Can't find first and/or second of pair in sam block of length

[CaroleBelliardo]

Hi,

I try to use your software but I return the following sentence :

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Opening /dev/null for write.
samblaster: Opening samp.split.sam for write.
samblaster: Loaded 291 header sequence entries.
samblaster: Can't find first and/or second of pair in sam block of length 1 for id: 31c20002-7721-47a8-88e3-9dc223225e9a
samblaster:    At location: Minc_v4_shac_contig_1:1
samblaster:    Are you sure the input is sorted by read ids?samblaster: Exiting early, the following stats are for processing preceeding the error
samblaster: Output           0 split reads to samp.split.sam
samblaster: Marked           0 of          3 (0.000%) total read ids as duplicates using 4016k memory in 0.000S CPU seconds and 0S wall time.
samblaster: Premature exit (return code 1).```

Do you have some idea of how I can fixe it please ? 

Thank you 

[GregoryFaust]

When you get the error:

samblaster: Can't find first and/or second of pair in sam block of length 1 for id:

it is almost always because of one of two issues, especially as in this case where the error occurred essentially at the beginning of the input SAM file.:

1. The input SAM file contains paired-end reads, but the file is not read-id grouped. Please either use SAM output directly from the alignment tool, or sort the input SAM file by read-id.
2. The input SAM file contains singleton long reads, but you failed to use the --ignoreUnmated option.

Please let me know if neither of these suggestions fixes your problem,

[learning1112]

Thank you so much, it help me a lot