I am attempting to convert a SAM file that I obtained as output from Bowtie, in to a BAM file so that I can use it in MACS2. (This is a input file).
Here is the command line I use when attempting to do this:
samtools view -bS /Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_HCT116.sam > Input_HCT116.bam
However, I continually get this error (I re-aligned the fastq files twice to make sure this wasn't a bowtie error, and the downstream sam to bam conversion error was the same):
[W::sam_read1] parse error at line 28 [main_samview] truncated file.
Here is what the data looks like:
Carlos$ samtools view -H /Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_HCT116.sam @HD VN:1.0 SO:unsorted @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @SQ SN:chrM LN:16571 @PG ID:Bowtie VN:1.1.2 CL:"bowtie --wrapper basic-0 -t /Users/Carlos/Downloads/hg19.ebwt/hg19 -S -m 1 -p 4 -q /Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_S1_L001_R1_001.fastq,/Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_S1_L002_R1_001.fastq,/Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_S1_L003_R1_001.fastq,/Users/Carlos/Desktop/Enhancer.Project/HCT116_Enhancers/Input_S1_L004_R1_001.fastq,"
I've attempted to solve this, and looked online but could find nothing that helps me understand what the error is and how to troubleshoot it. Can anyone help?