hg19all Download Issues

WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files

http://seqmule.usc.edu

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hg19all Download Issues #173

Closed coolsideofthepillow closed 5 years ago

coolsideofthepillow commented 6 years ago

Hello,

Thank you for the great collections of scripts.

I've followed the online guide and am at the point where I would like to download hg19. I've cd to the SeqMule folder but I receive the error:

"seqmule: command not found"

after

seqmule download -down hg19all

seqmule download -d hg19

I'm not fantastic with ubuntu so if I'm missing something obvious, my apologies.

As a side note, it appears that SeqMule does not load all repositories in Ubunutu 18.04 (does work as stated with 12.04) and the latest version of GATK I could get to work is 3.8.1 (GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar).

Many thanks, C

yunfeiguo commented 6 years ago

Hi did you add path to seqmule to your PATH environment variable? alternatively, you can run seqmule_folder/bin/seqmule where seqmule_folder is full path to directory of SeqMule. Thanks.

coolsideofthepillow commented 6 years ago

Hello yunfeigo,

Thank you for that, I did not add seqmule to PATH. Knew it would be something small. Thank you for that.

juanmluque commented 5 years ago

Hi Yunfei,

I have a good experience with SeqMule in Ubuntu 12 version (years ago), but when I try now to install SeqMule in Ubuntu 16 version (into other different computer)I have problems, for example to load the hg19all databases and GATK last version.Could you help me to install or load hg19all with other options differents to :

seqmule download -down hg19all (this option doesn t function me)

And what file I must install of GATK last version?. What version of Ubuntu is better to install SeqMule?

(*) Please, I would like to know your e-mail adress if I have to ask you so many questions or doubts, because your old e-mail I had it is not valid now.

Waiting for your answer,please, thank you very much for your help and best regards.

Juan M.

yunfeiguo commented 5 years ago

Hi @juanmluque please retrieve the GenomeAnalysisTK.jar file and put it in exe/ folder (where other programs are installed). Note the GATK4 has changed its API and therefore is not compatible with SeqMule at the moment. Please use older versions: https://software.broadinstitute.org/gatk/download/archive

What errors are you seeing using Ubuntu16?

You can send questions to seqmule-dev@googlegroups.com

juanmluque commented 5 years ago

Hi Yunfei, Thank you very much for your answer. Now I have problems to load the hg19all databases.I send you my output when i try to load these databases:

luque@luque-HP-Compaq-Pro-6300-MT:~/SeqMule$ seqmule download -down hg19all seqmule: command not found luque@luque-HP-Compaq-Pro-6300-MT:~/SeqMule$ perl seqmule download -down hg19allCan't open perl script "seqmule": No such file or directory

Could you help me ,please , to load these databases (I use now Ubuntu 16 version)?

Thank you very much and best regards.

Juan M.

El dom., 4 ago. 2019 a las 21:55, Yunfei Guo (notifications@github.com) escribió:

Hi @juanmluque https://github.com/juanmluque please retrieve the GenomeAnalysisTK.jar file and put it in exe/ folder (where other programs are installed). Note the GATK4 has changed its API and therefore is not compatible with SeqMule at the moment. Please use older versions: https://software.broadinstitute.org/gatk/download/archive

What errors are you seeing using Ubuntu16?

You can send questions to seqmule-dev@googlegroups.com

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILLVJIJK3UW5JEAOCKTQC4X4LA5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3QIQPA#issuecomment-518031420, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILI7W3J4XQOETP7VRT3QC4X4LANCNFSM4FCXW7VQ .

yunfeiguo commented 5 years ago

Assume seqmule is in the folder where you run the command, then please replace seqmule with ./seqmule

juanmluque commented 5 years ago

OK. Yunfei, I have solved the problem and the loading of hg19 all databases. Now i need to know what MINIMAL equirements of computer are necessary (memory, RAM memory, hard disk) to install and working without problems with SeqMule .For example to load hg19 all databases COMPLETELY WITHOUT SPACE PROBLEMS IN DISK when i am loading the databases.

Thank you very much for your help and best regards.

Juan M.

El lun., 5 ago. 2019 a las 15:21, Yunfei Guo (notifications@github.com) escribió:

Assume seqmule is in the folder where you run the command, then replace seqmule with ./seqmule.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILI5L3LHO76GPZ4NC3DQDASM3A5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3RZMBA#issuecomment-518231556, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILISIKLJW6WK3NPYKQ3QDASM3ANCNFSM4FCXW7VQ .

juanmluque commented 5 years ago

Hi Yunfei,

Enclosed I send you a SeqMule ERROR when I try to run 2 Example FASTQ files (normal_R1.fastq.gz and the other R2), it outputs ERROR in step 7 (gatklite....).Could you analize it and answer me what can I do? .I have tried run these files twice and always gives ERROR in step 7.

Thank you very much for your help.Best regards.

Juan M.

El dom., 4 ago. 2019 a las 21:55, Yunfei Guo (notifications@github.com) escribió:

Hi @juanmluque https://github.com/juanmluque please retrieve the GenomeAnalysisTK.jar file and put it in exe/ folder (where other programs are installed). Note the GATK4 has changed its API and therefore is not compatible with SeqMule at the moment. Please use older versions: https://software.broadinstitute.org/gatk/download/archive

What errors are you seeing using Ubuntu16?

You can send questions to seqmule-dev@googlegroups.com

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILLVJIJK3UW5JEAOCKTQC4X4LA5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3QIQPA#issuecomment-518031420, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILI7W3J4XQOETP7VRT3QC4X4LANCNFSM4FCXW7VQ .

yunfeiguo commented 5 years ago

RAM I would recommend at least 8GB, and disk at least 80GB, but to analyze WES or WGS data, you need much larger space.

Could you post the error message? Did you run ./Build freshinstall?

juanmluque commented 5 years ago

Thank you Yunfei. In my Bioinformatic Unit we are interested in a possible use or application of SeqMule to plant genomes like Arabidopsis thaliana for example.Do you know if are there any experiencie /information/publication with SeqMule or similar with other genomes different to human? Would it be possible to load another databases different to human and use SeqMule without problems? I am searching information about this ,but I do not find someting.It is important for us.

Thank you so much for your help. Best regards.

Juan Manuel Luque Bioinformatic Unit Biotechnology National Center-CSIC Madrid (Spain)

El martes, 6 de agosto de 2019, Yunfei Guo notifications@github.com escribió:

RAM I would recommend at least 8GB, and disk at least 80GB, but to analyze WES or WGS data, you need much larger space.

Could you post the error message? Did you run ./Build freshinstall?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILJNDDUPTDYAFZ6XFTLQDF23ZA5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3VDLFY#issuecomment-518665623, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILKSXJB7IZOHUYCAWDTQDF23ZANCNFSM4FCXW7VQ .

yunfeiguo commented 5 years ago

Hi @juanmluque SeqMule was designed for use with human genome. You can try and I can help with you if you encounter some fixable problems, but otherwise it's uncertain.

juanmluque commented 5 years ago

Hi Yunfei; I am triying solve the ERROR in step 7 (gatklite...) as you answered me and reading in FAQ : (...) Please make sure you are using Java 1.7 and put make it your default java program (put the folder containing java at the beginning of your PATH variable).I have tried do this , but the ERROR goes on. Also i have tried with : $ sudo apt -get install default -jre But the output is :

it does not make sense the command line option "g" (from -get) combined with the other options

I have located the jre (java 1.7) folder in my computer inside of the same folder than folder contains SeqMule.

Please, could you write me the commands line to solve this problem? Or another way to solve this problem.I have installed in my computer java 1.7 and java 1.8. My path to SeqMule folder is : $ cd /media/ubuntu/DATOS/SeqMule-master/bin . Where I must put the java folder jre in this pàth to solve this ERROR?

Thank you very much for your help.Best regards JUan M.

El mar., 6 ago. 2019 a las 13:08, Juan Manuel Luque Sánchez (< j6163mls@gmail.com>) escribió:

Hi Yunfei,

Enclosed I send you a SeqMule ERROR when I try to run 2 Example FASTQ files (normal_R1.fastq.gz and the other R2), it outputs ERROR in step 7 (gatklite....).Could you analize it and answer me what can I do? .I have tried run these files twice and always gives ERROR in step 7.

Thank you very much for your help.Best regards.

Juan M.

El dom., 4 ago. 2019 a las 21:55, Yunfei Guo (notifications@github.com) escribió:

Hi @juanmluque https://github.com/juanmluque please retrieve the GenomeAnalysisTK.jar file and put it in exe/ folder (where other programs are installed). Note the GATK4 has changed its API and therefore is not compatible with SeqMule at the moment. Please use older versions: https://software.broadinstitute.org/gatk/download/archive

What errors are you seeing using Ubuntu16?

You can send questions to seqmule-dev@googlegroups.com

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILLVJIJK3UW5JEAOCKTQC4X4LA5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3QIQPA#issuecomment-518031420, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILI7W3J4XQOETP7VRT3QC4X4LANCNFSM4FCXW7VQ .

juanmluque commented 5 years ago

Hi Yunfei, About this mail I sent you I would like to ask you,please: 1) What folders of SeqMule are necessary or essentials applied to analysis for example of Arabidopsis thaliana?. Could you name these folders? 2) Belonging to the Database folder in SeqMule ,what subfolders are necessary or essentials? .Could you name these subfolders? Would it be possible work SeqMule without problems ONLY with the subfolders (inside of Database folder) BWA (fasta files-reference genome of Arabidopsis thaliana) and subfolder (inside of Database folder) Arabidopsis reference genome illumina (bed files) and also (inside of database folder) vcf files and vcf.idx files of another genome databases of Arabidopsis ?. All of this would it be enough or we'd need include more folders or information in SeqMule for Arabidopsis?.

