Picard SamToFastq only extracts one read, then throws an error - bioinformatics

I'm trying to extract some FastQ files from bam files. Picard can do this with SamToFastq as it says in the documentation for this tool it accepts either a bam or sam file.
But when I run it, it only extracts one read, and then exits. Here is the error message. Any help is appreciated.
[davy#xxxx picard-tools-1.70]$ java -jar SamToFastq.jar I=/home/davy/xxx_trio_data/xxxx-1.bam F=/home/davy/xxx_trio_data/1005-1.fastq
[Wed Jun 20 14:14:21 BST 2012] net.sf.picard.sam.SamToFastq INPUT=/home/davy/xxx_trio_data/xxxx-1.bam FASTQ=/home/davy/xxxx_trio_data/xxxx-1.fastq OUTPUT_PER_RG=false RE_REVERSE=true INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Jun 20 14:14:21 BST 2012] Executing as davy#xxxxx.xxxx.xxxx.xx.xx on Linux 2.6.34.9-69.fc13.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_18-b18; Picard version: 1.70(1215)
[Wed Jun 20 14:14:21 BST 2012] net.sf.picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2029715456
FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1
at java.util.ArrayList.rangeCheck(ArrayList.java:571)
at java.util.ArrayList.get(ArrayList.java:349)
at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:118)

As it turns out, the data is paired end, not single read as I had initially thought, and picard require a second outfile in this instance specified with the SECOND_END_FASTQ option.

Related

dump ended with error (set phase) => Error: read ECONNRESET

I am using elasticdump to dump data from local machine to the server. But my dumps always ended with this error:
...
Tue, 20 Oct 2015 22:56:35 GMT | sent 100 objects to destination elasticsearch, wrote 100
Tue, 20 Oct 2015 22:56:35 GMT | got 100 objects from source elasticsearch (offset: 21200)
Tue, 20 Oct 2015 22:56:36 GMT | Error Emitted => read ECONNRESET
Tue, 20 Oct 2015 22:56:36 GMT | Total Writes: 21200
Tue, 20 Oct 2015 22:56:36 GMT | dump ended with error (set phase) => Error: read ECONNRESET
...
How should I solve this problem?
Is there a better way to dump data from local machine to the server? Thanks in advance!
It sounds like your issue is being caused by the elasticdump opening too many sockets to your elasticsearch cluster. You can use the --maxSockets option to limit the number of sockets opened.
For example:
$ elasticdump --input http://192.168.2.222:9200/index1 --output http://192.168.2.222:9200/index2 --type=data --maxSockets=5
You can find a detailed explanation of the issue here:
https://github.com/taskrabbit/elasticsearch-dump/issues/98

