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MayurDivate / GUAVASourceCode

Source code repository for GUAVA (ATAC-seq data analysis tool).
GNU General Public License v3.0
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Display shows nothing for annotated peaks, plot, GO and pathways #15

Open smbchu opened 5 years ago

smbchu commented 5 years ago

Hi! I am following your GUAVA manual and using the sample data. But my analysis cannot finish, I see this error code always.

Adapter trimming...Done fastq QC... Alignment... Please wait while bowtie2 alignment is finished..Done! Error code 101: Unexpected exit from analysis workflow (base)

What am I doing wrong? and what can I do?

smbchu commented 5 years ago

I see this before: dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib So, I did this in minicond2/bin

brew update
brew install openssl
ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/
ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/

Now, GUAVA finished. But the display shows nothing for annotated peaks, plot, GO and pathways. I checked the output folder and there is nothing inside functional_analysis folder Also, there is this warning:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/Users/smbchu/GUAVA/lib/poi-ooxml-3.16-beta2.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Is this warning related to the failed display? What should I do?

MayurDivate commented 5 years ago

Please share your log file. Mayur

smbchu commented 5 years ago

Hi! Thanks for your reply. BYL719_Rep1_R1_log.txt

smbchu commented 5 years ago

Dear Mayur Divate,

Thank you for your reply. I posted this on the site also.

Best regards, Sharlyn Mae Chua

On May 21, 2019, at 18:38, Mayur Divate notifications@github.com wrote:

Please share your log file. Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/15?email_source=notifications&email_token=AMCYQ65XYIXFLHJ6JO62NEDPWO7IVA5CNFSM4HNZSB7KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODV3LCNQ#issuecomment-494317878, or mute the thread https://github.com/notifications/unsubscribe-auth/AMCYQ6Z2MWTIJPD4DOE6C5DPWO7IVANCNFSM4HNZSB7A.

------------ Input Sumary ------------

R1 fastq: /Users/sharlynmaechua/Genomes/SampleData/BYL719_Rep1_R1.fastq R2 fatsq: /Users/sharlynmaechua/Genomes/SampleData/BYL719_Rep1_R2.fastq Genome Index: /Users/sharlynmaechua/Genomes/Hs_demo.fasta

Aligner: bowtie2 Max insert size: 2000 Min mapping quality: 30 chrs: chrM

Genome : hg19 (Homo sapiens) Adapter trimming using Cutadapt R1 => BYL719_Rep1_R1.fastq R2 => BYL719_Rep1_R2.fastq Adapter Sequence => CTGTCTCTTATACACATCT Trimmed R1 => BYL719_Rep1_R1_trimmed.fastq Trimmed R2 => BYL719_Rep1_R2_trimmed.fastq dir => BYL719_Rep1_R1_Adapter_Trimming Max N => 2 error rate => 0.1 Min len => 30

Peak calling: -q = 0.05

Cutadapt Adapter Trimming

This is cutadapt 1.13 with Python 2.7.16 Command line parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -f fastq -e 0.1 --trim-n --max-n 2 -m 30 -o /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_Adapter_Trimming/BYL719_Rep1_R1_trimmed.fastq -p /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_Adapter_Trimming/BYL719_Rep1_R2_trimmed.fastq /Users/sharlynmaechua/Genomes/SampleData/BYL719_Rep1_R1.fastq /Users/sharlynmaechua/Genomes/SampleData/BYL719_Rep1_R2.fastq Trimming 2 adapters with at most 10.0% errors in paired-end mode ... Finished in 68.89 s (51 us/read; 1.19 M reads/minute).

=== Summary ===

Total read pairs processed: 1,362,349 Read 1 with adapter: 4,788 (0.4%) Read 2 with adapter: 4,576 (0.3%) Pairs that were too short: 605 (0.0%) Pairs with too many N: 0 (0.0%) Pairs written (passing filters): 1,361,744 (100.0%)

Total basepairs processed: 132,966,277 bp Read 1: 66,482,010 bp Read 2: 66,484,267 bp Total written (filtered): 132,898,943 bp (99.9%) Read 1: 66,447,963 bp Read 2: 66,450,980 bp

=== First read: Adapter 1 ===

Sequence: CTGTCTCTTATACACATCT; Type: regular 3'; Length: 19; Trimmed: 4788 times.

