I'm using bbmap to map transcriptome reads to a set of target loci. I'm working with 12 samples with pair-end reads and 1 sample with single-end reads, all from NCBI's SRA. I'm having no problems with bbmap reading paired-end data and completing analyses correctly. It's the one sample with single-end reads that's causing two issues:
1. The first issue is that the input fasta file only has 288915 reads. I have confirmed this with grep ">" file.fasta | wc -l. However, bbmap reports "Reads used: 308655". I have no idea why the read count is inflated; again, this is not an issue with the paired-end data.
2. bbmap fails to recognize a sequence immediately after the fasta header: "Warning: A fasta header with no sequence was encountered: SRR768524.9631" The sequence in question is formatted exactly like all others in the file and I have checked the EOL, which is fine. Below is what a snippet of the fasta file looks like, with the 3rd sequence being the problematic one for bbmap.
I'm at a loss for figuring out how to resolve these issues. I appreciate any help in getting this to run properly on this last fasta file.
1. The first issue is that the input fasta file only has 288915 reads. I have confirmed this with grep ">" file.fasta | wc -l. However, bbmap reports "Reads used: 308655". I have no idea why the read count is inflated; again, this is not an issue with the paired-end data.
2. bbmap fails to recognize a sequence immediately after the fasta header: "Warning: A fasta header with no sequence was encountered: SRR768524.9631" The sequence in question is formatted exactly like all others in the file and I have checked the EOL, which is fine. Below is what a snippet of the fasta file looks like, with the 3rd sequence being the problematic one for bbmap.
>SRR768524.9629
CTATCAAAGGGAAATCCCGCTGGCCTGCTATCATACAGTCTTGAACCTCCACATGCAATATCAGCTGAATCTCCAACGTGGCCGCTGACAAATGGAGTAACTACGACTGCCAAAACGAAAGCGCGACCTCCTTTCCATCCCATGGGTAATTGGAGTCTTTGAGGAAATCCACATCGGCCAGCCTCTGAATAATGGAATGGTTCCTTCTGGTTGAGTGCACTGTTTATTGAAGTGTAAAGAGACCTGAATCCTTCTTGGTCATGGATAAAGAGGGGAGAATCTGTTGAACTTCTTTCCCACACATTAACACCCTCAGTCAATTTTACTGGGAAACGGTCAATTTCAAATAAGCTAGTTTTGCTTGGTCATAAGTGAGGAAATGTTCATCAGAATCATATTTCGGTCCAATGAATACTCTCACAATGGCATCATCAGCTTTT
>SRR768524.9630
ATAATGCAATTATAGATTGTTGGAGTGCAGGTAAAGCTACCACTGTTATGATTAAAGATAATCCAAAGGTTGAAATTCTTGATGTAGAAGATGTTAAGGTTGGAAAGATAAGACAATTTTGTGAGTTGGACTTGGCATTGAACATGGCCTTACGAAAGTATTTTGGTAGTGTGTTTGATAAAATGGCAGTTACATCTAATGAAACGCCGTGGAAAGTTGCTTGGAATCCATATTTTATGCCTCATCACATCGTGGCGATAGAGAACGACAAGTACGATGTCTTTTGTATAGATGTGAAAAGAATGGATAAGAATTTACCAGTCCAATTCACTGAGATATTGTGT
>SRR768524.9631