Thank you so much for your help. Best regards.

Juan M.

El mié., 7 ago. 2019 a las 7:01, Yunfei Guo (notifications@github.com) escribió:

Hi @juanmluque https://github.com/juanmluque SeqMule was designed for use with human genome. You can try and I can help with you if you encounter some fixable problems, but otherwise it's uncertain.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173?email_source=notifications&email_token=AMZYILJQCGSWGNUEV7RPEOTQDJJMHA5CNFSM4FCXW7V2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3XGRJY#issuecomment-518940839, or mute the thread https://github.com/notifications/unsubscribe-auth/AMZYILLSURDZVG6P5MDT3NLQDJJMHANCNFSM4FCXW7VQ .

yunfeiguo commented 5 years ago

Hi @juanmluque you can run

export PATH=your_path_to_java_bin:$PATH

Please replace your_path_java_bin with the actual path to the bin folder containing java.

Once you finish installing ./Build freshinstall, you should be able to start analysis, since you are not analyzing human genome, you can ignore database folders created by seqmule. Instead, you need to specify reference genome for Arabidopsis (--ref option).

yunfeiguo commented 5 years ago

Can you run the example without a problem? http://seqmule.openbioinformatics.org/en/latest/Tutorials/Quick%20start/

juanmluque commented 5 years ago

       Yunfei, sorry, I forgot the issue number (GitHub) is  #176 .

---------- Forwarded message --------- De: Juan Manuel Luque Sánchez j6163mls@gmail.com Date: mié., 4 sept. 2019 a las 14:44 Subject: Re: SeqMule for Analysis of Arabidopsis thaliana To: yunfei guo guoyunfei2008@outlook.com

Hi Yunfei, I have just sent you (by GitHUb -WGLab/SeqMule) my next question:

As you know , we are trying to apply SeqMule for Arabidopsis thaliana, and we would like to delete the messages: NOTICE: Reference genome build is hg 19 and NOTICE: dbsnp138 will be used for variant calling and recalibration when pipeline starts (or to change the message about hg 19 by other reference genome build). We have changed the next parameters: go_dbsnp=0 #dbSNP file for GATK only go_hapmap=0 #HapMap file for GATK go_dbsnpver=0 #dbSNP version for variant recalibration and annotation, default is 137 go_kg=0 #1000 Genome project VCF file go_buildver=0 #genome build version, default is hg19 and also: o_gatklite_forceSNPHardFilter=1 #if set to 1, force using hard filtering on SNP, otherwise seqmule use VQSR only if BAM size is larger than 1GB. CAUTION: do NOT set o_gatklite_forceSNPVQSR and o_gatklite_forceSNPHardFilter both to 1! and: o_gatklite_forceINDELHardFilter=1 #if set to 1, force using hard filtering on INDEL, otherwise seqmule use VQSR only if BAM size is larger than 15GB. CAUTION: do NOT set o_gatklite_forceINDELVQSR and o_gatklite_forceINDELHardFilte both to 1!

But the NOTICE messages are the same again (hg19 and dbsnp 138) when we run the pipeline.

Please, what can we do to solve this? Thank you very much. Best. Juan M.

El sáb., 24 ago. 2019 a las 15:13, yunfei guo (guoyunfei2008@outlook.com) escribió:

Hi Juan,

The seqmule version used to generate the script is different from the version you are executing. Please rerun the script generation. Thanks.

On Aug 23, 2019, at 1:57 AM, Juan Manuel Luque Sánchez j6163mls@gmail.com wrote:

Hi Yunfei, I have to ask you please about an ERROR with SeqMule (because I have searched in FAQ-SeqMule and internet, but I don't find anything about):

When I try $ perl seqmule run PRUEBA1.script (PRUEBA1 is a pipeline not ended that I want to restart), then the output is: Current version: 1.2.3 ERROR: incompatible execution script version Supported versions: 1.2

And I did the same yesterday with other different script WITHOUT PROBLEMS AND FINALLY RUN RIGHT TO THE END OF THE PROCESS/PIPELINE.

Could you help me, please?

Thank you very much.

Juan M.

El jue., 22 ago. 2019 a las 17:47, yunfei guo (guoyunfei2008@outlook.com) escribió:
Hi Juan,

Thanks for sharing the good news. Glad to hear that. Enjoy your research!

Best, Yunfei

On Aug 22, 2019, at 4:52 AM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Hi Yunfei, I have good news for you.For the first time the whole process or pipeline of SeqMule for Arabidopsis thaliana reach the end without problems and getting a result of variants.This is the pipeline we used:

$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture TAIR10_chr.all.bed -t 1 -prefix PRUEBA1 --ref TAIR10_chr.all.fasta -e

We had to change (with commands) the name Chr by chr in the TAIR10_chr.all.bed and TAIR10_chr.all.fasta , because SeqMule give us ERROR: NO UPPERCASE ALLOWED IN chr OF A CONTIG NAME: Chr C..... But when we changed those letters in these files, the process was fine until the end and giving results.Now we will analyze the results, and we will go on doing proofs.

Meanwhile thank you very much for your help.Best.

Juan M.

El mié., 21 ago. 2019 a las 5:44, yunfei guo (guoyunfei2008@outlook.com) escribió:
TAIR10_Chr.all.dict is NOT a .bed file but a .dict file. Please generate the correct .bed file using the fai2bed.pl from .fai file. Thanks.

On Aug 20, 2019, at 2:55 PM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Yunfei, I used(with the fai2bed.pl script) a .fai file of TAIR10_Arabidopsis and generated a TAIR10_Chr.all.dict file (that it is the same I sent you enclosed in my last mail ).But now I DON' T KNOW HOW CONVERT THIS .dict FILE IN A BED FILE (.bed).I have consulted and investigated several sources , but I still don't know how to do it.Please, could you help me to get this bed file of Arabidopsis?.And so to go on the proofs with SeqMule for Arabidopsis.

Thank you very much

Juan M.

El mar., 20 ago. 2019 a las 19:34, yunfei guo (< guoyunfei2008@outlook.com>) escribió:
The bed file contains non standard characters and cannot be used.

Please use .fai file to generate a BED file.

On Aug 20, 2019, at 9:50 AM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Hi Yunfei, I paste you what you ask me , and the output: ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~$ head /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed

w~��״�⣊U |�i�9�ݐ�� [��`/��ꮮ h� l�3�� ~}�� ^�>=��} n\��釫�O/�Ϗ��>~} ��vz��{��>��/�� ����D��O�tsw�x�ɽ޾��3-D��7��?я⟮iI���H -��I�� Y�] w 6��!ſ��J]�Кie-+sY�6 NZt%#]9��' �Y��ỡ�Ժj*��Z&դ�� 0 �3�Z�<�ꐢS �&�zZ1��yqcM "��]�նB�J,�! }� �%�� ~O ��"Y̹ڮ$O�L J�Z �Р�V�(�}M�3�)B�#[ Jy _�83Wk G�2)

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By other side, I have generated other bed file for Arabidopsis with fai2bed.pl script you recommended me, and this is TAIR10_Chr.all.dict (I send you also enclosed for you can see), but I don't know if this .dict file I can use as .bed file of Arabidopsis and put in your pipeline for SeqMule, or it must be converted to a .bed file ?.Could you answer me this question, please?. The Arabth.bed file was generated from Table browser of UCSC.

Thank you very much

Juan M.

El mar., 20 ago. 2019 a las 15:13, yunfei guo (< guoyunfei2008@outlook.com>) escribió:
Could you show me the first few lines of your bed file? i.e. run

head /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed

The bed file apparently contains some malformed lines.

On Aug 20, 2019, at 4:25 AM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Hi Yunfei, I have put the index files for TAIR10_arabdopsis.fasta and TAIR10_arabdopsis.fasta in the same bin folder (before they were in the database folder), and the pipeline start without problems until step 6 (it gives some ERRORS) and you can see the last outputs:

[M::main_mem] read 28714 sequences (2167099 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 10189, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (124, 143, 162) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (48, 238) [M::mem_pestat] mean and std.dev: (143.70, 28.53) [M::mem_pestat] low and high boundaries for proper pairs: (10, 276) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 28714 reads in 10.316 CPU sec, 10.359 real sec [main] Version: 0.7.8-r455 [main] CMD: /media/ubuntu/DATOS/SeqMule-master/exe/bwa/bwa mem -M -T 0 -A 1 -B 4 -O 6 -E 1 -L 5 -U 17 -R @RG\tID:READGROUP\tSM:PRUEBA1\tPL:ILLUMINA\tLB:LIBRARY TAIR10_Chr.all.fasta PRUEBA1_result/PRUEBA1.0.fastq.gz PRUEBA1_result/PRUEBA1.1.fastq.gz [main] Real time: 5750.395 sec; CPU: 5357.148 sec [bam_sort_core] merging from 7 files...

