Job ID = 1293988 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 969,351 reads read : 969,351 reads written : 969,351 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: 00:05:01 20969351 reads; of these: 20969351 (100.00%) were unpaired; of these: 6380682 (30.43%) aligned 0 times 12562981 (59.91%) aligned exactly 1 time 2025688 (9.66%) aligned >1 times 69.57% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3906975 / 14588669 = 0.2678 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 04:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.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 04:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.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 04:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.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 04:09:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:09:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:09:15: 1000000 INFO @ Mon, 03 Jun 2019 04:09:16: 1000000 INFO @ Mon, 03 Jun 2019 04:09:17: 1000000 INFO @ Mon, 03 Jun 2019 04:09:22: 2000000 INFO @ Mon, 03 Jun 2019 04:09:25: 2000000 INFO @ Mon, 03 Jun 2019 04:09:26: 2000000 INFO @ Mon, 03 Jun 2019 04:09:30: 3000000 INFO @ Mon, 03 Jun 2019 04:09:33: 3000000 INFO @ Mon, 03 Jun 2019 04:09:36: 3000000 INFO @ Mon, 03 Jun 2019 04:09:38: 4000000 INFO @ Mon, 03 Jun 2019 04:09:42: 4000000 INFO @ Mon, 03 Jun 2019 04:09:46: 5000000 INFO @ Mon, 03 Jun 2019 04:09:46: 4000000 INFO @ Mon, 03 Jun 2019 04:09:52: 5000000 INFO @ Mon, 03 Jun 2019 04:09:54: 6000000 INFO @ Mon, 03 Jun 2019 04:09:57: 5000000 INFO @ Mon, 03 Jun 2019 04:10:01: 6000000 INFO @ Mon, 03 Jun 2019 04:10:02: 7000000 INFO @ Mon, 03 Jun 2019 04:10:07: 6000000 INFO @ Mon, 03 Jun 2019 04:10:10: 8000000 INFO @ Mon, 03 Jun 2019 04:10:11: 7000000 INFO @ Mon, 03 Jun 2019 04:10:17: 9000000 INFO @ Mon, 03 Jun 2019 04:10:18: 7000000 INFO @ Mon, 03 Jun 2019 04:10:20: 8000000 INFO @ Mon, 03 Jun 2019 04:10:24: 10000000 INFO @ Mon, 03 Jun 2019 04:10:28: 8000000 INFO @ Mon, 03 Jun 2019 04:10:28: 9000000 INFO @ Mon, 03 Jun 2019 04:10:30: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:30: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:30: #1 total tags in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:30: #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 04:10:30: #1 tags after filtering in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:30: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:31: #2 number of paired peaks: 1468 INFO @ Mon, 03 Jun 2019 04:10:31: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:31: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:31: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:31: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:31: #2 predicted fragment length is 223 bps INFO @ Mon, 03 Jun 2019 04:10:31: #2 alternative fragment length(s) may be 4,223 bps INFO @ Mon, 03 Jun 2019 04:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10_model.r INFO @ Mon, 03 Jun 2019 04:10:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:10:36: 10000000 INFO @ Mon, 03 Jun 2019 04:10:37: 9000000 INFO @ Mon, 03 Jun 2019 04:10:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:41: #1 total tags in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:41: #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 04:10:42: #1 tags after filtering in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:42: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:43: #2 number of paired peaks: 1468 INFO @ Mon, 03 Jun 2019 04:10:43: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:43: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:43: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:43: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:43: #2 predicted fragment length is 223 bps INFO @ Mon, 03 Jun 2019 04:10:43: #2 alternative fragment length(s) may be 4,223 bps INFO @ Mon, 03 Jun 2019 04:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20_model.r INFO @ Mon, 03 Jun 2019 04:10:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:10:45: 10000000 INFO @ Mon, 03 Jun 2019 04:10:52: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:52: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:52: #1 total tags in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:52: #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 04:10:52: #1 tags after filtering in treatment: 10681694 INFO @ Mon, 03 Jun 2019 04:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:52: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:53: #2 number of paired peaks: 1468 INFO @ Mon, 03 Jun 2019 04:10:53: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:53: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:53: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:53: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:53: #2 predicted fragment length is 223 bps INFO @ Mon, 03 Jun 2019 04:10:53: #2 alternative fragment length(s) may be 4,223 bps INFO @ Mon, 03 Jun 2019 04:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05_model.r INFO @ Mon, 03 Jun 2019 04:10:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:11:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.10_summits.bed INFO @ Mon, 03 Jun 2019 04:11:18: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:11:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:11:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:11:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.20_summits.bed INFO @ Mon, 03 Jun 2019 04:11:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550622/SRX1550622.05_summits.bed INFO @ Mon, 03 Jun 2019 04:11:41: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (694 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。