No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1

Bases preceding removed adapters: A: 25.6% C: 28.3% G: 26.4% T: 19.7% none/other: 0.0%

Overview of removed sequences length count expect max.err error counts 3 3716 21286.7 0 3716 4 663 5321.7 0 663 5 200 1330.4 0 200 6 146 332.6 0 146 7 36 83.2 0 36 8 3 20.8 0 3 9 5 5.2 0 1 4 10 4 1.3 1 2 2 11 12 0.3 1 0 12 12 2 0.1 1 0 2 13 1 0.0 1 0 1

=== Second read: Adapter 2 ===

Sequence: CTGTCTCTTATACACATCT; Type: regular 3'; Length: 19; Trimmed: 4576 times.

No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1

Bases preceding removed adapters: A: 24.7% C: 28.8% G: 27.5% T: 19.0% none/other: 0.0%

Overview of removed sequences length count expect max.err error counts 3 3620 21286.7 0 3620 4 576 5321.7 0 576 5 169 1330.4 0 169 6 167 332.6 0 167 7 29 83.2 0 29 8 4 20.8 0 4 9 2 5.2 0 0 2 10 1 1.3 1 0 1 11 7 0.3 1 1 6 13 1 0.0 1 0 1

FastQC R1 fastq

Analysis complete for BYL719_Rep1_R1_trimmed.fastq

Started analysis of BYL719_Rep1_R1_trimmed.fastq Approx 5% complete for BYL719_Rep1_R1_trimmed.fastq Approx 10% complete for BYL719_Rep1_R1_trimmed.fastq Approx 15% complete for BYL719_Rep1_R1_trimmed.fastq Approx 20% complete for BYL719_Rep1_R1_trimmed.fastq Approx 25% complete for BYL719_Rep1_R1_trimmed.fastq Approx 30% complete for BYL719_Rep1_R1_trimmed.fastq Approx 35% complete for BYL719_Rep1_R1_trimmed.fastq Approx 40% complete for BYL719_Rep1_R1_trimmed.fastq Approx 45% complete for BYL719_Rep1_R1_trimmed.fastq Approx 50% complete for BYL719_Rep1_R1_trimmed.fastq Approx 55% complete for BYL719_Rep1_R1_trimmed.fastq Approx 60% complete for BYL719_Rep1_R1_trimmed.fastq Approx 65% complete for BYL719_Rep1_R1_trimmed.fastq Approx 70% complete for BYL719_Rep1_R1_trimmed.fastq Approx 75% complete for BYL719_Rep1_R1_trimmed.fastq Approx 80% complete for BYL719_Rep1_R1_trimmed.fastq Approx 85% complete for BYL719_Rep1_R1_trimmed.fastq Approx 90% complete for BYL719_Rep1_R1_trimmed.fastq Approx 95% complete for BYL719_Rep1_R1_trimmed.fastq

FastQC R2 fastq

Analysis complete for BYL719_Rep1_R2_trimmed.fastq

Started analysis of BYL719_Rep1_R2_trimmed.fastq Approx 5% complete for BYL719_Rep1_R2_trimmed.fastq Approx 10% complete for BYL719_Rep1_R2_trimmed.fastq Approx 15% complete for BYL719_Rep1_R2_trimmed.fastq Approx 20% complete for BYL719_Rep1_R2_trimmed.fastq Approx 25% complete for BYL719_Rep1_R2_trimmed.fastq Approx 30% complete for BYL719_Rep1_R2_trimmed.fastq Approx 35% complete for BYL719_Rep1_R2_trimmed.fastq Approx 40% complete for BYL719_Rep1_R2_trimmed.fastq Approx 45% complete for BYL719_Rep1_R2_trimmed.fastq Approx 50% complete for BYL719_Rep1_R2_trimmed.fastq Approx 55% complete for BYL719_Rep1_R2_trimmed.fastq Approx 60% complete for BYL719_Rep1_R2_trimmed.fastq Approx 65% complete for BYL719_Rep1_R2_trimmed.fastq Approx 70% complete for BYL719_Rep1_R2_trimmed.fastq Approx 75% complete for BYL719_Rep1_R2_trimmed.fastq Approx 80% complete for BYL719_Rep1_R2_trimmed.fastq Approx 85% complete for BYL719_Rep1_R2_trimmed.fastq Approx 90% complete for BYL719_Rep1_R2_trimmed.fastq Approx 95% complete for BYL719_Rep1_R2_trimmed.fastq