----------NOTICE---------- [ => SeqMule Execution Status: Running 5 of 19 steps: Filter BAM file by mapping quality, at mar ago 20 11:59:35 CEST 2019, Time Elapsed: 1 hr 42 min 16 s] [ => SeqMule Execution Status: step 4 is finished at mar ago 20 11:59:35 CEST 2019, bwamem alignment]

[samopen] SAM header is present: 7 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 6 of 19 steps: gatklite realn, at mar ago 20 12:05:26 CEST 2019, Time Elapsed: 1 hr 48 min 7 s] [ => SeqMule Execution Status: step 5 is finished at mar ago 20 12:05:26 CEST 2019, Filter BAM file by mapping quality]

INFO 11:05:30,333 ArgumentTypeDescriptor - Dynamically determined type of /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed to be BED INFO 11:05:30,373 HelpFormatter -

INFO 11:05:30,378 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2013/01/11 20:03:13 INFO 11:05:30,379 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:05:30,379 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:05:30,384 HelpFormatter - Program Args: -T RealignerTargetCreator -I PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.bam -R TAIR10_Chr.all.fasta -o /tmp/9785.47397996627.tmp.intervals -L /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed INFO 11:05:30,389 HelpFormatter - Date/Time: 2019/08/20 11:05:30 INFO 11:05:30,389 HelpFormatter -

INFO 11:05:30,389 HelpFormatter -

INFO 11:05:30,404 GenomeAnalysisEngine - Strictness is SILENT INFO 11:05:30,413 ReferenceDataSource - Dict file /media/ubuntu/DATOS/SeqMule-master/bin/TAIR10_Chr.all.dict does not exist. Trying to create it now. [Tue Aug 20 11:05:30 GMT+01:00 2019] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/media/ubuntu/DATOS/SeqMule-master/bin/TAIR10_Chr.all.fasta OUTPUT=/media/ubuntu/DATOS/SeqMule-master/bin/dict4544612316941911242.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 20 11:05:30 GMT+01:00 2019] Executing as ubuntu@ubuntu-Compaq-CQ58-Notebook-PC on Linux 4.4.0-157-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_95-b00; Picard version: null [Tue Aug 20 11:05:32 GMT+01:00 2019] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=224919552 INFO 11:05:32,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000, Using the new downsampling implementation INFO 11:05:32,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 11:05:32,942 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 WARN 11:05:34,774 RestStorageService - Error Response: PUT '/GATK_Run_Reports/N4luPhsFtHlJVINNdiniUW1wonsQ6Yt3.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1319, Content-MD5: FWO1KXgQ4Biz3jmVwmMsZQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 1563b5297810e018b3de3995c2632c65, Date: Tue, 20 Aug 2019 10:05:33 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:ipaptihLbLa5PHalhfBn0yU6xTA=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-157-generic; amd64; es; JVM 1.7.0_95), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: E538A8F2F2342832, x-amz-id-2: 9cI/rc7m+bAVFqwbqtkK8p5rC/9nIImfXXZfirwgGpw71aew7ipCm6/f9BXCMbY3tppWfYR1bfk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 20 Aug 2019 10:05:34 GMT, Connection: close, Server: AmazonS3]

ERROR

ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):

ERROR The invalid arguments or inputs must be corrected before

the GATK can proceed

ERROR Please do not post this error to the GATK forum

ERROR

ERROR See the documentation (rerun with -h) for this tool to

view allowable command-line arguments.

ERROR Visit our website and forum for extensive documentation

and answers to

ERROR commonly asked questions

http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: File associated with name

/media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed is malformed: Problem reading the interval file caused by

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ERROR

^[[?62;c^[[?62;c

----------ERROR---------- [ => SeqMule Execution Status: step 6 FAILED at mar ago 20 12:05:35 CEST 2019, gatklite realn] ERROR: command failed /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker /media/ubuntu/DATOS/SeqMule-master/bin/seqmule.08202019.3989.logs 6 "/media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced PRUEBA1.config -n 5 -ref TAIR10_Chr.all.fasta -java java -jmem 1750m -gatk /media/ubuntu/DATOS/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 1 -gatk-nt 2 -tmpdir /tmp -bed /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed -goldindel /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /media/ubuntu/DATOS/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.bam -out PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! After fixing the problem, please execute 'cd //media/ubuntu/DATOS/SeqMule-master/bin' and 'seqmule run PRUEBA1.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ubuntu@ ubuntu-Compaq-CQ58-Notebook-PC://media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta -e

It tells also that the Arabth.bed file is not good.I will try to get another different bed file for Arabidopsis thaliana, but ,please, revise the output and tell me if I must change or correct something. Thank you very much.Best.

Juan Manuel

El mar., 20 ago. 2019 a las 6:48, yunfei guo (< guoyunfei2008@outlook.com>) escribió:

Hi Juan,

Please make sure TAIR10_Chr.all.fasta and the index files are in the same folder. They don’t necessarily have to be placed in database folder.

Best, Yunfei

On Aug 19, 2019, at 5:40 AM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Hi Yunfei,

When I try the pipeline you recommend me in this mail, I have the next output:

ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~$ cd /media/ubuntu/DATOS/SeqMule-master/bin ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced seqmule/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Current version: 1.2.3 Cannot open seqmule/misc/predefined_config/bwa_samtools.config: Not a directory

And, after, when I try another pipeline (a variant), the output is: ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced Seqmule-master/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Current version: 1.2.3 Cannot open Seqmule-master/misc/predefined_config/bwa_samtools.config: No such file or directory ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ cd ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~$ /media/ubuntu/DATOS/SeqMule-master bash: /media/ubuntu/DATOS/SeqMule-master: Es un directorio ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced Seqmule-master/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Can't open perl script "seqmule": No existe el archivo o el directorio ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:~$ cd /media/ubuntu/DATOS/SeqMule-master/bin ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fastaCurrent version: 1.2.3 Reading configuration file... Done NOTICE: Commandline options will override advanced configuration. NOTICE: Parsing global settings... Done NOTICE: checking contig(chromosome) name consistency in TAIR10_Chr.all.fasta and /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed. NOTICE: use --no-check-chr to skip chromosome name checking NOTICE: contig names in capture file and reference match with each other. NOTICE: Input BED file detected, only variants in corresponding regions will be generated. CAUTION: You used your own reference file or index file, there is no guarantee that it will work with all programs. ERROR: use -g for whole-genome data, -e for exome (or captured) sequencing data ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta -e Current version: 1.2.3 Reading configuration file... Done NOTICE: Commandline options will override advanced configuration. NOTICE: Parsing global settings... Done NOTICE: checking contig(chromosome) name consistency in TAIR10_Chr.all.fasta and /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed. NOTICE: use --no-check-chr to skip chromosome name checking NOTICE: contig names in capture file and reference match with each other. NOTICE: Input BED file detected, only variants in corresponding regions will be generated. CAUTION: You used your own reference file or index file, there is no guarantee that it will work with all programs. Checking Phred score scheme: PRUEBA1_result/PRUEBA1.0.fastq.gz PRUEBA1_result/PRUEBA1.1.fastq.gz NOTICE: Analysis name: PRUEBA1 NOTICE: Input is exome (or captured) sequencing data NOTICE: BED file used for caculating coverage statistics and extracting variants: Arabth.bed NOTICE: Readgroup : READGROUP_PRUEBA1 NOTICE: Sequencing platform: ILLUMINA NOTICE: Library : LIBRARY NOTICE: Phred scoring scheme : 33 NOTICE: Reference genome build is hg19 NOTICE: dbsnp138 will be used for variant calling and recalibration. NOTICE: Java memory usage is limited to 1750m NOTICE: java executable path: java NOTICE: Max number of processes: 1 NOTICE: /tmp will be used for storing temporary files Generating script... ERROR: bwamem index file(s) missing (TAIR10_Chr.all.fasta) ubuntu@ubuntu-Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$

But however I got generate the bwa index files for TAIR10_Arabidopsis.fasta (and I put them inside of database folder).And also I used a bed file of Arabidopsis (Arabth.bed), as you can see in the pipeline. Please Yunfei, what can I do now ?

Thank you very much for your help.Best regards.

Juan Manuel

El mar., 13 ago. 2019 a las 17:57, yunfei guo (< guoyunfei2008@outlook.com>) escribió:

Hi Juan,

1) if you have a region of interest, i.e. a BED file for Arabidopsis, then use it, otherwise, you can use https://github.com/yunfeiguo/bioinfo_toolbox/blob/master/utilities/seq_related/fai2bed.pl to generate one from *.fai file. 2) you’ll need to generate index files for your reference genome, .e.g. bwa, bowtie2 etc. Then run analysis. A simple example would be

seqmule pipeline -a sample_lane1_R1.fq.gz,sample_lane2_R1.fq.gz -b sample_lane1_R2.fq.gz,sample_lane2_R2.fq.gz -capture your_own.bed -m -advanced seqmule/misc/predefined_config/bwa_samtools.config -quick -t 4 -prefix mySample --ref arabidopsis.fasta

Note, you need to replace the illustrative filenames with your own. For more, check out http://seqmule.openbioinformatics.org/en/latest/Manuals/pipeline/

Best, Yunfei

On Aug 13, 2019, at 2:18 AM, Juan Manuel Luque Sánchez < j6163mls@gmail.com> wrote:

Hi Yunfei, how are you?

