Please provide us with the following information so we can help you out:

The Software:

• Meerkat

The Problem:

• http://compbio.med.harvard.edu/Meerkat/
• The website is not functioning, and I am trying to install this program for academic purposes.

Details:

• It says: An error has occurred
  Error 8
  compbio.med.harvard.edu
  2021-04-12 18:45:31 UTC

• I also attempted to report this issue here: https://gitreports.com/issue/parklab/Software-Issues?email_public=on

• but it gives a 404 Error.

Submitter: Deepak Kumar Jha
Hi,
I am a post in the Daley lab, here at BCH and I am trying to use Repeat Enrichment Estimator tool, and I am having the following issues:

1. I cannot seem to create an account. and 2. The demo does not seem to load (it times-out).
   Thanks for helping to solve these issues.
   Deepak

Submitter: Scott O.
This is a test

Please provide us with the following information so we can help you out:

The Software:

Repeat enrichment estimator

The Problem:

I have tried to create the sequence assembly file for mm10 following the instructions in the readme file of the source code but it does not seem that the canonical repeat sequence concatenate with instance sequences identified by the default RepeatMasker scan.

Details:

here is the head of mm10.combined.fa that I obtain

HY5
agttggtccgagtgttgtgggttattgttaagttgatttaacattgtctccccccacaaccgcgcttgactagcttgctgttttNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
tRNA-Gln-CAG
ggttccatggtgtaatggtaagcactctggactctgaatccagcgatccgagttcaagtctcggtggaacctccaNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

message:
reading repbase /home/data/tools/RepeatMasker/Libraries/RepeatMaskerLib.embl ... done (45184 repeats).
reading repeatmasker file mm10.fa.out.gz ... done (18538 repeat types).
matching canonical names ... done (matched 1279 repeat types out of 18538).
organism-matched repeats: [Lx6_3end Lx9_3end Lx8b_3end Lx11_3end Lx7_3end Lx8_3end L1_Rod2_orf2 7SLRNA_short_ MERVL_2A Lx10_3end RodERV21]
initializing genome sequence database ... done ids=[chr10 chr12 chr14 chr16 chr18 chr1_GL456210_random chr1_GL456212_random chr1_GL456221_random chr1 chr3 chr4_GL456350_random chr4_JH584292_random chr4_JH584294_random chr5_JH584297_random chr5_JH584299_random chr5 chr7 chr9 chrM chrUn_GL456359 chrUn_GL456360 chrUn_GL456366 chrUn_GL456368 chrUn_GL456379 chrUn_GL456382 chrUn_GL456393 chrX_GL456233_random chrY_JH584301_random chrY_JH584303_random chrY chr11 chr13 chr15 chr17 chr19 chr1_GL456211_random chr1_GL456213_random chr2 chr4_GL456216_random chr4_JH584293_random chr4_JH584295_random chr4 chr5_GL456354_random chr5_JH584296_random chr5_JH584298_random chr6 chr7_GL456219_random chr8 chrUn_GL456239 chrUn_GL456367 chrUn_GL456370 chrUn_GL456372 chrUn_GL456378 chrUn_GL456381 chrUn_GL456383 chrUn_GL456385 chrUn_GL456387 chrUn_GL456389 chrUn_GL456390 chrUn_GL456392 chrUn_GL456394 chrUn_GL456396 chrUn_JH584304 chrX chrY_JH584300_random chrY_JH584302_random]
(CGAGG)n ... 0 valid out of 4 specified sequences (0)
RMER19B ... 0 valid out of 5497 specified sequences (0)
PB1D7 ... 0 valid out of 24234 specified sequences (0)
L2-1_Crp ... 0 valid out of 2 specified sequences (0)
MER70A ... 0 valid out of 184 specified sequences (0)
RLTR15 ... 0 valid out of 2419 specified sequences (0)
MARE6 ... 0 valid out of 45 specified sequences (0)
(GAAAA)n ... 0 valid out of 369 specified sequences (0)
(GAA)n ... 0 valid out of 1428 specified sequences (0)
LTR33A_ ... 0 valid out of 459 specified sequences (0)
Eulor9C ... 0 valid out of 70 specified sequences (0)
(CAAT)n ... 0 valid out of 377 specified sequences (0)