Bowtie2 log

1361744 reads; of these: 1361744 (100.00%) were paired; of these: 248 (0.02%) aligned concordantly 0 times 1269643 (93.24%) aligned concordantly exactly 1 time 91853 (6.75%) aligned concordantly >1 times 99.98% overall alignment rate

Quality filter log

sam to sorted bam log

BYL719_Rep1_R1_aligned_csrt.bamidxstats

chr6 171115067 2641338 0 chrM 16571 6426 0

BYL719_Rep1_R1_aligned_csrt.bamidxstats

chr6 171115067 2641338 0 chrM 16571 6426 0

Picard Mark duplicate log

INFO 2019-05-22 09:04:49 MarkDuplicates

** NOTE: Picard's command line syntax is changing.

** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

** The command line looks like this in the new syntax:

** MarkDuplicates -REMOVE_DUPLICATES true -I /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_csrt.bam -O /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_duplicate_filtered.bam -M /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_duplicate_filtered.bam_matrix.txt

09:04:55.184 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sharlynmaechua/miniconda2/share/picard-2.20.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Wed May 22 09:04:55 JST 2019] MarkDuplicates INPUT=[/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_csrt.bam] OUTPUT=/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_duplicate_filtered.bam METRICS_FILE=/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_duplicate_filtered.bam_matrix.txt REMOVE_DUPLICATES=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed May 22 09:04:55 JST 2019] Executing as sharlynmaechua@Sharlyns-MacBook-Air.local on Mac OS X 10.14.3 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.1-SNAPSHOT INFO 2019-05-22 09:04:55 MarkDuplicates Start of doWork freeMemory: 530814384; totalMemory: 536870912; maxMemory: 1073741824 INFO 2019-05-22 09:04:55 MarkDuplicates Reading input file and constructing read end information. INFO 2019-05-22 09:04:55 MarkDuplicates Will retain up to 3890368 data points before spilling to disk. WARNING 2019-05-22 09:04:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: SRR3929040.38746638. Cause: String 'SRR3929040.38746638' did not start with a parsable number. INFO 2019-05-22 09:05:01 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: chr6:54,784,052 INFO 2019-05-22 09:05:01 MarkDuplicates Tracking 2 as yet unmatched pairs. 2 records in RAM. INFO 2019-05-22 09:05:07 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 5s. Last read position: chr6:126,193,688 INFO 2019-05-22 09:05:07 MarkDuplicates Tracking 10 as yet unmatched pairs. 10 records in RAM. INFO 2019-05-22 09:05:11 MarkDuplicates Read 2647764 records. 0 pairs never matched. INFO 2019-05-22 09:05:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 218429904; totalMemory: 542113792; maxMemory: 1073741824 INFO 2019-05-22 09:05:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2019-05-22 09:05:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2019-05-22 09:05:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2019-05-22 09:05:13 MarkDuplicates Sorting list of duplicate records. INFO 2019-05-22 09:05:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 535668832; totalMemory: 811597824; maxMemory: 1073741824 INFO 2019-05-22 09:05:14 MarkDuplicates Marking 648838 records as duplicates. INFO 2019-05-22 09:05:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2019-05-22 09:05:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2019-05-22 09:05:30 MarkDuplicates Before output close freeMemory: 530074776; totalMemory: 536870912; maxMemory: 1073741824 INFO 2019-05-22 09:05:30 MarkDuplicates After output close freeMemory: 530074776; totalMemory: 536870912; maxMemory: 1073741824 [Wed May 22 09:05:30 JST 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.59 minutes. Runtime.totalMemory()=536870912