I am Juan Manuel Luque (from CNB-CSIC at Madrid) and I write by this via/e-mail to ask you about SeqMule for Analysis of Arabidopsis thaliana (you remember it, we are trying it).I am doing the first proof to run SeqMule for Arabidopsis thaliana.I downloaded vcf.gz files of Arabidopsis thaliana and TAIR10_Chr.all.fasta.gz files (for Arabidopsis thaliana) , both files as databases and reference genome (and I put both files inside of database folder of SeqMule).I have seen in the beginning of process(pipeline) that SeqMule use or tell us it will use BED FILES of hg19. The process (pipeline of SeqMule) about our first prooff is not over still.

1)Do you think I have to get the bed files of Arabidopsis thaliana and put it into the database folder?. But ,in this case, what order or script I must write for SeqMule uses by default the Arabidopsis bed file instead of the hg19 bed file (when start the run of pipeline).

2) What other new orders or scripts are necessaries in SeqMule for the analysis of Arabidopsis was correct, without problems?.For example I don't know if it is necessary to write an order or script for SeqMule uses by default the databases I downloaded of Arabidopsis (instead of the hg19 databases).

Please if you could answer and help us WITH DETAIL AND WITH ORDERS / SCRIPTS I asked you before (if it was necessary) ,I will thank you very much. Thank you very much for your help and best regards

Juan Manuel Luque

juanmluque commented 3 years ago

Dear Yunfei,

A long time since i wrote you the last time. I want tio ask you, please, why one year ago (more or less) I worked well with SeqMule (without problems with gatk) and with java 1.8 version, and now (yesterday) with the same java 1.8 version (without changes in my SeqMule) I get123 ERROR WITH gatk : SeqMule Execution Status: step 7 FAILED ,gatklite realn] ERROR: command failed. (As # 123 issue in Wiki SeqMule).

Why before (1 year ago) no problem and now yes?. May I install now java 1.7 version in my computer to solve the problem, and may I delete java 1.8 version?

Waiting for your answer, please, thank you very much for your help.

Best regards

Juan Manuel Luque

El jue, 5 sept 2019 a las 10:02, Juan Manuel Luque Sánchez (< @.***>) escribió:

       Yunfei, sorry, I forgot the issue number (GitHub) is  #176 .
---------- Forwarded message --------- De: Juan Manuel Luque Sánchez @.> Date: mié., 4 sept. 2019 a las 14:44 Subject: Re: SeqMule for Analysis of Arabidopsis thaliana To: yunfei guo @.>

Hi Yunfei, I have just sent you (by GitHUb -WGLab/SeqMule) my next question:

As you know , we are trying to apply SeqMule for Arabidopsis thaliana, and we would like to delete the messages: NOTICE: Reference genome build is hg 19 and NOTICE: dbsnp138 will be used for variant calling and recalibration when pipeline starts (or to change the message about hg 19 by other reference genome build). We have changed the next parameters: go_dbsnp=0 #dbSNP file for GATK only go_hapmap=0 #HapMap file for GATK go_dbsnpver=0 #dbSNP version for variant recalibration and annotation, default is 137 go_kg=0 #1000 Genome project VCF file go_buildver=0 #genome build version, default is hg19 and also: o_gatklite_forceSNPHardFilter=1 #if set to 1, force using hard filtering on SNP, otherwise seqmule use VQSR only if BAM size is larger than 1GB. CAUTION: do NOT set o_gatklite_forceSNPVQSR and o_gatklite_forceSNPHardFilter both to 1! and: o_gatklite_forceINDELHardFilter=1 #if set to 1, force using hard filtering on INDEL, otherwise seqmule use VQSR only if BAM size is larger than 15GB. CAUTION: do NOT set o_gatklite_forceINDELVQSR and o_gatklite_forceINDELHardFilte both to 1!

But the NOTICE messages are the same again (hg19 and dbsnp 138) when we run the pipeline.

Please, what can we do to solve this? Thank you very much. Best. Juan M.

El sáb., 24 ago. 2019 a las 15:13, yunfei guo @.***>) escribió:
Hi Juan,

The seqmule version used to generate the script is different from the version you are executing. Please rerun the script generation. Thanks.

On Aug 23, 2019, at 1:57 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei, I have to ask you please about an ERROR with SeqMule (because I have searched in FAQ-SeqMule and internet, but I don't find anything about):

When I try $ perl seqmule run PRUEBA1.script (PRUEBA1 is a pipeline not ended that I want to restart), then the output is: Current version: 1.2.3 ERROR: incompatible execution script version Supported versions: 1.2

And I did the same yesterday with other different script WITHOUT PROBLEMS AND FINALLY RUN RIGHT TO THE END OF THE PROCESS/PIPELINE.

Could you help me, please?

Thank you very much.

Juan M.

El jue., 22 ago. 2019 a las 17:47, yunfei guo @.***>) escribió:
Hi Juan,

Thanks for sharing the good news. Glad to hear that. Enjoy your research!

Best, Yunfei

On Aug 22, 2019, at 4:52 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei, I have good news for you.For the first time the whole process or pipeline of SeqMule for Arabidopsis thaliana reach the end without problems and getting a result of variants.This is the pipeline we used:

$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture TAIR10_chr.all.bed -t 1 -prefix PRUEBA1 --ref TAIR10_chr.all.fasta -e

We had to change (with commands) the name Chr by chr in the TAIR10_chr.all.bed and TAIR10_chr.all.fasta , because SeqMule give us ERROR: NO UPPERCASE ALLOWED IN chr OF A CONTIG NAME: Chr C..... But when we changed those letters in these files, the process was fine until the end and giving results.Now we will analyze the results, and we will go on doing proofs.

Meanwhile thank you very much for your help.Best.

Juan M.

El mié., 21 ago. 2019 a las 5:44, yunfei guo @.***>) escribió:
TAIR10_Chr.all.dict is NOT a .bed file but a .dict file. Please generate the correct .bed file using the fai2bed.pl from .fai file. Thanks.

On Aug 20, 2019, at 2:55 PM, Juan Manuel Luque Sánchez < @.***> wrote:

Yunfei, I used(with the fai2bed.pl script) a .fai file of TAIR10_Arabidopsis and generated a TAIR10_Chr.all.dict file (that it is the same I sent you enclosed in my last mail ).But now I DON' T KNOW HOW CONVERT THIS .dict FILE IN A BED FILE (.bed).I have consulted and investigated several sources , but I still don't know how to do it.Please, could you help me to get this bed file of Arabidopsis?.And so to go on the proofs with SeqMule for Arabidopsis.

Thank you very much

Juan M.

El mar., 20 ago. 2019 a las 19:34, yunfei guo (< @.***>) escribió:
The bed file contains non standard characters and cannot be used.

Please use .fai file to generate a BED file.

On Aug 20, 2019, at 9:50 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei, I paste you what you ask me , and the output: @.***Compaq-CQ58-Notebook-PC:~$ head /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed

w~��״�⣊U |�i�9�ݐ�� [��`/��ꮮ h� l�3�� ~}�� ^�>=��} n\��釫�O/�Ϗ��>~} ��vz��{��>��/�� ����D��O�tsw�x�ɽ޾��3-D��7��?я⟮iI���H -��I�� Y�] w 6��!ſ��J]�Кie-+sY�6 NZt%#]9��' �Y��ỡ�Ժj*��Z&դ�� 0 �3�Z�<�ꐢS �&�zZ1��yqcM "��]�նB�J,�! }� �%�� ~O ��"Y̹ڮ$O�L J�Z �Р�V�(�}M�3�)B�#[ Jy _�83Wk G�2)

7�" C�Zm%��F��j�7 �d� ,sV!J��҆6��5�tp�E Fq(�� BOv�P�Đ.�P�D�4��#F�� f�Z�� V�]��k B$s7QK� �J� ]ai�� #�� g��0�M�#%g��vA�<�~G G�CU�kk��VWUF��j�{�� iʓ"�]E�B 5yOͷUȷ|A �/�}� MWT[ %d2� �P�90�F�A�Ӑ�)Gjp(-hq�u�. v�$��-2��N]�\�72| �p�So ��N $�[Qr�k6EM�� Z]3p#穭T�:Q��M��ZK� �� :+ �XA! 8D � � ��"Cǵ�n!j�� T U�zQ�1-��V�nV�� s8DI��y�]��4%[+F� �s�;�i � “� X��s'j�{v��dK�멚z��J�$��+ ڻ8��(h�� )�� <�,@�J�Hً��"��1�%p s� QX�WJ� �L�(� I�t��2�і �*�� k��YYP=�'�.܅$� �v��Cwu�E۩O��T��DQ ��S:9U4��,Z�6��Y 0dR��uT(k��ăA� >��Rr� W а ɳ)e�f��2�% ��l�� f>';Q%a�(�� .L\V�jNS�[�9��N�˚��GT~�_B�z�!��$�JG ��.uF� ��Q�� Z��` 8,4=,� �T�A�" �� ]'��a�sж�� Z ��bv � 8� �� ˝��6��ȾP�� R/�!�I��q+ � F� �aÍ��ܢ!�� ]F 捆^ ��P� � a� ΀ �&QgQ�#0 0�۷q$ᰈ��ѱ��I� ��!� �fз�Ȋ�W h Ԯ�� h7��i � ��-��0
                        �٫H&�eTK�/� �%/���}�X�-+��0�&CX�� m�
��/5��g�A船��E> �$�}��u �m v2� 82Ս#��2� �!PmA Ґr,@ۃA��%9�" h��#� �~8 "��0 Sg�<f�� c��Z?m|��u�} 1?i ��?p4 �o��A�b�B� �^�4 n�#�֘��C��C ǮO߸N�G�bc2�� opq'�+�;�x�(n�U��(� p6}��<� ��8�� W ��QS��hSe^px��a�:��e��o�lŦ�9� �g��}�V�K��әbqs׍'a�Gg�;��9��A�N�:�Pۅb �� <I�}��&� ��Y�9GH��ғt,��>��;$a��{ �f��Ρ9^� U��I,��SS�0��i )�Q��n��A)�k֌2��ʇ+��T�9�I��) ��vw,�V�w��g �-"�vȡ�P��׆u*�':��9L%\& � ��R�F!�Y0c�lr_�a��8L�?4��Lnar��vۓ��S|��R�KVQ;5��: ���2�:� �&�lc~�<��^=�#��s\ǚ�I�v�j�9 �� GPcp� �1 ��ۨDq��X ܢ^�2(m?D� �~#��,�#�\� 4A��H�<�.8�/��U� �B��ߤL+68��6�*�� n�,p� �ʸ +�R�1p��a�� 26�0�~ڋ�� Qt��^ԯ��ˀW� �� / �� ;� V� �_!�)�}m4OIR/D�� (�JhG!�{ ��w?ā� �Nr#�ߟw� �� @.***Compaq-CQ58-Notebook-PC:~$