CouchDB 1.6.1 on Windows 08 r2 - os_process_error exit status 1

I have an installation of couchdb which has been working well for a few weeks now. Today it started to throw an os_process_error exit status 1 when attempting to look at any view. The documents in the DB are very small and the views a quite simple. Total DB size is 20mb, largest document is 2mb, i have noticed that the ERL process pegs the CPU at 99%.
I've looked at:
CouchDB delay building index (CouchDB 1.5.0 on Windows Server 2008 R2)
Specific couchdb views suddenly start timing out
I've increased my time out to 50000 seconds, then lowered it to 500 to see if i could find the document which was killing everything but nothing shows up. Stale views still work as well.
Below is the debug error:
[Mon, 10 Nov 2014 19:22:19 GMT] [debug] [<0.118.0>] Successful cookie auth as: "sking"
[Mon, 10 Nov 2014 19:22:19 GMT] [info] [<0.118.0>] 192.168.247.158 - - GET /_config/native_query_servers/ 200
[Mon, 10 Nov 2014 19:22:19 GMT] [error] [<0.231.0>] OS Process Error <0.233.0> :: {os_process_error,
{exit_status,1}}
[Mon, 10 Nov 2014 19:22:19 GMT] [error] [emulator] Error in process <0.231.0> with exit value: {{nocatch,{os_process_error,{exit_status,1}}},[{couch_os_process,prompt,2,[{file,"c:/cygwin/relax/APACHE~2.1/src/couchdb/couch_os_process.erl"},{line,57}]},{couch_query_servers,map_doc_raw,2,[{file,"c:/cygwin/relax...
[Mon, 10 Nov 2014 19:22:19 GMT] [debug] [<0.117.0>] Minor error in HTTP request: {os_process_error,
{exit_status,1}}
[Mon, 10 Nov 2014 19:22:19 GMT] [debug] [<0.117.0>] Stacktrace: [{couch_mrview_util,get_view,4,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/COUCH_~3/src/couch_mrview_util.erl"},
{line,49}]},
{couch_mrview,query_view,6,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/COUCH_~3/src/couch_mrview.erl"},
{line,75}]},
{couch_httpd,etag_maybe,2,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/couchdb/couch_httpd.erl"},
{line,610}]},
{couch_mrview_http,design_doc_view,5,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/COUCH_~3/src/couch_mrview_http.erl"},
{line,188}]},
{couch_httpd_db,do_db_req,2,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/couchdb/couch_httpd_db.erl"},
{line,234}]},
{couch_httpd,handle_request_int,5,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/couchdb/couch_httpd.erl"},
{line,318}]},
{mochiweb_http,headers,5,
[{file,
"c:/cygwin/relax/APACHE~2.1/src/mochiweb/mochiweb_http.erl"},
{line,94}]},
{proc_lib,init_p_do_apply,3,
[{file,"proc_lib.erl"},{line,239}]}]
[Mon, 10 Nov 2014 19:22:19 GMT] [info] [<0.117.0>] 192.168.247.158 - - GET /tcs/_design/company/_view/Company_Id?limit=101 500
[Mon, 10 Nov 2014 19:22:19 GMT] [error] [<0.117.0>] httpd 500 error response:
{"error":"os_process_error","reason":"{exit_status,1}"}
I figured this out but I am not sure why it happened. There was a HUGE document 57mb which had been uploaded to the DB but it was not visible in Futon or anywhere else.
I only found it after digging into the debug log further. I could not access the document via a CURL Get. I ended up having to use CURL -X DELETE with the specific revision then a purge to get rid of the document. Soon as the document was deleted everything worked as expected.

Why aren't my Windows Apache log messages being written to the ErrorLog location specified in my VirtualHost?