Thank you,

Vanessa

Submitter: Owen Miller
Email: [email protected]
Hi,
I'm using Meerkat as part of my masters project to map structural variants within cancer genomes. I'm having issues with the filtering step: I always get an empty (0 byte) file as the output. Having manually inspected my .variants output files, I can identify positions shared between my normal sample and my tumor samples, but the filtering script isn't giving me any output at all.

Here's the script i'm running:

somatic_sv.pl
-i /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8A/run_2/Polyp_8A.mkdub.variants
-o /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8A/run_2/Polyp_8A.mkdub.somatica.variants
-F /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8Normal/run_2
-R /data/BCI-EvoCa2/owen/reference_genome_hg19/RepeatMasker_refGene_hg19.txt.gz

Here is the steps I ran before this point:

pre_process.pl
-b Polyp_8A.mkdub.bam
-I /data/BCI-EvoCa2/marc/refs/hg19/ucsc.hg19.fasta
-A /data/BCI-EvoCa2/marc/refs/hg19/ucsc.hg19.fasta.fai
-k 1500
-t 10
-s 20
-q 15
-l 0

replace sample blacklist.gz with normal blacklist.gz

rm Polyp_8A.mkdub.blacklist.gz
ln -s /data/BCI-EvoCa2/owen/07_Meerkat/Results/Polyp.08.WGS/Polyp_8Normal/run_2/Polyp_8Normal.mkdub.blacklist.gz Polyp_8A.mkdub.blacklist.gz

meerkat.pl
-b Polyp_8A.mkdub.bam
-F /data/BCI-EvoCa2/marc/refs/hg19/
-m 0
-t 10
-s 20
-d 5
-p 3
-o 1
-l 0

mechanism.pl
-b Polyp_8A.mkdub.bam
-R /data/BCI-EvoCa2/owen/reference_genome_hg19/RepeatMasker_refGene_hg19.txt.gz

Any idea as to why I might not be getting any output from the filtering step?

Submitter: Scott Ouellette
Email: [email protected]
Howdy

Submitter: Scott Ouellette
Email: [email protected]

Testing feature from schneidmaster/gitreports.com#119

Submitter: scott
Email: [email protected]
blank title

Submitter: Sergio Ruiz
I would like to use SigMA to infer how relevant is mut. signature 3 in a set of samples which have been sequenced through whole exome sequencing, but I´m not sure which option fits with our sequencing platform, either WES 37Mb or 64Mb.
Best regards,
Sergio

Submitter: Scott Bruce Ouellette
test

Submitter: scott

Submitter: Scott Bruce Ouellette
Email: [email protected]

Submitter: Juhwan Lee
Email: [email protected]
Hi, i'm graduate student in Korea. Major in Bioinformatics.

I want to use your program tools "BIC-Seq2". I can download it in your website, but can not find the manual that how to use it.
Additionally, i notice that your home page is changing from "http://www.compbio.med.harvard.edu/BIC-seq/" to https://compbio.hms.harvard.edu/index.
i wish you give reply ASAP.

Thank you.

Submitter: phoebe.xin.leung
Email: [email protected]
Dear Sir or Madam,
I met some problem when I install bre,though I'v make mybamtools and bamreader successfully, following the manual.
below are my codes:
tar xjvf dre.tbz✔
cd dre✔
#Edit Makefile and set BTROOT to the path to which mybamtools was extracted.
#vi Makefile
#BTROOT = /home/ywliao/bin/Meerkat/src/mybamtools/ ✔
make ✘