By other side, I have generated other bed file for Arabidopsis with fai2bed.pl script you recommended me, and this is TAIR10_Chr.all.dict (I send you also enclosed for you can see), but I don't know if this .dict file I can use as .bed file of Arabidopsis and put in your pipeline for SeqMule, or it must be converted to a .bed file ?.Could you answer me this question, please?. The Arabth.bed file was generated from Table browser of UCSC.

Thank you very much

Juan M.

El mar., 20 ago. 2019 a las 15:13, yunfei guo (< @.***>) escribió:
Could you show me the first few lines of your bed file? i.e. run

head /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed

The bed file apparently contains some malformed lines.

On Aug 20, 2019, at 4:25 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei, I have put the index files for TAIR10_arabdopsis.fasta and TAIR10_arabdopsis.fasta in the same bin folder (before they were in the database folder), and the pipeline start without problems until step 6 (it gives some ERRORS) and you can see the last outputs:

[M::main_mem] read 28714 sequences (2167099 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 10189, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (124, 143, 162) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (48, 238) [M::mem_pestat] mean and std.dev: (143.70, 28.53) [M::mem_pestat] low and high boundaries for proper pairs: (10, 276) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_process_seqs] Processed 28714 reads in 10.316 CPU sec, 10.359 real sec [main] Version: 0.7.8-r455 [main] CMD: /media/ubuntu/DATOS/SeqMule-master/exe/bwa/bwa mem -M -T 0 -A 1 -B 4 -O 6 -E 1 -L 5 -U 17 -R @RG\tID:READGROUP\tSM:PRUEBA1\tPL:ILLUMINA\tLB:LIBRARY TAIR10_Chr.all.fasta PRUEBA1_result/PRUEBA1.0.fastq.gz PRUEBA1_result/PRUEBA1.1.fastq.gz [main] Real time: 5750.395 sec; CPU: 5357.148 sec [bam_sort_core] merging from 7 files...

----------NOTICE---------- [ => SeqMule Execution Status: Running 5 of 19 steps: Filter BAM file by mapping quality, at mar ago 20 11:59:35 CEST 2019, Time Elapsed: 1 hr 42 min 16 s] [ => SeqMule Execution Status: step 4 is finished at mar ago 20 11:59:35 CEST 2019, bwamem alignment]

[samopen] SAM header is present: 7 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 6 of 19 steps: gatklite realn, at mar ago 20 12:05:26 CEST 2019, Time Elapsed: 1 hr 48 min 7 s] [ => SeqMule Execution Status: step 5 is finished at mar ago 20 12:05:26 CEST 2019, Filter BAM file by mapping quality]

INFO 11:05:30,333 ArgumentTypeDescriptor - Dynamically determined type of /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed to be BED INFO 11:05:30,373 HelpFormatter -

INFO 11:05:30,378 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-gdcdccbb, Compiled 2013/01/11 20:03:13 INFO 11:05:30,379 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:05:30,379 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 11:05:30,384 HelpFormatter - Program Args: -T RealignerTargetCreator -I PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.bam -R TAIR10_Chr.all.fasta -o /tmp/9785.47397996627.tmp.intervals -L /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed INFO 11:05:30,389 HelpFormatter - Date/Time: 2019/08/20 11:05:30 INFO 11:05:30,389 HelpFormatter -

INFO 11:05:30,389 HelpFormatter -

INFO 11:05:30,404 GenomeAnalysisEngine - Strictness is SILENT INFO 11:05:30,413 ReferenceDataSource - Dict file /media/ubuntu/DATOS/SeqMule-master/bin/TAIR10_Chr.all.dict does not exist. Trying to create it now. [Tue Aug 20 11:05:30 GMT+01:00 2019] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/media/ubuntu/DATOS/SeqMule-master/bin/TAIR10_Chr.all.fasta OUTPUT=/media/ubuntu/DATOS/SeqMule-master/bin/dict4544612316941911242.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Aug 20 11:05:30 GMT+01:00 2019] Executing as @.***Compaq-CQ58-Notebook-PC on Linux 4.4.0-157-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_95-b00; Picard version: null [Tue Aug 20 11:05:32 GMT+01:00 2019] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=224919552 INFO 11:05:32,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000, Using the new downsampling implementation INFO 11:05:32,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 11:05:32,942 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 WARN 11:05:34,774 RestStorageService - Error Response: PUT '/GATK_Run_Reports/N4luPhsFtHlJVINNdiniUW1wonsQ6Yt3.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1319, Content-MD5: FWO1KXgQ4Biz3jmVwmMsZQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 1563b5297810e018b3de3995c2632c65, Date: Tue, 20 Aug 2019 10:05:33 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:ipaptihLbLa5PHalhfBn0yU6xTA=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-157-generic; amd64; es; JVM 1.7.0_95), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: E538A8F2F2342832, x-amz-id-2: 9cI/rc7m+bAVFqwbqtkK8p5rC/9nIImfXXZfirwgGpw71aew7ipCm6/f9BXCMbY3tppWfYR1bfk=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 20 Aug 2019 10:05:34 GMT, Connection: close, Server: AmazonS3]

ERROR

ERROR A USER ERROR has occurred (version 2.3-9-gdcdccbb):

ERROR The invalid arguments or inputs must be corrected before

the GATK can proceed

ERROR Please do not post this error to the GATK forum

ERROR

ERROR See the documentation (rerun with -h) for this tool to

view allowable command-line arguments.

ERROR Visit our website and forum for extensive documentation

and answers to

ERROR commonly asked questions

http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: File associated with name

/media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed is malformed: Problem reading the interval file caused by

ERROR Line: D½ÜüãóíÓëËÍíóíO·tsw÷x³É½Þ¾»¾»»úËýÃ3-D””7¢åï?Ñ

âŸ®iIË_ ƒH
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7È" CëZm%¤°FåÑjÈ7 ‘dü ,sV!J‚ ÄÒ†6™´5¡tp¤E Fq(›

ERROR

^[[?62;c^[[?62;c

----------ERROR---------- [ => SeqMule Execution Status: step 6 FAILED at mar ago 20 12:05:35 CEST 2019, gatklite realn] ERROR: command failed /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker /media/ubuntu/DATOS/SeqMule-master/bin/seqmule.08202019.3989.logs 6 "/media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced PRUEBA1.config -n 5 -ref TAIR10_Chr.all.fasta -java java -jmem 1750m -gatk /media/ubuntu/DATOS/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 1 -gatk-nt 2 -tmpdir /tmp -bed /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed -goldindel /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /media/ubuntu/DATOS/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /media/ubuntu/DATOS/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.bam -out PRUEBA1_result/PRUEBA1.0_bwamem.sort.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! After fixing the problem, please execute 'cd //media/ubuntu/DATOS/SeqMule-master/bin' and 'seqmule run PRUEBA1.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ubuntu@ ubuntu-Compaq-CQ58-Notebook-PC://media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta -e

It tells also that the Arabth.bed file is not good.I will try to get another different bed file for Arabidopsis thaliana, but ,please, revise the output and tell me if I must change or correct something. Thank you very much.Best.

Juan Manuel

El mar., 20 ago. 2019 a las 6:48, yunfei guo (< @.***>) escribió:

Hi Juan,

Please make sure TAIR10_Chr.all.fasta and the index files are in the same folder. They don’t necessarily have to be placed in database folder.

