Code:
magicblast -query A16_S4_4_S22_S23_R1.fastq.gz -query_mate A16_S4_4_S22_S23_R2.fastq.gz -db USDA1106_reference -num_threads 24 -infmt fastq | samtools sort -n | samtools view -bS > A16_S4_4_S22_S23.nsort.bam
Error suggests a truncation error in the sam file:
[W::sam_read1_sam] Parse error at line 4991269
samtools sort: truncated file. Aborting
[main_samview] fail to read the header from "-".
Generating the sam file without the pipe:
tail -n 1 A16_S4_4_S22_S23.sam
VH00707:155:2222VWGNX:2:1315:15697:42799 141 * 0 0 * * 0 0 AGAGAGTGCAACATCCCGATTTTTAATATTATTCTACTAGTATTATTACACTACAAGAATTTATTTAATTAGTGACAAATTCAAAAT(magicblast)
Notice the '(magicblast)' text at the end of the file, which is also line 4991269.
Any suggestions?
Code:
magicblast -query A16_S4_4_S22_S23_R1.fastq.gz -query_mate A16_S4_4_S22_S23_R2.fastq.gz -db USDA1106_reference -num_threads 24 -infmt fastq | samtools sort -n | samtools view -bS > A16_S4_4_S22_S23.nsort.bamError suggests a truncation error in the sam file:
Generating the sam file without the pipe:
Notice the '(magicblast)' text at the end of the file, which is also line 4991269.
Any suggestions?