there's errors:
g++ -c -O3 -I /pub6/Temp/lx/software/bs/Meerkat/src/mybamtools/src dre.cpp
dre.cpp: In function ‘std::map<std::__cxx11::basic_string, std::pair<double, double> > read_isinfo(std::__cxx11::string)’:
dre.cpp:90:49: error: no matching function for call to ‘make_pair<double, double>(double&, int)’
isinfo[rg] = make_pair<double,double>(val, 0);
^
In file included from /IJob/J21/gcc-7.1.0/include/c++/7.1.0/bits/stl_algobase.h:64:0,
from /IJob/J21/gcc-7.1.0/include/c++/7.1.0/bits/char_traits.h:39,
from /IJob/J21/gcc-7.1.0/include/c++/7.1.0/ios:40,
from /IJob/J21/gcc-7.1.0/include/c++/7.1.0/ostream:38,
from /IJob/J21/gcc-7.1.0/include/c++/7.1.0/iostream:39,
from dre.cpp:1:

my statement: it always throws an error, cannot find function make_pair().is there something wrong with 'make' or 'gcc'?

my tools' version:GNU Make 3.81 ; gcc (GCC) 7.1.0

I would sincerely appreciate it if you can reply!
Best wishes!
Phoebe.X.L

Submitter: Scott Ouellette
Email: [email protected]
Check public email submission

Please provide us with the following information so we can help you out:

The Software:

meerkat pre-process.pl

The Problem:

no insertion size information (prefix/prefix.is) were generated.

Details:

The pre-process.pl script seems successfully run. Please see log

$ cat cartilage_P18S_loc1.srt.dupmark.pre.log
warning: cannot open reagroup blacklist 'null'
Options:
input BAM: /mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.bam
prefix: /mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark
generating blacklist: coverage >= 1500 reads
max insert size: 1000 bases
soft clip threshold: 60 bases
fragment size: 35 bases
insert size samples: 0 reads
blacklisted read groups:
trim reads: 15
max N bps per read: 5
output files:
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.unmapped.fq.gz
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.softclips.fq.gz
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.isinfo
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.unmapped.rdist
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.softclips.rdist
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.sr.1.fq.gz
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.sr.2.fq.gz
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.blacklist.gz
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark/ (directory)
Forcing immediate execution.
/mnt/isilon/sfgi/suc1/analyses/grant/dnaSeq/HME/meerkat/cartilage_P18S_loc1/cartilage_P18S_loc1.srt.dupmark.bam:
1178625399 reads
1877040 unaligned
54744079 clipped (42308175 hashed)
151 bps in the longest read
Quality string info:
quality score range: [35, 70]
* Sanger [33, 126]
Solexa/Illumina 1.0 [59, 126]
Illumina 1.3 [64, 126]
Illumina 1.5 [66, 126]
Final read counts after rejection due to quality (-q 15 -m 120):
unmapped reads: 1543650 (333390 rejected)
clipped reads: 54545066 (199013 rejected)
Readgroup [cartilage_P18S_loc1]: 1178625399 reads

However, the insertion size file is empty and insertion size plotting failed in R

ls -lhtr cartilage_P18S_loc1.srt.dupmark
total 1.8G
-rw-r--r-- 1 suc1 sfgi 679M Jan 29 12:53 cartilage_P18S_loc1_1.fq.gz
-rw-r--r-- 1 suc1 sfgi 834M Jan 29 12:53 cartilage_P18S_loc1_2.fq.gz
-rw-r--r-- 1 suc1 sfgi 0 Jan 29 12:53 cartilage_P18S_loc1.is

Tue Jan 29 09:46:51 2019 Pre-process v.0.189 started
Error in hist.default(data, xlim = c(0, 10000), breaks = 1000, xlab = "Insert size", :
'x' must be numeric
Calls: hist -> hist.default
Execution halted
Tue Jan 29 12:54:04 2019 Pre-process finished
Time used: 3:7:13

I tried to increase insertion size to 10000 bp, in case that no insertion is smaller than 1000 bp. It still failed. I used picard CollectInsertSizeMetrics.jar to calculate insert size. Here are the report

METRICS CLASS picard.analysis.InsertSizeMetrics

MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
140 50 2 247030253 163.993181 103.729549 294915720 FR 21 39 59 81 101 125 153 193 373 1393

Thus insertion size is as expected --- majority pair insertion size falls into 1000bp range.