Best, Yunfei

On Aug 19, 2019, at 5:40 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei,

When I try the pipeline you recommend me in this mail, I have the next output:

@.Compaq-CQ58-Notebook-PC:~$ cd /media/ubuntu/DATOS/SeqMule-master/bin @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced seqmule/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Current version: 1.2.3 Cannot open seqmule/misc/predefined_config/bwa_samtools.config: Not a directory

And, after, when I try another pipeline (a variant), the output is: @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced Seqmule-master/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Current version: 1.2.3 Cannot open Seqmule-master/misc/predefined_config/bwa_samtools.config: No such file or directory @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ cd @.Compaq-CQ58-Notebook-PC:~$ /media/ubuntu/DATOS/SeqMule-master bash: /media/ubuntu/DATOS/SeqMule-master: Es un directorio @.Compaq-CQ58-Notebook-PC:~$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -m -advanced Seqmule-master/misc/predefined_config/bwa_samtools.config -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta Can't open perl script "seqmule": No existe el archivo o el directorio @.Compaq-CQ58-Notebook-PC:~$ cd /media/ubuntu/DATOS/SeqMule-master/bin @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fastaCurrent version: 1.2.3 Reading configuration file... Done NOTICE: Commandline options will override advanced configuration. NOTICE: Parsing global settings... Done NOTICE: checking contig(chromosome) name consistency in TAIR10_Chr.all.fasta and /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed. NOTICE: use --no-check-chr to skip chromosome name checking NOTICE: contig names in capture file and reference match with each other. NOTICE: Input BED file detected, only variants in corresponding regions will be generated. CAUTION: You used your own reference file or index file, there is no guarantee that it will work with all programs. ERROR: use -g for whole-genome data, -e for exome (or captured) sequencing data @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$ perl seqmule pipeline -a Arabthcontrol_R1.fastq.gz -b Arabthcontrol_R2.fastq.gz -capture Arabth.bed -t 1 -prefix PRUEBA1 --ref TAIR10_Chr.all.fasta -e Current version: 1.2.3 Reading configuration file... Done NOTICE: Commandline options will override advanced configuration. NOTICE: Parsing global settings... Done NOTICE: checking contig(chromosome) name consistency in TAIR10_Chr.all.fasta and /media/ubuntu/DATOS/SeqMule-master/bin/Arabth.bed. NOTICE: use --no-check-chr to skip chromosome name checking NOTICE: contig names in capture file and reference match with each other. NOTICE: Input BED file detected, only variants in corresponding regions will be generated. CAUTION: You used your own reference file or index file, there is no guarantee that it will work with all programs. Checking Phred score scheme: PRUEBA1_result/PRUEBA1.0.fastq.gz PRUEBA1_result/PRUEBA1.1.fastq.gz NOTICE: Analysis name: PRUEBA1 NOTICE: Input is exome (or captured) sequencing data NOTICE: BED file used for caculating coverage statistics and extracting variants: Arabth.bed NOTICE: Readgroup : READGROUP_PRUEBA1 NOTICE: Sequencing platform: ILLUMINA NOTICE: Library : LIBRARY NOTICE: Phred scoring scheme : 33 NOTICE: Reference genome build is hg19 NOTICE: dbsnp138 will be used for variant calling and recalibration. NOTICE: Java memory usage is limited to 1750m NOTICE: java executable path: java NOTICE: Max number of processes: 1 NOTICE: /tmp will be used for storing temporary files Generating script... ERROR: bwamem index file(s) missing (TAIR10_Chr.all.fasta) @.Compaq-CQ58-Notebook-PC:/media/ubuntu/DATOS/SeqMule-master/bin$

But however I got generate the bwa index files for TAIR10_Arabidopsis.fasta (and I put them inside of database folder).And also I used a bed file of Arabidopsis (Arabth.bed), as you can see in the pipeline. Please Yunfei, what can I do now ?

Thank you very much for your help.Best regards.

Juan Manuel

El mar., 13 ago. 2019 a las 17:57, yunfei guo (< @.***>) escribió:

Hi Juan,

1) if you have a region of interest, i.e. a BED file for Arabidopsis, then use it, otherwise, you can use https://github.com/yunfeiguo/bioinfo_toolbox/blob/master/utilities/seq_related/fai2bed.pl to generate one from *.fai file. 2) you’ll need to generate index files for your reference genome, .e.g. bwa, bowtie2 etc. Then run analysis. A simple example would be

seqmule pipeline -a sample_lane1_R1.fq.gz,sample_lane2_R1.fq.gz -b sample_lane1_R2.fq.gz,sample_lane2_R2.fq.gz -capture your_own.bed -m -advanced seqmule/misc/predefined_config/bwa_samtools.config -quick -t 4 -prefix mySample --ref arabidopsis.fasta

Note, you need to replace the illustrative filenames with your own. For more, check out http://seqmule.openbioinformatics.org/en/latest/Manuals/pipeline/

Best, Yunfei

On Aug 13, 2019, at 2:18 AM, Juan Manuel Luque Sánchez < @.***> wrote:

Hi Yunfei, how are you?

I am Juan Manuel Luque (from CNB-CSIC at Madrid) and I write by this via/e-mail to ask you about SeqMule for Analysis of Arabidopsis thaliana (you remember it, we are trying it).I am doing the first proof to run SeqMule for Arabidopsis thaliana.I downloaded vcf.gz files of Arabidopsis thaliana and TAIR10_Chr.all.fasta.gz files (for Arabidopsis thaliana) , both files as databases and reference genome (and I put both files inside of database folder of SeqMule).I have seen in the beginning of process(pipeline) that SeqMule use or tell us it will use BED FILES of hg19. The process (pipeline of SeqMule) about our first prooff is not over still.

1)Do you think I have to get the bed files of Arabidopsis thaliana and put it into the database folder?. But ,in this case, what order or script I must write for SeqMule uses by default the Arabidopsis bed file instead of the hg19 bed file (when start the run of pipeline).

2) What other new orders or scripts are necessaries in SeqMule for the analysis of Arabidopsis was correct, without problems?.For example I don't know if it is necessary to write an order or script for SeqMule uses by default the databases I downloaded of Arabidopsis (instead of the hg19 databases).

Please if you could answer and help us WITH DETAIL AND WITH ORDERS / SCRIPTS I asked you before (if it was necessary) ,I will thank you very much. Thank you very much for your help and best regards

Juan Manuel Luque

yunfeiguo commented 3 years ago

Dear Juan,

Which GATK version are you using? If it is not GATKLite, I would recommend using GATKLite because we have full control over its version and dependencies. Thanks.

juanmluque commented 3 years ago

Dear Yunfei,

Thank you very much for your answer, but mi GATK version installed is the correct (old version installed many years ago)) and I have GenomeAnalysisTK.jar file well put in exe/ folder.One year ago my SeqMule worked well without problems, but now (one year after) the same SeqMule program gives me problems with gatk: ERROR with gatk, SeqMule Execution Status step 7 FAILED, gatk realm], ERROR command failed. (as # 123 issue in Wiki SeqMule).My java version installed is 1.8.May I install java 1.7 version instead of and delete java 1.8 version to solve this problem?

Waiting for your answer ASAP , please, thank you very much. Best.

Juan Manuel Luque

El dom, 4 ago 2019 a las 21:55, Yunfei Guo @.***>) escribió:

Hi @juanmluque https://github.com/juanmluque please retrieve the GenomeAnalysisTK.jar file and put it in exe/ folder (where other programs are installed). Note the GATK4 has changed its API and therefore is not compatible with SeqMule at the moment. Please use older versions: https://software.broadinstitute.org/gatk/download/archive

What errors are you seeing using Ubuntu16?

You can send questions to @.***

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juanmluque commented 3 years ago

Yes Yunfei,

I always am using GATKLite since the first time I installed SeqMule (many years ago).My java is 1.8 version (and it worked well 1 year ago), but now I have problems : gatklite realn].

What can I do?. Thank you very much. Best.

Juan Manuel Luque

El lun, 7 jun 2021 a las 16:22, Yunfei Guo @.***>) escribió:

Dear Juan,

Which GATK version are you using? If it is not GATKLite, I would recommend using GATKLite because we have full control over its version and dependencies. Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-855972440, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMZYILO2ABQ3CS7P5S5HC23TRTIZJANCNFSM4FCXW7VQ .

yunfeiguo commented 3 years ago

Which version of GATK were you using?

juanmluque commented 3 years ago

Dear Yunfei,

I'm sorry, but I don't remember the GATK version I used since 2012 or 2013 when I installed for the first time your SeqMule program in my computer.How could I know this GATK version in my computer used for me ?. If you can help me to know it, then I will see it.I never had this problem with gatk since I installed SeqMule and this gatk version.

Waiting for your answer, please. Thank you .

Juan Manuel

El lun, 7 jun 2021 a las 17:40, Yunfei Guo @.***>) escribió:

Which version of GATK were you using?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856048601, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMZYILIQ6LFXTND4AWSOKUTTRTR7BANCNFSM4FCXW7VQ .

juanmluque commented 3 years ago

Dear Yunfei,

Now when I try to process with SeqMule the example fastq files(normalR1 and normalR2) downloaded from the Quick start guide, always I get the next ERROR: [bam_header_read] EOF marker is absent. The input is probably truncated. [bwa_idx_load] Failed to allocate 775451185 bytes at bwa.c line 291: Cannot allocate memory [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!

----------ERROR---------- [ => SeqMule Execution Status: step 4 FAILED at lun jun 7 21:59:27 CEST 2021, bwamem alignment] ERROR: command failed

Please, would it be possible to send me 2 small and good new fastq files (R1 and R2) to process with my SeqMule (or a link to download them)?.

Waiting for your answer, please, thank you very much Best.

Juan Manuel

El lun, 7 jun 2021 a las 17:40, Yunfei Guo @.***>) escribió:

Which version of GATK were you using?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856048601, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMZYILIQ6LFXTND4AWSOKUTTRTR7BANCNFSM4FCXW7VQ .

yunfeiguo commented 3 years ago

If your issue is similar to #123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

juanmluque commented 3 years ago

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with

more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7 "/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN -advanced example.config -n 6 -ref /home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta -java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel /home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf -dbsnp /home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf -samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam " !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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yunfeiguo commented 3 years ago

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ .

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juanmluque commented 3 years ago

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7 "/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref /home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel /home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp /home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam " !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ>

.

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yunfeiguo commented 3 years ago

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7 "/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref /home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel /home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp /home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam " !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ>

.

D You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/WGLab/SeqMule/issues/173#issuecomment-856737034>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AB3A7TUDREFNXH4BEHMDI43TRYGVPANCNFSM4FCXW7VQ>.

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juanmluque commented 3 years ago

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ>

.

D You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/WGLab/SeqMule/issues/173#issuecomment-856737034>, or unsubscribe<

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yunfeiguo commented 3 years ago

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ>

.

D You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/WGLab/SeqMule/issues/173#issuecomment-856737034>, or unsubscribe<

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juanmluque commented 3 years ago

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997,

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yunfeiguo commented 3 years ago

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed /home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997,

or

unsubscribe <

https://github.com/notifications/unsubscribe-auth/AMZYILJHN5PPS3CRPTTM4KTTRV2LZANCNFSM4FCXW7VQ>

.

D You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/WGLab/SeqMule/issues/173#issuecomment-856737034>, or unsubscribe<

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juanmluque commented 3 years ago

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

or

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yunfeiguo commented 3 years ago

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

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juanmluque commented 3 years ago

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

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yunfeiguo commented 3 years ago

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk /home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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juanmluque commented 3 years ago

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs 16 "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -prefix example_result/example -ref /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta -s example -venn example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! After fixing the problem, please execute 'cd /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! @.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$ NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE: /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

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yunfeiguo commented 3 years ago

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker /home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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juanmluque commented 3 years ago

Hi Yunfei,

From what link I can download Rscript? And then, in what folder or path of ubuntu I can install Rscript better?. I work now with R-4.0.3 in my computer (Ubuntu).

Thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 14:22, Yunfei Guo @.***>) escribió:

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs

16 "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule

stats -tmpdir /tmp -prefix example_result/example -ref /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-s example -venn example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf"

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin'

and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE: /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed

contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats

line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker

/home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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yunfeiguo commented 3 years ago

If you have R already, just put its folder on PATH.

发件人: juanmluque @.> 发送时间: Friday, June 18, 2021 1:58:47 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

From what link I can download Rscript? And then, in what folder or path of ubuntu I can install Rscript better?. I work now with R-4.0.3 in my computer (Ubuntu).

Thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 14:22, Yunfei Guo @.***>) escribió:

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs

16 "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule

stats -tmpdir /tmp -prefix example_result/example -ref /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-s example -venn example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf"

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin'

and 'seqmule run example.script' to resume analysis. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE: /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed

contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats

line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker

/home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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juanmluque commented 3 years ago

Hi Yunfei,

This is my last output when I put my R-4.0.3 folder on path: $ PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH $ PATH=/home/juanm/Descargas/R-4.0.3/bin:$PATH

And this is the error again in step 14 (generating Venn diagram): ................................................. .................................................

................................................

-NOTICE----------[ => SeqMule Execution Status: Running 14 of 18 steps: Generate Venn digram, at mar jun 22 11:15:46 CEST 2021, Time Elapsed: 0 hr 9 min 15 s][ => SeqMule Execution Status: step 13 is finished at mar jun 22 11:15:46 CEST 2021, Extract consensus calls]Current version: 1.2.3NOTICE: normalzing VCF with Vt...NOTICE: done normalzing.NOTICE: Converting input file to ANNOVAR format, variants that failed to pass filtering will be ignored.NOTICE: Counting non-empty lines in /tmp/82851973.9254378403_normalized.vcfNOTICE: Counting non-empty lines in /tmp/82856820.95054631026_nofiltered.vcfNOTICE: 243 records removed because of being filtered.NOTICE: output files will be written to /tmp/82851411.73143015166_annovar_raw..avinputNOTICE: Finished reading 3123 lines from VCF fileNOTICE: A total of 1217 locus in VCF file passed QC threshold, representing 1208 SNPs (631 transitions and 577 transversions) and 9 indels/substitutionsNOTICE: Finished writting 1208 SNPs (631 transitions and 577 transversions) and 9 indels/substitutions for 1 samplesNOTICE: Converting input file to ANNOVAR format, variants that failed to pass filtering will be ignored.NOTICE: Counting non-empty lines in /tmp/82853945.21968577735_normalized.vcfNOTICE: Counting non-empty lines in /tmp/82857705.91747387525_nofiltered.vcfNOTICE: 0 records removed because of being filtered.NOTICE: output files will be written to /tmp/82857200.76139594071_annovar_raw..avinputNOTICE: Finished reading 2027 lines from VCF fileNOTICE: A total of 128 locus in VCF file passed QC threshold, representing 122 SNPs (75 transitions and 47 transversions) and 7 indels/substitutionsNOTICE: Finished writting 121 SNPs (75 transitions and 46 transversions) and 7 indels/substitutions for 1 samplesNOTICE: Converting input file to ANNOVAR format, variants that failed to pass filtering will be ignored.NOTICE: Counting non-empty lines in /tmp/82851957.93231634742_normalized.vcfNOTICE: Counting non-empty lines in /tmp/82856556.46495643091_nofiltered.vcfNOTICE: 0 records removed because of being filtered.NOTICE: output files will be written to /tmp/82851933.07800438824_annovar_raw..avinputNOTICE: Finished reading 195 lines from VCF fileNOTICE: A total of 138 locus in VCF file passed QC threshold, representing 132 SNPs (79 transitions and 53 transversions) and 7 indels/substitutionsNOTICE: Finished writting 117 SNPs (72 transitions and 45 transversions) and 7 indels/substitutions for 1 samplesNOTICE: VennDiagram not installed, now try to install it.inferring 'repos = NULL' from 'pkgs' installing source package ‘VennDiagram’ ... package ‘VennDiagram’ successfully unpacked and MD5 sums checked using staged installation R byte-compile and prepare package for lazy loading help* installing help indices building package indices testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location* testing if installed package keeps a record of temporary installation path DONE (VennDiagram)NOTICE: Generating Venn diagram...Loading required package: VennDiagramLoading required package: gridError in .External2(C_X11, paste0("tiff::", comp, ":", filename), g$width, : no fue posible iniciar el dispositivo TIFFCalls: venn.diagram -> tiffAdemás: Warning message:In tiff(filename = filename, height = height, width = width, units = units, : no tiff support in this version of REjecución interrumpidaERROR: Execution failed, please run PRUEBADROS1_result/PRUEBADROS1_SNV_venn.R manuallyNOTICE: Cleaning...----------ERROR----------[ => SeqMule Execution Status: step 14 FAILED at mar jun 22 11:16:02 CEST 2021, Generate Venn digram]ERROR: command failed /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06222021.5891.logs 14 "/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -prefix PRUEBADROS1_result/PRUEBADROS1 -ref Drosophila_melanogaster.BDGP6.32.dna.nonchromosomal.fa -s PRUEBADROS1 -venn PRUEBADROS1_result/PRUEBADROS1.0_bwamem.sort.readfiltered.realn.0_gatklite.extract.vcf,PRUEBADROS1_result/PRUEBADROS1.0_bwamem.sort.readfiltered.0_samtools.extract.vcf,PRUEBADROS1_result/PRUEBADROS1.0_bwamem.sort.readfiltered.0_freebayes.extract.vcf" !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! After fixing the problem, please execute 'cd /media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin' and 'seqmule run PRUEBADROS1.script' to resume analysis. @.Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

And the error looks like: no tiff support in this version of R What R version has tiff support?.My R version is now R-4.0.3.

Waiting for your answer, please, thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 20:02, Yunfei Guo @.***>) escribió:

If you have R already, just put its folder on PATH.

发件人: juanmluque @.> 发送时间: Friday, June 18, 2021 1:58:47 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

From what link I can download Rscript? And then, in what folder or path of ubuntu I can install Rscript better?. I work now with R-4.0.3 in my computer (Ubuntu).

Thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 14:22, Yunfei Guo @.***>) escribió:

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs

16

"/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule

stats -tmpdir /tmp -prefix example_result/example -ref

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-s example -venn

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf"

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin'

and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE:

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed

contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats

line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker

/home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

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juanmluque commented 3 years ago

Hi Yunfei,

Could you read my last mail that I sent you?.Please, if you know what R version works well and supports tiffs for generating Venn diagram in SeqMule, write me (I use R-4.0.3, but it doesn't work for this problem in my case).

Thank you very much for your help. Best.

Juan Manuel

El vie, 18 jun 2021 a las 20:02, Yunfei Guo @.***>) escribió:

If you have R already, just put its folder on PATH.

发件人: juanmluque @.> 发送时间: Friday, June 18, 2021 1:58:47 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

From what link I can download Rscript? And then, in what folder or path of ubuntu I can install Rscript better?. I work now with R-4.0.3 in my computer (Ubuntu).

Thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 14:22, Yunfei Guo @.***>) escribió:

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs

16

"/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule

stats -tmpdir /tmp -prefix example_result/example -ref

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-s example -venn

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf"

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin'

and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE:

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed

contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats

line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker

/home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

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yunfeiguo commented 3 years ago

Hi Juan,

Could you try R 3.1.3? And make sure you have VennDiagram package installed for R.

From: juanmluque @.> Sent: Sunday, June 27, 2021 3:24 PM To: WGLab/SeqMule @.> Cc: Yunfei Guo @.>; Comment @.> Subject: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help. Best.