I'm attempting to override the ErrorLog location in my httpd.conf file by specifying it in my .vhost, but it's creating the file only and still writing to the .conf one.
I have the following in my httpd.conf file:
# ErrorLog: The location of the error log file.
# If you do not specify an ErrorLog directive within a <VirtualHost>
# container, error messages relating to that virtual host will be
# logged here. If you *do* define an error logfile for a <VirtualHost>
# container, that host's errors will be logged there and not here.
#
ErrorLog "logs/error.log"
# Virtual hosts
Include conf/vhosts/xyz_apache.vhost
Then I have this in my xyz_apache.vhost file (on one line):
ErrorLog "C:/Program Files (x86)/Apache Software Foundation/
Apache2.2/logs/xyzerrors.log"
If I start up apache and look in my logs directory to see what was created, I see a blank xyzerrors.log and an error.log file with startup messages in it ("Starting thread to listen on port 80, etc.).
Any idea why this might be happening, or advice as to how I can fix it? The xyzerrors.log file was clearly created, so it seems my file paths and spelling of "ErrorLog" and my vhost configuration and all the obvious parts should be correct. But it's writing to the file specified in my httpd.conf, which, if I understand correctly, should only be the backup location, should there not be one specified in the .vhost. I wondered if permissions might be an issue somehow (maybe it didn't have write access to the xyzerror.log it created so it wrote to error.log instead?), but both files are in the same directory. Is there another configuration piece I missed?
I verified what was happening by renaming the .conf ErrorLog and deleting the .vhost ErrorLog, and again saw the .vhost log created and the .conf log created and written to. I have similar setups running in Linux with no problems.
Update: Here's another piece. I was fixing an issue with lxml (I got an error, installed a newer version of it, then restarted apache), and noticed that a couple of messages appeared in my xyzerror.log. Here's what it looks like:
error.log
[Wed Oct 09 09:14:52 2013] [notice] Child 42900: Starting thread to listen on port 80.
[Wed Oct 09 09:48:11 2013] [error] ERROR:django.request:Internal Server Error: /admin/
[Wed Oct 09 09:48:11 2013] [error] Traceback (most recent call last):
[Wed Oct 09 09:48:11 2013] [error] ImportError: DLL load failed: A dynamic link library (DLL) initialization routine failed. (Rest of traceback omitted)
[Wed Oct 09 09:54:50 2013] [notice] Parent: Received shutdown signal -- Shutting down the server.
Apache server interrupted...
Apache server interrupted...
Apache server interrupted...
Apache server interrupted...
Apache server interrupted...
Released the start mutex
[Wed Oct 09 09:54:52 2013] [notice] Child 42900: All worker threads have exited.
[Wed Oct 09 09:54:52 2013] [notice] Child 42900: Child process is exiting
[Wed Oct 09 09:54:52 2013] [notice] Parent: Child process exited successfully.
[Wed Oct 09 09:54:53 2013] [warn] mod_wsgi: Compiled for Python/2.7.
[Wed Oct 09 09:54:53 2013] [warn] mod_wsgi: Runtime using Python/2.7.2.
[Wed Oct 09 09:54:53 2013] [notice] Apache/2.2.22 (Win32) mod_wsgi/3.3 Python/2.7.2 configured -- resuming normal operations
[Wed Oct 09 09:54:53 2013] [notice] Server built: Jan 28 2012 11:16:39
[Wed Oct 09 09:54:53 2013] [notice] Parent: Created child process 40284
[Wed Oct 09 09:54:53 2013] [warn] mod_wsgi: Compiled for Python/2.7.
[Wed Oct 09 09:54:53 2013] [warn] mod_wsgi: Runtime using Python/2.7.2.
[Wed Oct 09 09:54:53 2013] [notice] Child 40284: Child process is running
[Wed Oct 09 09:54:53 2013] [notice] Child 40284: Acquired the start mutex.
[Wed Oct 09 09:54:53 2013] [notice] Child 40284: Starting 64 worker threads.
[Wed Oct 09 09:54:53 2013] [notice] Child 40284: Starting thread to listen on port 80.
xyzerror.log
[Wed Oct 09 09:47:54 2013] [info] [client 127.0.0.1] mod_wsgi (pid=42900, process='', application='XYZ.sysname.mydomain.local|'): Loading WSGI script 'C:/Users/etc/etc/XYZ_wsgi.py'.
[Wed Oct 09 09:48:11 2013] [error] [client 127.0.0.1] client denied by server configuration: C:/Users/etc/etc/site_media
So maybe these aren't ErrorLog messages and I need to investigate my CustomLog settings? I'm seeing similar behavior with those (an xyzaccess.log file is being written but my access.log in my .conf is being written to), but I didn't include it here for simplicity.
Update 2:
If I continue to browse my site and watch the log files, I see that logs are eventually getting written to the xyzerror.log (and the xyzaccess.log) in my vhost location. Only the initial startup messages ("listening on port..", etc.) and one site-related error were in the conf location.
Can anyone explain or suggest a solution?
Apache 2.2/Windows 7/Django 1.5/Python 2.7
if I understand correctly, should only be the backup location, should there not be one specified in the .vhost
Not at all !
This is normal behaviour, because the ErrorLog directive can either apply globally, or to the VirtualHost it is declared in.
Think about it. When an error is reported to the error log for apache internal events, such as startup events or module loading failure, how can it use a specific virtual host's error log, since virtual host resolution is not even possible yet ?
Apache knows which Virtual Host to use only when a client makes a request and the request is identified to refer to a specific virtual host, either via IP resolution or Hostname resolution.
Therefore, only those errors will appear in your vhost-specific error log, such as PHP errors pertaining to that vhost, or HTTP errors such as 401 or 404 codes.

