fastq-dump: mbedtls_ssl_handshake returned -28800 #75

serge2016 · 2017-05-05T08:47:00Z

Hello!
I am trying to get an SRA with fastq-dump, but I am getting a lot of such errors! Despite this, *.fastq files are enlarging!
What's wrong? How to get rid of these errors?

bg@universe:~/TOOLS/fastqdump$ $VDBCONFIGBIN --import keys/prj_11248.ngc ./
keys/prj_11248.ngc was imported.
Repository directory is: '/home/bg/TOOLS/fastqdump'.
bg@universe:~/TOOLS/fastqdump$ $FASTQDUMP --split-3 --readids --outdir ./ SRR2771707
2017-05-05T08:30:52 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:30:52 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000005.9'
2017-05-05T08:30:52 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:30:52 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000005.9'
2017-05-05T08:30:53 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:30:53 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000022.10'
2017-05-05T08:30:58 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:30:58 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000004.11'
2017-05-05T08:30:58 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:30:58 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000004.11'
2017-05-05T08:31:05 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:06 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:07 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:07 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000023.10'
2017-05-05T08:31:08 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:08 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000012.11'
2017-05-05T08:31:13 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:14 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:14 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000005.9'
2017-05-05T08:31:14 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:31:14 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000005.9'
2017-05-05T08:35:14 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:14 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000007.13'
2017-05-05T08:35:14 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:14 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000007.13'
2017-05-05T08:35:19 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:19 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:19 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000005.9'
2017-05-05T08:35:21 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:21 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000003.11'
2017-05-05T08:35:21 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:26 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:26 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000001.10'
2017-05-05T08:35:26 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:26 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000001.10'
2017-05-05T08:35:33 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:33 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000013.10'
2017-05-05T08:35:33 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:33 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000016.9'
2017-05-05T08:35:33 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:33 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000016.9'
2017-05-05T08:35:36 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:36 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000002.11'
2017-05-05T08:35:37 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:37 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000006.11'
2017-05-05T08:35:37 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:37 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000006.11'
2017-05-05T08:35:37 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:38 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:38 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000016.9'
2017-05-05T08:35:38 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:38 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000016.9'
2017-05-05T08:35:39 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:35:39 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000002.11'
2017-05-05T08:37:56 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:37:56 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:37:57 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:37:57 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000015.9'
2017-05-05T08:37:58 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:37:58 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000023.10'
2017-05-05T08:37:58 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:37:58 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000023.10'
2017-05-05T08:37:59 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:38:00 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:38:06 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T08:38:06 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000004.11'
2017-05-05T08:38:06 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )

The text was updated successfully, but these errors were encountered:

BenLangmead · 2017-05-05T13:40:26Z

I have the same issue

BenLangmead · 2017-05-05T13:43:02Z

Looks as though it's trying to use HTTPS / SSL to open a url that is simply HTTP?

kwrodarmer · 2017-05-05T16:21:55Z

The http URL gets redirected to https. We're looking into it.

kwrodarmer · 2017-05-05T18:29:05Z

@serge2016 - Are you running jobs on a cluster? Not clear if this will have any influence on the investigation, but just wanted to be clear.

kwrodarmer · 2017-05-05T18:29:58Z

@BenLangmead - are you still having this problem?

serge2016 · 2017-05-05T18:42:53Z

@kwrodarmer I am running this from cloud server. I cant say, that it is a cluster.

kwrodarmer · 2017-05-05T18:45:06Z

@serge2016 - is the problem still happening? I can't duplicate it here (yet).

serge2016 · 2017-05-05T18:48:22Z

Right now I'he got:

$ $FASTQDUMP --split-3 --readids --outdir ./ SRR2771707
2017-05-05T18:44:57 fastq-dump.2.8.2 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -28800 ( SSL - The requested feature is not available )
2017-05-05T18:44:57 fastq-dump.2.8.2 err: connection failed while opening file within cryptographic module - error with https open 'http://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/NC_000009.11'
2017-05-05T18:44:57 fastq-dump.2.8.2 err: table incorrect while opening manager within database module - failed SRR2771707

=============================================================
An error occurred during processing.
A report was generated into the file '/home/bg/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

But a minute later is't ok:

$ $FASTQDUMP -I -X 1 -Z --split-spot SRR2771707
Read 1 spots for SRR2771707
Written 1 spots for SRR2771707

So there is something wrong, as I think.

kwrodarmer · 2017-05-05T18:54:19Z

I deleted the data you posted, because they are controlled-access data and cannot be published.

For future correspondence on this issue containing any specifics about your system and this sample run, please write directly to sra-tools@ncbi.nlm.nih.gov rather than posting publicly on GitHub.

Yes, there is clearly something wrong, and it is intermittent. This shows that your configuration is fine, and that the tools are working correctly. We are seeing networking errors. It would help to know which cloud service you are using, and specifically the IP address(es) of the host(s) you are using so that we can monitor the access in our logs. You also have an error report XML file that you should send to us if you're comfortable doing so.