Juan Manuel

El vie, 18 jun 2021 a las 20:02, Yunfei Guo @.***>) escribió:

If you have R already, just put its folder on PATH.

发件人: juanmluque @.> 发送时间: Friday, June 18, 2021 1:58:47 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

From what link I can download Rscript? And then, in what folder or path of ubuntu I can install Rscript better?. I work now with R-4.0.3 in my computer (Ubuntu).

Thank you very much.

Juan Manuel

El vie, 18 jun 2021 a las 14:22, Yunfei Guo @.***>) escribió:

Looks like Rscript is missing. Please install Rscript and follow same steps for java to put R folder in PATH.

发件人: juanmluque @.> 发送时间: Thursday, June 17, 2021 7:15:15 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Thank you very much Yunfei,

At last the problem of Step 7 (gatk) has been solved, and the process is almost ended (20 steps), but in step 16 gives me an ERROR:

----------ERROR----------[ => SeqMule Execution Status: step 16 FAILED at jue jun 17 12:19:25 CEST 2021, Generate Venn digram]ERROR: command failed

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/secondary/worker

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/seqmule.06172021.3880.logs

16

"/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../bin/seqmule

stats -tmpdir /tmp -prefix example_result/example -ref

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-s example -venn

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf,example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf"

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin'

and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.**Compaq-CQ58-Notebook-PC:/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin$

NOTICE: all chromosome names in BED can be found in BAM header. NOTICE: Calculating coverage ... NOTICE: Start reading from SAMTools depth command ... NOTICE: normalzing VCF with Vt... NOTICE: done normalzing. NOTICE: keep variants if they are unfiltered in any one of the input files. NOTICE: extracting variants shared by at least 2 input files. NOTICE:

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/misc/hg19_exome.bed

contains 46205397 base pairs Statistics written to example_result/example_cov_stat.txt and example_result/example_cov_stat_detail.txt sh: 1: Rscript: not found ERROR: Failed to plot example_result/example_cov_stat_detail.txt at

/media/juanm/d631a66f-81da-495d-8136-67bc214cb51d/DATOS/SeqMule-master/bin/secondary/stats

line 782. NOTICE: Extracting primary alignments Generating alignment stats Output written to example_result/example_aln_stat.txt NOTICE: Cleaning... NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

The strange is that after the ERROR in step 16 , instead of stopping the pipeline .the process has gone on until : NOTICE: 19 variants written to example_result/example.extract_consensus.vcf. NOTICE: Cleaning...

And now still is Cleaning (but it lasts 45 minutes aprox.).Is this well or normal? May I wait for ending Cleaning or may I stop it?

Waiting for your answer, please, thank you very much. Best

Juan Manuel

El jue, 17 jun 2021 a las 2:16, Yunfei Guo @.***>) escribió:

Hi Juan, please prepend java bin folder to PATH, eg PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

发件人: juanmluque @.> 发送时间: Wednesday, June 16, 2021 2:28:14 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Here I write you my problem now:

$ export PATH = /usr/lib/jvm/jdk1.7.0_80/bin

$ perl seqmule pipeline ....(examples)

The order perl is available in /usr/bin/perl The order was not found because / usr/ bin is not included in the PATH enviroment variable. perl: it is not found the order

What can I do? Could you help me please? Thank you very much for your help

Best

Juan Manuel

El jue., 10 jun. 2021 19:27, Yunfei Guo @.***> escribió:

👍👍

发件人: juanmluque @.> 发送时间: Thursday, June 10, 2021 11:44:13 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Thank you very much for your help.Perfect, as you say(including /bin at the end of path):

@.***Compaq-CQ58-Notebook-PC:~$ export PATH=/usr/lib/jvm/jdk1.7.0_80/bin

@.***Compaq-CQ58-Notebook-PC:~$ java -version

java version "1.7.0_80"

Java(TM) SE Runtime Environment (build 1.7.0_80-b15)

Java HotSpot(TM) 64-Bit Server VM (build 24.80-b11, mixed mode)

@.**Compaq-CQ58-Notebook-PC:~$

Now, I have to delete folders and data not useful , to get more memory to solve the error I have in bwa-alignment step.

Best

Juan Manuel

El mié, 9 jun 2021 a las 16:02, Yunfei Guo @.***>) escribió:

export PATH=/usr/lib/jvm/jdk1.7.0_80/bin:$PATH

Then when you run java -version you will see 1.7.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 8:37:43 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

Then what may I do?.Could you explain and help me, please, because I don't know how to write the path to solve this problem.What path may I write?.Could you write this path, please?

Thank you very much.

Juan Manuel

El mié, 9 jun 2021 a las 13:49, Yunfei Guo @.***>) escribió:

It is not about JAVA_HOME. It is the PATH variable.

发件人: juanmluque @.> 发送时间: Wednesday, June 9, 2021 3:47:38 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, This is the configuration of JAVA_HOME I did yesterday for the java 1.7 version I installed in /usr/lib/jvm:

$ sudo nano /etc/environment $ JAVA_HOME="/usr/lib/jvm/jdk1.7.0_80/bin/java" $ source /etc/environment $ echo $JAVA_HOME

/usr/lib/jvm/jdk1.7.0_80/bin/java

Is this well done?

In the /usr/lib/jvm also is java 8 version (openjdk) and when I do java-version only appear(output) java 8 version (but not java 1.7 version).

PLEASE , COULD YOU WRITE ME YOUR CORRECT CONFIGURATION FOR JAVA_HOME OF MY JAVA 1.7 VERSION?

Thank you very much.

Juan Manuel

El mar, 8 jun 2021 a las 22:05, Yunfei Guo @.***>) escribió:

If java -version does not show the correct version, it means java 1.7 is not on path. Make sure java 1.7 folder precedes other java folders on PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 3:21:48 PM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei, I have put well the java 1.7 bin folder on PATH(with echo $JAVA_HOME it gives well the path), but when I do: $ java -version Only appear(output) the openjdk 1.8 java version that I had installed before(several years ago) in /usr/lib/jvm.But it does not appear(output) jdk 1.7 java version(that I installed yesterday).Why not? I don't understand it.And SeqMule doesn't work again.

What can I do?.Could you help me, please?. Thank you very much

Juan Manuel

El mar, 8 jun 2021 a las 15:41, Yunfei Guo @.***>) escribió:

Have put the java 1.7 bin folder on PATH? See https://opensource.com/article/17/6/set-path-linux for an example of modifying PATH.

发件人: juanmluque @.> 发送时间: Tuesday, June 8, 2021 8:49:27 AM 收件人: WGLab/SeqMule @.> 抄送: Yunfei Guo @.>; Comment @.> 主题: Re: [WGLab/SeqMule] hg19all Download Issues (#173)

Hi Yunfei,

I have switched my Java version (1.8) by Java 1.7 in a computer with more memory.But this is the ERROR:

[samopen] SAM header is present: 84 sequences.

----------NOTICE---------- [ => SeqMule Execution Status: Running 7 of 20 steps: gatklite realn, at mar jun 8 14:23:35 CEST 2021, Time Elapsed: 0 hr 3 min 41 s] [ => SeqMule Execution Status: step 6 is finished at mar jun 8 14:23:35 CEST 2021, Filter BAM file by mapping quality]

/tmp/seqmule94.74879085946681623155015script: línea 4: java: orden no encontrada (order not found)

----------ERROR---------- [ => SeqMule Execution Status: step 7 FAILED at mar jun 8 14:23:36 CEST 2021, gatklite realn] ERROR: command failed

/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/worker

/home/usuario/SeqMule-master/bin/seqmule.06082021.31798.logs 7

"/home/usuario/SeqMule-master/bin/secondary/../../bin/secondary/runGATKLITEREALN

-advanced example.config -n 6 -ref

/home/usuario/SeqMule-master/bin/secondary/../../database/human_g1k_v37.fasta

-java java -jmem 1750m -gatk

/home/usuario/SeqMule-master/exe/gatklite/GenomeAnalysisTKLite.jar -threads 4 -gatk-nt 2 -tmpdir /tmp -bed /home/usuario/SeqMule-master/misc/hg19_exome.bed -goldindel

/home/usuario/SeqMule-master/bin/secondary/../../database/Mills_and_1000G_gold_standard.indels.b37.vcf

-dbsnp

/home/usuario/SeqMule-master/bin/secondary/../../database/dbsnp_hg19_138.vcf

-samtools /home/usuario/SeqMule-master/exe/samtools/samtools -pl ILLUMINA -bam example_result/example.0_bwamem.sort.rmdup.readfiltered.bam -out

example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.bam "

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

After fixing the problem, please execute 'cd /home/usuario/SeqMule-master/bin' and 'seqmule run example.script' to resume analysis.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

@.***System-Product-Name:~/SeqMule-master/bin$

Please Yunfei, could you send me the COMPLETE INSTRUCTIONS to install java 1.7 (and where and how to download the right java 1.7 version) in my computer (to my directory : /usr/lib/jvm). I am desperate with this problem.

Thank you very much for your help. Best.

Juan Manuel

El mar, 8 jun 2021 a las 3:58, Yunfei Guo @.***>) escribió:

If your issue is similar to #123 https://github.com/WGLab/SeqMule/issues/123, then you should try switching java version to 1.7.

Your last problem seems to be due to insufficient memory. Try closing some memory-consuming programs on your machine or switch to higher memory machine.

D You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/WGLab/SeqMule/issues/173#issuecomment-856378997>,

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