BYL719_Rep1_R1_aligned_duplicate_filtered.bamidxstats

chr6 171115067 1998736 0 chrM 16571 190 0

Indexing duplicate filered bam

samtool properly aligned bam (-f3) log

bam indexing for chromosome filtering

chromosome filetering log

BYL719_Rep1_R1_aligned_chr_filtered.bamidxstats

chr6 171115067 1998736 0 chrM 16571 0 0

Black list region filtering

BYL719_Rep1_R1_aligned_blacklist_filtered.bamidxstats

chr6 171115067 1991459 0 chrM 16571 0 0

bam to query sorted sam log

BYL719_Rep1_R1_aligned_ATACseq.bamidxstats

chr6 171115067 1991448 0 chrM 16571 0 0

BYL719_Rep1_R1_aligned_ATACseq.bamidxstats

chr6 171115067 1991448 0 chrM 16571 0 0

Bam To bedgraph

true

sort bedgraph

true

ucsc bdgToBigwig

**** InsertSizelog START ****

INFO 2019-05-22 09:07:59 CollectInsertSizeMetrics

** NOTE: Picard's command line syntax is changing.

** For more information, please see: ** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

** The command line looks like this in the new syntax:

** CollectInsertSizeMetrics -I /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_ATACseq.bam -O /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.txt -H /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.pdf -M 0.05

09:08:06.133 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sharlynmaechua/miniconda2/share/picard-2.20.1-0/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib [Wed May 22 09:08:06 JST 2019] CollectInsertSizeMetrics HISTOGRAM_FILE=/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.pdf MINIMUM_PCT=0.05 INPUT=/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_ATACseq.bam OUTPUT=/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.txt DEVIATIONS=10.0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Wed May 22 09:08:06 JST 2019] Executing as sharlynmaechua@Sharlyns-MacBook-Air.local on Mac OS X 10.14.3 x86_64; OpenJDK 64-Bit Server VM 11.0.1+13-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.20.1-SNAPSHOT INFO 2019-05-22 09:08:10 SinglePassSamProgram Processed 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr6:78,043,032 INFO 2019-05-22 09:08:12 RExecutor Executing R script via command: Rscript /var/folders/72/chcrsvt95c5c03gpfdspg6vh0000gn/T/sharlynmaechua/script3837131417853579888.R /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.txt /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_picard_insert_size.pdf BYL719_Rep1_R1_aligned_ATACseq.bam INFO 2019-05-22 09:08:13 ProcessExecutor null device INFO 2019-05-22 09:08:13 ProcessExecutor 1 [Wed May 22 09:08:13 JST 2019] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=536870912

** MACS2 Peak calling log **

INFO @ Wed, 22 May 2019 09:08:14:

Command line: callpeak -t /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_ATACseq.bam -f BAM -g hs --keep-dup all --outdir /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_PEAK_CALLING -n BYL719_Rep1_R1 -q 0.05 --bdg --trackline --nomodel --nolambda

ARGUMENTS LIST:

name = BYL719_Rep1_R1

format = BAM

ChIP-seq file = ['/Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_aligned_ATACseq.bam']

control file = None

effective genome size = 2.70e+09

band width = 300

model fold = [5, 50]

qvalue cutoff = 5.00e-02

Larger dataset will be scaled towards smaller dataset.

