/DEGAP.py --mode gapfiller --seqleft ~/Dsuz/genome/Y_Dsuz/left.fa --seqright ~/Dsuz/genome/Y_Dsuz/right.fa -t 40 --reads ~/Dsuz/data/hifi/Dsuz_male_all.hifi.fa -o ./Output --flag leftand the error isThe log file contains the following errors:
Although these errors appeared, the program did not terminate, and it continued running. I would like to clarify:
Will these missing index files affect the final results of the gap-filling process? Is this a bug, or could my version of the software be outdated or misconfigured? How can I resolve this issue to ensure that the necessary .bam index files are generated or loaded correctly? Thank you for your assistance!
Best regards, Shuangxiong