From the perl script, .is file should be generated by bamreader command. However, when I run bamreader alone, it does not generate .is either.

Could you please help?

Submitter: Javier Rodriguez Hernaez
I get the following error when running the hint pre step:

"ERROR: /media/javier/data/backup.mac/RStudio_PRJS/hint/data/fastq/T_ALL-rep2-Arima_R1_001.fastq.gz"

docker run suwangbio/hint hint pre -d T_ALL-rep2-Arima_R1_001.fastq.gz,T_ALL-rep2-Arima_R2_001.fastq.gz -a /media/javier/data/install/bwa-0.7.17 -i /media/javier/data/install/bwa.index_mm10/mm10/mm10.fa --refdir /media/javier/data/install/hintref_mm10/mm10/ --informat fastq --outformat cooler -g mm10 -n test -o /media/javier/data/test_hint/ --pairtoolspath /home/javier/anaconda3/bin/pairtools --samtoolspath /home/javier/anaconda3/bin/samtools --coolerpath /home/javier/anaconda3/bin/cooler

The Software:

Meerkat

The Problem:

I have a software compiling issue while installing src packages for Meerkat. After compling mybamtools successfully, I failed to compile another three binary files (bamreader, dre and sclus) based on pre-build mybamtools.

Details:

I have change BTROOT to the bamtools path (/mnt/isilon/sfgi/programs/Meerkat/src/mybamtools), and add -lz to first compiling step
$(CXX) -L $(BTLIB) $(PROFILE) -o bamreader Histogram.o ReadGroup.o bamreader.o gzstream.o -lbamtools -lbamtools-utils -lz

The error seems a lib linkage issue.

g++ -L /mnt/isilon/sfgi/programs/Meerkat/src/mybamtools/lib -o bamreader Histogram.o ReadGroup.o bamreader.o gzstream.o -lbamtools -lbamtools-utils -lz
ReadGroup.o:ReadGroup.cpp:function std::ReadGroup::~ReadGroup(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)'
ReadGroup.o:ReadGroup.cpp:function std::ReadGroup::~ReadGroup(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)'
ReadGroup.o:ReadGroup.cpp:function std::ReadGroup::~ReadGroup(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)'
ReadGroup.o:ReadGroup.cpp:function std::ReadGroup::~ReadGroup(): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)'
ReadGroup.o:ReadGroup.cpp:function clipAlignment(BamTools::BamAlignment&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)'
ReadGroup.o:ReadGroup.cpp:function clipAlignment(BamTools::BamAlignment&): error: undefined reference to 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)'

I tried to use three different versions of GCC to compile (GCC/4.8.2, GCC/4.9.2, GCC/6.3.0-2.27). None of them worked. Could you please help?

Please provide us with the following information so we can help you out:

The Software:

Meerkat Download website

The Problem:

After Inputing details for academic use, the PHP page fails to serve the file

Details:

Not sure what is happening but it would be great to gain access to this software.

Submitter: scott
Email: [email protected]
test

Please provide us with the following information so we can help you out:

The Software:

Meerkat (bamreader, dre and sclus)

The Problem:

Compiling issue

Details:

Hi,

While I have successfully compiled bamtools I failed to compile the other 3 binaries (bamreader,dre and sclus_ with the error message below. Is meerkat compatible with OSX ? I am sorry but i am newbie in programming and I have been struggling for a while so any help would be great !!

