Job ID = 1292349 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,389,010 reads read : 17,389,010 reads written : 17,389,010 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: 00:05:08 17389010 reads; of these: 17389010 (100.00%) were unpaired; of these: 3030226 (17.43%) aligned 0 times 12341708 (70.97%) aligned exactly 1 time 2017076 (11.60%) aligned >1 times 82.57% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6040200 / 14358784 = 0.4207 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 @ Sun, 02 Jun 2019 18:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:38: 1000000 INFO @ Sun, 02 Jun 2019 18:11:39: 1000000 INFO @ Sun, 02 Jun 2019 18:11:39: 1000000 INFO @ Sun, 02 Jun 2019 18:11:45: 2000000 INFO @ Sun, 02 Jun 2019 18:11:48: 2000000 INFO @ Sun, 02 Jun 2019 18:11:48: 2000000 INFO @ Sun, 02 Jun 2019 18:11:53: 3000000 INFO @ Sun, 02 Jun 2019 18:11:56: 3000000 INFO @ Sun, 02 Jun 2019 18:11:57: 3000000 INFO @ Sun, 02 Jun 2019 18:12:00: 4000000 INFO @ Sun, 02 Jun 2019 18:12:05: 4000000 INFO @ Sun, 02 Jun 2019 18:12:06: 4000000 INFO @ Sun, 02 Jun 2019 18:12:08: 5000000 INFO @ Sun, 02 Jun 2019 18:12:13: 5000000 INFO @ Sun, 02 Jun 2019 18:12:15: 5000000 INFO @ Sun, 02 Jun 2019 18:12:16: 6000000 INFO @ Sun, 02 Jun 2019 18:12:21: 6000000 INFO @ Sun, 02 Jun 2019 18:12:23: 7000000 INFO @ Sun, 02 Jun 2019 18:12:23: 6000000 INFO @ Sun, 02 Jun 2019 18:12:29: 7000000 INFO @ Sun, 02 Jun 2019 18:12:31: 8000000 INFO @ Sun, 02 Jun 2019 18:12:32: 7000000 INFO @ Sun, 02 Jun 2019 18:12:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:12:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:12:33: #1 total tags in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:12:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:12:33: #1 tags after filtering in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:12:33: #1 finished! INFO @ Sun, 02 Jun 2019 18:12:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:12:34: #2 number of paired peaks: 314 WARNING @ Sun, 02 Jun 2019 18:12:34: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 02 Jun 2019 18:12:34: start model_add_line... INFO @ Sun, 02 Jun 2019 18:12:34: start X-correlation... INFO @ Sun, 02 Jun 2019 18:12:34: end of X-cor INFO @ Sun, 02 Jun 2019 18:12:34: #2 finished! INFO @ Sun, 02 Jun 2019 18:12:34: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 18:12:34: #2 alternative fragment length(s) may be 4,109,138 bps INFO @ Sun, 02 Jun 2019 18:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10_model.r INFO @ Sun, 02 Jun 2019 18:12:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:12:38: 8000000 INFO @ Sun, 02 Jun 2019 18:12:40: 8000000 INFO @ Sun, 02 Jun 2019 18:12:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:12:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:12:41: #1 total tags in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:12:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:12:41: #1 tags after filtering in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:12:41: #1 finished! INFO @ Sun, 02 Jun 2019 18:12:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:12:41: #2 number of paired peaks: 314 WARNING @ Sun, 02 Jun 2019 18:12:41: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 02 Jun 2019 18:12:41: start model_add_line... INFO @ Sun, 02 Jun 2019 18:12:42: start X-correlation... INFO @ Sun, 02 Jun 2019 18:12:42: end of X-cor INFO @ Sun, 02 Jun 2019 18:12:42: #2 finished! INFO @ Sun, 02 Jun 2019 18:12:42: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 18:12:42: #2 alternative fragment length(s) may be 4,109,138 bps INFO @ Sun, 02 Jun 2019 18:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20_model.r INFO @ Sun, 02 Jun 2019 18:12:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:12:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:12:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:12:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:12:43: #1 total tags in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:12:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:12:43: #1 tags after filtering in treatment: 8318584 INFO @ Sun, 02 Jun 2019 18:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:12:43: #1 finished! INFO @ Sun, 02 Jun 2019 18:12:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:12:44: #2 number of paired peaks: 314 WARNING @ Sun, 02 Jun 2019 18:12:44: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Sun, 02 Jun 2019 18:12:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:12:44: start X-correlation... INFO @ Sun, 02 Jun 2019 18:12:44: end of X-cor INFO @ Sun, 02 Jun 2019 18:12:44: #2 finished! INFO @ Sun, 02 Jun 2019 18:12:44: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 18:12:44: #2 alternative fragment length(s) may be 4,109,138 bps INFO @ Sun, 02 Jun 2019 18:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05_model.r INFO @ Sun, 02 Jun 2019 18:12:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:12:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.10_summits.bed INFO @ Sun, 02 Jun 2019 18:13:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.20_summits.bed INFO @ Sun, 02 Jun 2019 18:13:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341787/SRX341787.05_summits.bed INFO @ Sun, 02 Jun 2019 18:13:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。