TGTTACTGGGTAGGGCTGTGGCACTGGGACCTTGACTGGATAGGGTACATGCTTCTCGACTGGTACTGGGTATGGCTTGGGAATGTGGACAGGGTATGGCCTATCGACTGGGACCTTCACGGGATAGGGAACTTTCTTCTCGATATGGACTGGATAAGGTACTGGTACCTCCTTGTGGATGGTGATAGCTTTAATGTGGCCGTGTTCCTCATGTCCTCCGAGTTCATAGCCACCTCCATATCCGTATCCTCCTAAGTCATGTCCACCTCCATATCCTCCATGTCCACCGCCGTATCCTCCAAGCTCATAACCACCTCCATATCCTAAGCCAAGAAGTCCTCGTTTCTCCTGCTTCTTGTCATCTGTTGGTGCCGCTGCTTTGTCGGTCTTGGATTCGGCCTTCTTCTCTTCAGCTGATGCTGTGGCAAGCAGTGCCAACAGCCCTACCCACAGTACCTTGGATTGCATTGTTGAGTCGTGGTGTGGTCGGCGTCTCCCAA
>SRR768524.9632
AATTCCCAACGACCAAGTATCTGAACATGAGTGGATCAATGCTGAGATCCTGCCTGCTACTGCTATTCCTAGCTTACTGTGTGTCCTGCTATAGAAGTCATGTTCCTAGAGGCGGGAGTTACTCTCTACCGCCTGGAGTTAATCCAACATTCCCAGGAAGGAACCAAGGACTGCCTCCGGCTTATCATGGAAAATTCAAGAGATCACTGGAAGGAGGTTTAGAACCTGAAGATGGTGGTGTCCTTGCAGTTGATGAACCTGCTGATTATCTGAAAGTCAAAAGGTCAGTGGAAGATGTTGAAGGTGAATTCCTTGTGAACGAAGAACCTCAAGAATTTGAGACACTGAGAGCGCGCCGTGACGTCAGAATAATTCATCCAACT
>SRR768524.9633
TTCCAAACTGTCGATTCATGATGTACACAATACCAAAAAAGGCAAATAAGAAATAAAAGT
CTATCAAAGGGAAATCCCGCTGGCCTGCTATCATACAGTCTTGAACCTCCACATGCAATATCAGCTGAATCTCCAACGTGGCCGCTGACAAATGGAGTAACTACGACTGCCAAAACGAAAGCGCGACCTCCTTTCCATCCCATGGGTAATTGGAGTCTTTGAGGAAATCCACATCGGCCAGCCTCTGAATAATGGAATGGTTCCTTCTGGTTGAGTGCACTGTTTATTGAAGTGTAAAGAGACCTGAATCCTTCTTGGTCATGGATAAAGAGGGGAGAATCTGTTGAACTTCTTTCCCACACATTAACACCCTCAGTCAATTTTACTGGGAAACGGTCAATTTCAAATAAGCTAGTTTTGCTTGGTCATAAGTGAGGAAATGTTCATCAGAATCATATTTCGGTCCAATGAATACTCTCACAATGGCATCATCAGCTTTT
>SRR768524.9630
ATAATGCAATTATAGATTGTTGGAGTGCAGGTAAAGCTACCACTGTTATGATTAAAGATAATCCAAAGGTTGAAATTCTTGATGTAGAAGATGTTAAGGTTGGAAAGATAAGACAATTTTGTGAGTTGGACTTGGCATTGAACATGGCCTTACGAAAGTATTTTGGTAGTGTGTTTGATAAAATGGCAGTTACATCTAATGAAACGCCGTGGAAAGTTGCTTGGAATCCATATTTTATGCCTCATCACATCGTGGCGATAGAGAACGACAAGTACGATGTCTTTTGTATAGATGTGAAAAGAATGGATAAGAATTTACCAGTCCAATTCACTGAGATATTGTGT
>SRR768524.9631
TGTTACTGGGTAGGGCTGTGGCACTGGGACCTTGACTGGATAGGGTACATGCTTCTCGACTGGTACTGGGTATGGCTTGGGAATGTGGACAGGGTATGGCCTATCGACTGGGACCTTCACGGGATAGGGAACTTTCTTCTCGATATGGACTGGATAAGGTACTGGTACCTCCTTGTGGATGGTGATAGCTTTAATGTGGCCGTGTTCCTCATGTCCTCCGAGTTCATAGCCACCTCCATATCCGTATCCTCCTAAGTCATGTCCACCTCCATATCCTCCATGTCCACCGCCGTATCCTCCAAGCTCATAACCACCTCCATATCCTAAGCCAAGAAGTCCTCGTTTCTCCTGCTTCTTGTCATCTGTTGGTGCCGCTGCTTTGTCGGTCTTGGATTCGGCCTTCTTCTCTTCAGCTGATGCTGTGGCAAGCAGTGCCAACAGCCCTACCCACAGTACCTTGGATTGCATTGTTGAGTCGTGGTGTGGTCGGCGTCTCCCAA
>SRR768524.9632
AATTCCCAACGACCAAGTATCTGAACATGAGTGGATCAATGCTGAGATCCTGCCTGCTACTGCTATTCCTAGCTTACTGTGTGTCCTGCTATAGAAGTCATGTTCCTAGAGGCGGGAGTTACTCTCTACCGCCTGGAGTTAATCCAACATTCCCAGGAAGGAACCAAGGACTGCCTCCGGCTTATCATGGAAAATTCAAGAGATCACTGGAAGGAGGTTTAGAACCTGAAGATGGTGGTGTCCTTGCAGTTGATGAACCTGCTGATTATCTGAAAGTCAAAAGGTCAGTGGAAGATGTTGAAGGTGAATTCCTTGTGAACGAAGAACCTCAAGAATTTGAGACACTGAGAGCGCGCCGTGACGTCAGAATAATTCATCCAACT
>SRR768524.9633
TTCCAAACTGTCGATTCATGATGTACACAATACCAAAAAAGGCAAATAAGAAATAAAAGT
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