Many thanks,

Salim

g++ -c -O3 -I /Users/salim/Desktop/software/Meerkat/src/mybamtools//src bamreader.cpp
bamreader.cpp:16:10: fatal error: 'tr1/unordered_map' file not found
#include <tr1/unordered_map>
^~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [bamreader.o] Error 1
(base) salim@Salims-iMac:~/Desktop/software/Meerkat/src/bamreader$

Submitter: Rashesh Sanghvi
Email: [email protected]
Hello,
I am currently benchmarking bicseq2 version 0.2.4 for incorporating in our pipeline. We have been using nbicseq v0.7a in our pipeline.
While testing I ran multiple iterations of bicseq2 on the same samples, to determine the reproducibility of the CNV calls. I noticed that probably 1 out of 10 iterations had noisy focal events being called.
I increased the subsampling fraction of the reads to 0.001. I saw the same issue. These samples have a single read length(151 bp). Coverage is 50X normal 90X tumor.
I am attaching the CNV plots for the same.

1. Have you seen this issue before? If yes then, what would you suggest as the solution?
2. Is there a way to increase the reproducibility from iteration to iteration?

Your support and suggestions are appreciated.

Thank you,
Rashesh

Hello,
I am currently benchmarking bicseq2 version 0.2.4 for incorporating in our pipeline. We have been using nbicseq v0.7a in our pipeline.
While testing I ran multiple iterations of bicseq2 on the same samples, to determine the reproducibility of the CNV calls. I noticed that probably 1 out of 10 iterations had noisy focal events being called.

I increased the subsampling fraction of the reads to 0.001. I saw the similar issue. These samples have a single read length(151 bp). Coverage is 50X normal 90X tumor.
I am attaching the CNV plots for the same.

1. Have you seen this issue before? If yes then, what would you suggest as the solution?
2. Is there a way to increase the reproducibility from iteration to iteration?

Your support and suggestions are appreciated.

Thank you,
Rashesh

Submitter: scott
Email: [email protected]

Submitter: Benjamin Darbro
Title says it all. Getting:

Forbidden
You don't have permission to access /Meerkat/ on this server.
Apache/2.4.7 (Ubuntu) Server at compbio.med.harvard.edu Port 80

when I go to http://compbio.med.harvard.edu/Meerkat/

Submitter: Javier Rodriguez Hernaez
Email: [email protected]
I get this error when running the hint pre step:

docker run suwangbio/hint hint pre -d T_ALL-rep2-Arima_R1_001.fastq.gz,T_ALL-rep2-Arima_R2_001.fastq.gz -a /media/javier/data/install/bwa-0.7.17 -i /media/javier/data/install/bwa.index_mm10/mm10/mm10.fa --refdir /media/javier/data/install/hintref_mm10/mm10/ --informat fastq --outformat cooler -g mm10 -n test -o /media/javier/data/test_hint/ --pairtoolspath /home/javier/anaconda3/bin/pairtools --samtoolspath /home/javier/anaconda3/bin/samtools --coolerpath /home/javier/anaconda3/bin/cooler

It doesnt recognize the path to my hic fastq files. I tred multiple things, like quoting the paths but still get the same error.

Email: [email protected]
Submitter: Mark Youngblood
Hi,

I am trying to install Meerkat for use with Illumina WGS data. I downloaded the software and example data from this website: http://compbio.med.harvard.edu/Meerkat/. To test the installation, I have been trying to process the example dataset, however my final output files appear to be empty (example.intra.refined.typ.sorted; example.inter.refined.typ.sorted; example.variants). I have confirmed that I am using the correct software versions specified in the manual. The only abnormality I see when running Meerkat is that I receive an R error during the preprocessing step related to a missing file "Rscript execution error: No such file or directory". Digging into the code, it seems to be looking for a file "example.insert.r" that I think is supposed to be created by Bamreader? However, when I run Bamreader by itself, I do not see this file as a part of the log output (example.pre.log). I am not sure if this error is what is causing the final output files to be empty, but it is the only abnormality when I run the three steps. The first two steps take about 10 minutes to execute, but the final step (mechanism) executes instantly. I do not see any errors in example.dre.log or bwa.err.

I would really appreciate any help you are able to provide. I can send any log files that are needed. Thanks so much for your help and for publishing this tool,

Submitter: Scott Ouellette
Email: [email protected]
TEST