I only have one sample so this should be easy, but somehow I have the error that I don't have the "sample indices" for it. I tried removing the --individual line from the command but this didn't work. Here's the error.
WARNING: the following samples are not present in haplotype table for chromosome 2L: Wilding5
Traceback (most recent call last):
File "/home/dyern/lstm_scratch/WASP/CHT/bam2h5.py", line 760, in
main()
File "/home/dyern/lstm_scratch/WASP/CHT/bam2h5.py", line 676, in main
raise ValueError("got sample indices for %d individuals, "
ValueError: got sample indices for 0 individuals, but expected to get index for one individual (Wilding5)
Not entirely sure if I formatted my samples,.txt file correctly, so this may be the issue.
Here it is
Wilding5 Wilding5 /home/dyern/lstm_data/reads/Anogam_InfravecCraig/input/concatenated_RNAseq_reads/Wilding_5_R1.fastq.gz /home/dyern/lstm_data/reads/Anogam_InfravecCraig/input/concatenated_RNAseq_reads/Wilding_5_R2.fastq.gz
I only have one sample so this should be easy, but somehow I have the error that I don't have the "sample indices" for it. I tried removing the --individual line from the command but this didn't work. Here's the error.
WARNING: the following samples are not present in haplotype table for chromosome 2L: Wilding5 Traceback (most recent call last): File "/home/dyern/lstm_scratch/WASP/CHT/bam2h5.py", line 760, in
main()
File "/home/dyern/lstm_scratch/WASP/CHT/bam2h5.py", line 676, in main
raise ValueError("got sample indices for %d individuals, "
ValueError: got sample indices for 0 individuals, but expected to get index for one individual (Wilding5)
Not entirely sure if I formatted my samples,.txt file correctly, so this may be the issue. Here it is Wilding5 Wilding5 /home/dyern/lstm_data/reads/Anogam_InfravecCraig/input/concatenated_RNAseq_reads/Wilding_5_R1.fastq.gz /home/dyern/lstm_data/reads/Anogam_InfravecCraig/input/concatenated_RNAseq_reads/Wilding_5_R2.fastq.gz