Job ID = 2011934 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T18:23:58 fasterq-dump.2.9.6 sys: timeout exhausted while creating file within network system module - Failed to Make Connection in KClientHttpOpen to 'www.ncbi.nlm.nih.gov:443' 2019-07-05T18:23:58 fasterq-dump.2.9.6 err: invalid accession 'SRR1284648' spots read : 2,083,460 reads read : 2,083,460 reads written : 2,083,460 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1284648.sra.cache’: 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: 00:00:22 2083460 reads; of these: 2083460 (100.00%) were unpaired; of these: 374386 (17.97%) aligned 0 times 683512 (32.81%) aligned exactly 1 time 1025562 (49.22%) aligned >1 times 82.03% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1124765 / 1709074 = 0.6581 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 @ Sat, 06 Jul 2019 03:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:26:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:26:27: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:27: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 06 Jul 2019 03:26:28: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:26:28: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:26:30: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:26:30: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:26:30: #1 total tags in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:26:30: #1 tags after filtering in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:26:30: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:31: #2 number of paired peaks: 1067 INFO @ Sat, 06 Jul 2019 03:26:31: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:31: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:31: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:31: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:31: #2 predicted fragment length is 237 bps INFO @ Sat, 06 Jul 2019 03:26:31: #2 alternative fragment length(s) may be 3,237,250 bps INFO @ Sat, 06 Jul 2019 03:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05_model.r INFO @ Sat, 06 Jul 2019 03:26:31: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:26:31: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:26:31: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:26:31: #1 total tags in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:26:31: #1 tags after filtering in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:26:31: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:32: #2 number of paired peaks: 1067 INFO @ Sat, 06 Jul 2019 03:26:32: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:32: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:32: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:32: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:32: #2 predicted fragment length is 237 bps INFO @ Sat, 06 Jul 2019 03:26:32: #2 alternative fragment length(s) may be 3,237,250 bps INFO @ Sat, 06 Jul 2019 03:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10_model.r INFO @ Sat, 06 Jul 2019 03:26:32: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:26:32: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:26:32: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:26:32: #1 total tags in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:26:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:26:32: #1 tags after filtering in treatment: 584309 INFO @ Sat, 06 Jul 2019 03:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:26:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:26:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:26:32: #2 number of paired peaks: 1067 INFO @ Sat, 06 Jul 2019 03:26:32: start model_add_line... INFO @ Sat, 06 Jul 2019 03:26:32: start X-correlation... INFO @ Sat, 06 Jul 2019 03:26:32: end of X-cor INFO @ Sat, 06 Jul 2019 03:26:32: #2 finished! INFO @ Sat, 06 Jul 2019 03:26:32: #2 predicted fragment length is 237 bps INFO @ Sat, 06 Jul 2019 03:26:32: #2 alternative fragment length(s) may be 3,237,250 bps INFO @ Sat, 06 Jul 2019 03:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20_model.r INFO @ Sat, 06 Jul 2019 03:26:32: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:26:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:26:36: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.05_summits.bed INFO @ Sat, 06 Jul 2019 03:26:36: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (426 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:26:37: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.10_summits.bed INFO @ Sat, 06 Jul 2019 03:26:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541161/SRX541161.20_summits.bed INFO @ Sat, 06 Jul 2019 03:26:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 3 millis CompletedMACS2peakCalling