fastq-dump 分段错误
1615 人阅读 | 时间：2021年08月28日 16:13
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你好， 我正在尝试下载大约 150 个 SRR 加入的列表 我正在使用fastq-dump，因为我需要将与这些 SRR 访问相关的 SRA 文件转换为 FASTQ 文件。 我运行了以下命令： while read SRR ; do
fasterq-dump --outdir ${RAWDATA} --temp ${RAWDATA} --threads 64 --details ${SRR}
done < SRR.list
我的命令已经处理了约 150 个 SRR 加入中的 50 个，但已经有 12 个 SRR 加入以分段错误结束。 例如，这里是SRR062102的日志： cursor-cache : 5,242,880 bytes
buf-size : 1,048,576 bytes
mem-limit : 52,428,800 bytes
threads : 64
scratch-path : '${RAWDATA}/fasterq.tmp.ip-172-31-18-192.ec2.internal.38715/'
output-format: FASTQ split 3
output-file : '${RAWDATA}/SRR062102.fastq'
output-dir : '${RAWDATA}'
append-mode : 'NO'
stdout-mode : 'NO'
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #1 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #27349921 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #1012961 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #1519441 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #2025921 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #28362881 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #25830481 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #26843441 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #27856401 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #3545361 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #26336961 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:07 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #2532401 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #7597201 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #8610161 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #8103681 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #10129601 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #11649041 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #12155521 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #12662001 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #20259201 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #21272161 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #22791601 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #22285121 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #23298081 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #23804561 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #24311041 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #25324001 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #24817521 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #506481 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #28869361 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #29375841 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #29882321 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #30895281 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:08 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #31908241 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #18233281 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #18739761 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #19246241 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #5571281 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #4051841 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:09 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #4558321 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:10 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #9116641 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:10 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #13674961 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:10 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #15700881 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:10 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #16207361 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:10 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #19752721 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:15 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #14687921 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:16 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #6584241 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:20 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #13168481 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:25 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #30388801 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:32 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #21778641 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:34 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #15194401 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:36 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #10636081 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:39 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_String( #14181441 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:49 fasterq-dump.2.10.0 err: cmn_iter.c cmn_read_uint8_array( #16713841 ).VCursorCellDataDirect() -> RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)
2019-09-06T11:58:49 fasterq-dump.2.10.0 err: row #16713841 : READ.len(202) != QUALITY.len(0) (F)
2019-09-06T11:58:49 fasterq-dump.2.10.0 fatal: SIGNAL - Segmentation fault好像和#221有关 |
请不要在 fastq-dump 中为一个加入使用超过 8 个线程。这些线程将只是竞争 I/O - 带宽，并且大部分时间都在休眠。但是您可以同时进行多次加入——如果您有那么多可用的内核。超时可能有很多不同的原因。其中一些可以在我们的网站上。如果你负担得起：首先预取每个加入 - 然后运行 fastq-dump 和预取加入。 |
TlaskalV
@thbtmntgn，你还有这个问题吗？ |
klymenko
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