Weird behavior with gwan v3.12.26

I just installed the latest Xmas gift from gwan team, but I'm having some problems:
Segmentation fault with archlinux .
On Ubuntu strange behavior.
I can't run any script on it.
About #1, Archlinux is up to date and uses the 2.16 GLIBC.
About #2, I'm loading http://188.165.219.99:8080/100.html sometimes it display 100 X, sometimes an error page (with CSS) and sometimes an error page without CSS.
About #3, I can't run any csp script:
http://188.165.219.99:8080/?hello.c
http://188.165.219.99:8080/?hello.rb
http://188.165.219.99:8080/?hello.php
None of the above work. Has the csp url changed?
I have installed php5-cli and ruby on my ubuntu.
For informations:
# ldd --version
ldd (Ubuntu EGLIBC 2.11.1-0ubuntu7.11) 2.11.1
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.
Here the log on archlinux
# cat logs/gwan.log
[Thu Dec 27 14:03:44 2012 GMT] ------------------------------------------------
[Thu Dec 27 14:03:44 2012 GMT] G-WAN 3.12.26 64-bit (Dec 26 2012 13:58:12)
[Thu Dec 27 14:03:44 2012 GMT] ------------------------------------------------
[Thu Dec 27 14:03:44 2012 GMT] Local Time: Thu, 27 Dec 2012 16:03:44 GMT+2
[Thu Dec 27 14:03:44 2012 GMT] RAM: (1.60 GiB free + 0 shared + 834.57 MiB buffers) / 23.64 GiB total
[Thu Dec 27 14:03:44 2012 GMT] Physical Pages: 1.60 GiB / 23.64 GiB
[Thu Dec 27 14:03:44 2012 GMT] DISK: 1.71 TiB free / 1.88 TiB total
[Thu Dec 27 14:03:44 2012 GMT] 336 processes, including pid:1545 './gwan'
[Thu Dec 27 14:03:44 2012 GMT] Multi-Core, HT enabled
[Thu Dec 27 14:03:44 2012 GMT] 1x Intel(R) Xeon(R) CPU W3520 # 2.67GHz (4 Core(s)/CPU, 2 thread(s)/Core)
[Thu Dec 27 14:03:44 2012 GMT] using 4 workers 0[1111]3
[Thu Dec 27 14:03:44 2012 GMT] among 8 threads 0[11110000]7
[Thu Dec 27 14:03:44 2012 GMT] 64-bit little-endian (least significant byte first)
1: segmentation fault with archlinux
Many informations are listed at the top of the /logs/wgan.log file. It would immensely help to see it (that's what log files are for).
2: on ubuntu strange behavior
Not knowing the nature of the "strange behavior" nor the Ubuntu version makes difficult to answer your question (if that's a question).
3: I can't run any script on it
We received more than 50 emails this morning alove. None (but yours) reports that scripts fail to run. So far, people report great results with all languages.
Check your files permissions (can the G-WAN account read the script files?) and verify that the relevant compilers / runtimes are installed.
Ogla's report suggests that javascript embedded in HTML (the new release does minifying there) migh be the cause of the cut files.
Other than that, the fact that the daemon mode is broken in v3.12.25/26 may explain your problems if you run in daemon mode.

Apache crash on launch - W2008 Server

I installed Xampp on my Windows Server 2008. It worked fine, untill I decided to install some updates.
Now Apache doesn't start any more and I get these errors;
[Wed Aug 29 23:31:20.328125 2012] [core:warn] [pid 1540:tid 312] AH00098: pid file
C:/xampp/apache/logs/httpd.pid overwritten -- Unclean shutdown of previous Apache run?
[Wed Aug 29 23:31:20.968750 2012] [ssl:warn] [pid 1540:tid 312] AH01873: Init:Session Cache is not configured [hint: SSLSessionCache]
I'm trying to install Cacti on the server to monitor everything... Don't think it's relevant, but just saying
If you still need it:
http://httpd.apache.org/docs/2.4/upgrading.html#post_234
Apache 2.4 will not start with added SSL support on windows until additional module (compare to Apache 2.2 configuration) was enabled: socache_shmcb_module
This additional info is at the beginning of the httpd-ssl.conf, but it takes time to read it :)
# Required modules: mod_log_config, mod_setenvif, mod_ssl, socache_shmcb_module (for default value of SSLSessionCache)

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