Again, please send confidential information only to sra-tools@ncbi.nlm.nih.gov rather than posting here. We will follow up with any conclusions or recommendations for action in this ticket.

serge2016 · 2017-05-05T19:02:54Z

@kwrodarmer, sorry, it was one read! I wanted to show, that it works.
Check the email, please.

kwrodarmer · 2017-05-05T19:05:00Z

@serge2016 - thank you very much. Waiting for email now...

kwrodarmer · 2017-05-05T19:18:39Z

@serge2016 - please tell more about your environment. Did you pre-download the run? If so, how? Are there any restrictions on your network connectivity as you run? You have your user-cache disabled. Is this for space concerns, or for cluster usage?

osris · 2017-05-05T19:27:20Z

@BenLangmead the error message is misleading. the issue is deeper in the networking protocols. we've had some software updates on servers this week and a few odd behaviors have cropped up. the issue seems to be intermittent. if it still occurs for you, and you send some details about your environment?
thanks

serge2016 · 2017-05-05T19:29:29Z

@kwrodarmer, no, I didn't do any pre-downloads (with prefetch). In my first post there are both command I use to get the reads.
Here is the config I use:

/repository/remote/main/CGI/resolver-cgi = "https://www.ncbi.nlm.nih.gov/Traces/names/names.cgi"
/repository/remote/protected/CGI/resolver-cgi = "https://www.ncbi.nlm.nih.gov/Traces/names/names.cgi"
/repository/user/cache-disabled = "true"
/repository/user/default-path = "/tmp/ncbi"
/repository/user/main/public/apps/file/volumes/flat = "files"
/repository/user/main/public/apps/nakmer/volumes/nakmerFlat = "nannot"
/repository/user/main/public/apps/nannot/volumes/nannotFlat = "nannot"
/repository/user/main/public/apps/refseq/volumes/refseq = "refseq"
/repository/user/main/public/apps/sra/volumes/sraFlat = "sra"
/repository/user/main/public/apps/wgs/volumes/wgsFlat = "wgs"
/repository/user/main/public/cache-enabled = "false"
/repository/user/main/public/root = "/tmp/ncbi/public"
/tools/ascp/max_rate = "1000m"

I am running Ubuntu 16.04.1 LTS.
What else do you need to know?

kwrodarmer · 2017-05-05T19:33:10Z

I'm asking why you have your cache disabled - is it intentional, and if so, why? I don't think it's related to the problem you're experiencing, although it might very well change the behavior of your errors. We're working on discovering the problem itself, so thank you for your patience.

serge2016 · 2017-05-05T19:34:00Z

I've disabled the cache for to save free space.

kwrodarmer · 2017-05-05T19:35:52Z

This makes perfect sense. It should still work, just wanted to know if there was anything else.

kwrodarmer · 2017-05-05T20:01:25Z

Hope you're still there tonight - what do we know about proxies? The type of error you are seeing is happening within the TLS library. When we test a direct tool to server connection on our end, using systems outside of NCBI, we don't see any such problems. Whenever proxies are involved, it changes the game completely.

serge2016 · 2017-05-05T20:54:06Z

I know nothing about proxies :(
But I can test or do something to test!

kwrodarmer · 2017-05-05T22:57:20Z

Then please run the program test-sra SRR2771707 and capture its output to a text file. You should send this file to us at sra-tools@ncbi.nlm.nih.gov for analysis. This must be run from your dbGaP workspace directory, as you have used for fastq-dump.

BenLangmead · 2017-05-12T13:32:02Z

I ran a large job that involved using SRA toolkit (fastq-dump) to download several (~95) accessions. For two accessions, they could not be downloaded even with repeated attempts. I'm attaching 7 log files giving stderr output for 3 attempts for one accession and 4 attempts for the other. As you can see, the error discussed above occurs repeatedly. The exact number of times it occurs before fastq-dump aborts varies. But it always eventually aborts and spits out an XML report, which is included in each file I'm attaching.

Some of the output included in these files is from my software, i.e. the lines that look like this:

 1:18AM UTC on May 12, 2017 | wrote keep alive message to status stream
 1:20AM UTC on May 12, 2017 | writing keep alive message to status stream

But the rest are from fastq-dump. @kwrodarmer or others, could you help me diagnose?

sra_errors.zip

moritzschaefer · 2018-12-19T15:29:09Z

bump. I still observe this on arch linux

qicaibiology · 2019-08-19T19:08:41Z

I also have the same problem when running on server

klymenko · 2020-05-19T02:49:47Z

@serge2016 , try our latest 2.10.6 toolkit.

qicaibiology · 2020-05-19T22:20:04Z

@serge2016 , try our latest 2.10.6 toolkit.

I downloaded the SRA2.10.6 tookit. But after I export the PATH, it looks that a lot of common function cannot be used like ls, head. For example after I download the SRA2.10.6 toolkit, I configured it as the github munal. Then I tried the:

fastq-dump --stdout SRR390728 | head -n 8
-bash: head: command not found
2020-05-19T22:13:21 fastq-dump.2.10.6 err: table incorrect while opening manager within database module - failed to open 'SRR390728'
fastq-dump quit with error code 3

Where is the problem?

klymenko · 2020-05-19T22:49:47Z

You rewrote the PATH instead of updating it.
What was your export command?

qicaibiology · 2020-05-19T22:55:36Z

You rewrote the PATH instead of updating it.
What was your export command?

PATH=$:/scratch/midway2/caiqi/sratoolkit.2.10.6-centos_linux64/bin
export PATH

klymenko · 2020-05-19T22:57:35Z

use:
PATH=$PATH:/scratch/midway2/caiqi/sratoolkit.2.10.6-centos_linux64/bin

logout/login before running export.

qicaibiology · 2020-05-19T23:01:29Z

use:
PATH=$PATH:/scratch/midway2/caiqi/sratoolkit.2.10.6-centos_linux64/bin

logout/login before running export.

It is working now. Thank you very much!

PhilPalmer mentioned this issue Jan 11, 2019

storage exhausted while writing file within file system module rvalieris/parallel-fastq-dump#19

Closed

klymenko closed this as completed May 20, 2020

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fastq-dump: mbedtls_ssl_handshake returned -28800 #75

fastq-dump: mbedtls_ssl_handshake returned -28800 #75

serge2016 commented May 5, 2017

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fastq-dump: mbedtls_ssl_handshake returned -28800 #75

fastq-dump: mbedtls_ssl_handshake returned -28800 #75

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edited by kwrodarmer