Range for calculating regional lambda is: 10000 bps

Broad region calling is off

Paired-End mode is off

INFO @ Wed, 22 May 2019 09:08:14: #1 read tag files... INFO @ Wed, 22 May 2019 09:08:14: #1 read treatment tags... INFO @ Wed, 22 May 2019 09:08:19: 1000000 INFO @ Wed, 22 May 2019 09:08:23: #1 tag size is determined as 47 bps INFO @ Wed, 22 May 2019 09:08:23: #1 tag size = 47 INFO @ Wed, 22 May 2019 09:08:23: #1 total tags in treatment: 995724 INFO @ Wed, 22 May 2019 09:08:23: #1 finished! INFO @ Wed, 22 May 2019 09:08:23: #2 Build Peak Model... INFO @ Wed, 22 May 2019 09:08:23: #2 Skipped... INFO @ Wed, 22 May 2019 09:08:23: #2 Use 200 as fragment length INFO @ Wed, 22 May 2019 09:08:23: #3 Call peaks... INFO @ Wed, 22 May 2019 09:08:23: # local lambda is disabled! INFO @ Wed, 22 May 2019 09:08:23: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!! INFO @ Wed, 22 May 2019 09:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 May 2019 09:08:24: #3 In the peak calling step, the following will be performed simultaneously: INFO @ Wed, 22 May 2019 09:08:24: #3 Write bedGraph files for treatment pileup (after scaling if necessary)... BYL719_Rep1_R1_treat_pileup.bdg INFO @ Wed, 22 May 2019 09:08:24: #3 Write bedGraph files for control lambda (after scaling if necessary)... BYL719_Rep1_R1_control_lambda.bdg INFO @ Wed, 22 May 2019 09:08:24: #3 Pileup will be based on sequencing depth in treatment. INFO @ Wed, 22 May 2019 09:08:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 May 2019 09:08:32: #4 Write output xls file... /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_PEAK_CALLING/BYL719_Rep1_R1_peaks.xls INFO @ Wed, 22 May 2019 09:08:34: #4 Write peak in narrowPeak format file... /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_PEAK_CALLING/BYL719_Rep1_R1_peaks.narrowPeak INFO @ Wed, 22 May 2019 09:08:35: #4 Write summits bed file... /Users/sharlynmaechua/GUAVA/GUAVA_output/BYL719_Rep1_R1_OUTPUT/BYL719_Rep1_R1_PEAK_CALLING/BYL719_Rep1_R1_summits.bed INFO @ Wed, 22 May 2019 09:08:36: Done!

**** Fragment distribution plot log ****

null device 1

Registered S3 methods overwritten by 'ggplot2': method from [.quosures rlang c.quosures rlang print.quosures rlang

**** ChIPpeakAnno log ****

library(ChIPpeakAnno) でエラー: ‘ChIPpeakAnno’ という名前のパッケージはありません 実行が停止されました

GUAVA ATAC-seq data analysis

Started at:Wed May 22 08:54:39 JST 2019 Finished at:Wed May 22 09:08:41 JST 2019

MayurDivate commented 5 years ago

Hi, From the log, it looks like one of the R package is missing. i.e. ChIPpeakAnno. When the Japanese error message from the log translated, it says "Package NOT FOUND".

Installing above package should fix the issue.

Cheers, Mayur

smbchu commented 5 years ago

Hi,

I tried to run configure.sh again and I saw this

Installing R packages > >> > [1] ">>> >> > Loading BIOCONDUCTOR > >> >>>" file(filename, "r", encoding = encoding) でエラー: cannot open the connection to 'https://bioconductor.org/biocLite.R' 呼び出し: source -> file 追加情報: 警告メッセージ: file(filename, "r", encoding = encoding) で: URL 'https://bioconductor.org/biocLite.R': status was 'SSL connect error' 実行が停止されました SSL connect error?

Best, Sharlyn Chua

On May 24, 2019, at 15:53, Mayur Divate notifications@github.com wrote:

Hi, From the log, it looks like one of the R package is missing. i.e. ChIPpeakAnno. When the Japanese error message from the log translated, it says "Package NOT FOUND".

Installing above package should fix the issue.

Cheers, Mayur

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MayurDivate/GUAVASourceCode/issues/15?email_source=notifications&email_token=AMCYQ64KRUWSVHOLNVFPOCTPW6GGFA5CNFSM4HNZSB7KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWEKKTA#issuecomment-495494476, or mute the thread https://github.com/notifications/unsubscribe-auth/AMCYQ637PMQKVG46V2OAMV3PW6GGFANCNFSM4HNZSB7A.

MayurDivate commented 5 years ago

Hi Sharlyn Chua,

Recent Bioconductor update changed BiocLite() to BiocManage(). I will suggest to use BioManger() and install all missing Bioconductor packages.

However, I am working on it. The new release of GUAVA will fix this issue.

Best wishes, Mayur