rwdavies
commented
3 years ago Is it reproducible? This looks like a weird bam error through an external library. Otherwise, it might be worth validating the bams individually? See for example https://gatk.broadinstitute.org/hc/en-us/articles/360036854731-ValidateSamFile-Picard-
Also, these bams seem massive, with ~1M reads. You might consider shrinking the region being considered, and parallelize, to speed up, if it's taking too long.
linlin-pp
please help me！
[2021-03-06 22:52:34] downsample sample B04231 - 42 of 868872 reads removed [2021-03-06 22:52:37] downsample sample B04118 - 20 of 1111518 reads removed [2021-03-06 22:52:40] downsample sample B04346 - 17 of 819278 reads removed [2021-03-06 22:52:42] downsample sample A04676 - 43 of 1031030 reads removed [2021-03-06 22:52:44] downsample sample A04010 - 36 of 944007 reads removed [E::bgzf_uncompress] inflate failed: progress temporarily not possible, or in() / out() returned an error [E::bgzf_read_block] inflate_block error -1 [E::bgzf_read] bgzf_read_block error -1 after 13 of 31 bytes [2021-03-06 22:52:57] downsample sample A04777 - 37 of 1269588 reads removed [2021-03-06 22:53:02] downsample sample A04793 - 5 of 566671 reads removed [2021-03-06 22:53:05] downsample sample A02316 - 6 of 791159 reads removed [2021-03-06 22:53:05] downsample sample B04072 - 57 of 998359 reads removed [2021-03-06 22:53:15] downsample sample A04858 - 19 of 979535 reads removed [2021-03-06 22:53:16] downsample sample A04223 - 7 of 698919 reads removed
[2021-03-06 23:16:52] downsample sample B04788 - 81 of 1145196 reads removed [2021-03-06 23:17:26] downsample sample A04696 - 73 of 1056619 reads removed [2021-03-06 23:18:04] downsample sample B04790 - 81 of 1118561 reads removed [2021-03-06 23:18:06] Done generating inputs [2021-03-06 23:18:06] Copying files onto tempdir [2021-03-06 23:24:14] Done copying files onto tempdir [2021-03-06 23:24:14] Generate allele count [2021-03-06 23:30:37] Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Error in check_mclapply_OK(out2) : An error occured during STITCH. The first such error is above Calls: STITCH -> buildAlleleCount -> check_mclapply_OK In addition: Warning messages: 1: In mclapply(1:length(sampleRanges), mc.cores = nCores, FUN = loadBamAndConvert_across_a_range, : scheduled core 3 encountered error in user code, all values of the job will be affected 2: In mclapply(sampleRanges, mc.cores = nCores, FUN = buildAlleleCount_subfunction, : scheduled core 3 encountered error in user code, all values of the job will be affected Execution halted thank you！