Job ID = 1293377 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T14:10:55 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T14:10:55 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/era19/ERR/ERR1856/ERR1856431' 2019-06-02T14:11:05 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'ERR1856431' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 48,530,619 reads read : 48,530,619 reads written : 48,530,619 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:27 48530619 reads; of these: 48530619 (100.00%) were unpaired; of these: 40786230 (84.04%) aligned 0 times 3665191 (7.55%) aligned exactly 1 time 4079198 (8.41%) aligned >1 times 15.96% overall alignment rate Time searching: 00:19:27 Overall time: 00:19:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 7077962 / 7744389 = 0.9139 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 00:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # 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 @ Mon, 03 Jun 2019 00:13:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:13:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # 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 @ Mon, 03 Jun 2019 00:13:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:13:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # 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 @ Mon, 03 Jun 2019 00:13:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:13:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:13:19: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 00:13:19: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 00:13:19: #1 total tags in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:13:19: #1 tags after filtering in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:13:19: #1 finished! INFO @ Mon, 03 Jun 2019 00:13:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:13:20: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 00:13:20: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 00:13:20: #1 total tags in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:13:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:13:20: #1 tags after filtering in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:13:20: #1 finished! INFO @ Mon, 03 Jun 2019 00:13:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:13:20: #2 number of paired peaks: 4188 INFO @ Mon, 03 Jun 2019 00:13:20: start model_add_line... INFO @ Mon, 03 Jun 2019 00:13:20: start X-correlation... INFO @ Mon, 03 Jun 2019 00:13:20: end of X-cor INFO @ Mon, 03 Jun 2019 00:13:20: #2 finished! INFO @ Mon, 03 Jun 2019 00:13:20: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 00:13:20: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 00:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20_model.r INFO @ Mon, 03 Jun 2019 00:13:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:13:20: #2 number of paired peaks: 4188 INFO @ Mon, 03 Jun 2019 00:13:20: start model_add_line... INFO @ Mon, 03 Jun 2019 00:13:20: start X-correlation... INFO @ Mon, 03 Jun 2019 00:13:20: end of X-cor INFO @ Mon, 03 Jun 2019 00:13:20: #2 finished! INFO @ Mon, 03 Jun 2019 00:13:20: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 00:13:20: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 00:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10_model.r INFO @ Mon, 03 Jun 2019 00:13:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:13:21: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 00:13:21: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 00:13:21: #1 total tags in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:13:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 00:13:21: #1 tags after filtering in treatment: 666427 INFO @ Mon, 03 Jun 2019 00:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:13:21: #1 finished! INFO @ Mon, 03 Jun 2019 00:13:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:13:21: #2 number of paired peaks: 4188 INFO @ Mon, 03 Jun 2019 00:13:21: start model_add_line... INFO @ Mon, 03 Jun 2019 00:13:21: start X-correlation... INFO @ Mon, 03 Jun 2019 00:13:21: end of X-cor INFO @ Mon, 03 Jun 2019 00:13:21: #2 finished! INFO @ Mon, 03 Jun 2019 00:13:21: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 00:13:21: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 00:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05_model.r INFO @ Mon, 03 Jun 2019 00:13:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:13:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 00:13:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:13:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:13:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.10_summits.bed INFO @ Mon, 03 Jun 2019 00:13:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.20_summits.bed INFO @ Mon, 03 Jun 2019 00:13:24: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918290/ERX1918290.05_summits.bed INFO @ Mon, 03 Jun 2019 00:13:25: Done! BigWig に変換しました。 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1021 records, 4 fields): 6 millis CompletedMACS2peakCalling