Job ID = 4303135 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,786,959 reads read : 38,786,959 reads written : 38,786,959 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552300.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: 00:08:34 38786959 reads; of these: 38786959 (100.00%) were unpaired; of these: 11204133 (28.89%) aligned 0 times 23002661 (59.31%) aligned exactly 1 time 4580165 (11.81%) aligned >1 times 71.11% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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 12 files... [bam_rmdupse_core] 12272433 / 27582826 = 0.4449 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.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 @ Thu, 12 Dec 2019 01:05:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:05:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:05:59: 1000000 INFO @ Thu, 12 Dec 2019 01:06:04: 2000000 INFO @ Thu, 12 Dec 2019 01:06:09: 3000000 INFO @ Thu, 12 Dec 2019 01:06:14: 4000000 INFO @ Thu, 12 Dec 2019 01:06:19: 5000000 INFO @ Thu, 12 Dec 2019 01:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.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 @ Thu, 12 Dec 2019 01:06:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:06:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:06:24: 6000000 INFO @ Thu, 12 Dec 2019 01:06:30: 7000000 INFO @ Thu, 12 Dec 2019 01:06:30: 1000000 INFO @ Thu, 12 Dec 2019 01:06:35: 2000000 INFO @ Thu, 12 Dec 2019 01:06:35: 8000000 INFO @ Thu, 12 Dec 2019 01:06:41: 3000000 INFO @ Thu, 12 Dec 2019 01:06:41: 9000000 INFO @ Thu, 12 Dec 2019 01:06:46: 4000000 INFO @ Thu, 12 Dec 2019 01:06:47: 10000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:06:52: 5000000 INFO @ Thu, 12 Dec 2019 01:06:52: 11000000 INFO @ Thu, 12 Dec 2019 01:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.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 @ Thu, 12 Dec 2019 01:06:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:06:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:06:57: 6000000 INFO @ Thu, 12 Dec 2019 01:06:58: 12000000 INFO @ Thu, 12 Dec 2019 01:07:01: 1000000 INFO @ Thu, 12 Dec 2019 01:07:03: 7000000 INFO @ Thu, 12 Dec 2019 01:07:03: 13000000 INFO @ Thu, 12 Dec 2019 01:07:08: 2000000 INFO @ Thu, 12 Dec 2019 01:07:09: 8000000 INFO @ Thu, 12 Dec 2019 01:07:09: 14000000 INFO @ Thu, 12 Dec 2019 01:07:14: 3000000 INFO @ Thu, 12 Dec 2019 01:07:15: 15000000 INFO @ Thu, 12 Dec 2019 01:07:15: 9000000 INFO @ Thu, 12 Dec 2019 01:07:17: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:07:17: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:07:17: #1 total tags in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:07:17: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:07:17: #1 tags after filtering in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:07:17: #1 finished! INFO @ Thu, 12 Dec 2019 01:07:17: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:07:18: #2 number of paired peaks: 758 WARNING @ Thu, 12 Dec 2019 01:07:18: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 12 Dec 2019 01:07:18: start model_add_line... INFO @ Thu, 12 Dec 2019 01:07:18: start X-correlation... INFO @ Thu, 12 Dec 2019 01:07:18: end of X-cor INFO @ Thu, 12 Dec 2019 01:07:18: #2 finished! INFO @ Thu, 12 Dec 2019 01:07:18: #2 predicted fragment length is 217 bps INFO @ Thu, 12 Dec 2019 01:07:18: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 12 Dec 2019 01:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05_model.r INFO @ Thu, 12 Dec 2019 01:07:18: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:07:21: 10000000 INFO @ Thu, 12 Dec 2019 01:07:21: 4000000 INFO @ Thu, 12 Dec 2019 01:07:26: 11000000 INFO @ Thu, 12 Dec 2019 01:07:28: 5000000 INFO @ Thu, 12 Dec 2019 01:07:31: 12000000 INFO @ Thu, 12 Dec 2019 01:07:35: 6000000 INFO @ Thu, 12 Dec 2019 01:07:37: 13000000 INFO @ Thu, 12 Dec 2019 01:07:41: 7000000 INFO @ Thu, 12 Dec 2019 01:07:43: 14000000 INFO @ Thu, 12 Dec 2019 01:07:48: 15000000 INFO @ Thu, 12 Dec 2019 01:07:49: 8000000 INFO @ Thu, 12 Dec 2019 01:07:49: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:07:49: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:07:49: #1 total tags in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:07:49: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:07:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:07:50: #1 tags after filtering in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:07:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:07:50: #1 finished! INFO @ Thu, 12 Dec 2019 01:07:50: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:07:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:07:51: #2 number of paired peaks: 758 WARNING @ Thu, 12 Dec 2019 01:07:51: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 12 Dec 2019 01:07:51: start model_add_line... INFO @ Thu, 12 Dec 2019 01:07:51: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:07:51: start X-correlation... INFO @ Thu, 12 Dec 2019 01:07:51: end of X-cor INFO @ Thu, 12 Dec 2019 01:07:51: #2 finished! INFO @ Thu, 12 Dec 2019 01:07:51: #2 predicted fragment length is 217 bps INFO @ Thu, 12 Dec 2019 01:07:51: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 12 Dec 2019 01:07:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10_model.r INFO @ Thu, 12 Dec 2019 01:07:51: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:07:56: 9000000 INFO @ Thu, 12 Dec 2019 01:08:02: 10000000 INFO @ Thu, 12 Dec 2019 01:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:08:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:08:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.05_summits.bed INFO @ Thu, 12 Dec 2019 01:08:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7207 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:08:09: 11000000 INFO @ Thu, 12 Dec 2019 01:08:16: 12000000 INFO @ Thu, 12 Dec 2019 01:08:23: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:08:23: 13000000 INFO @ Thu, 12 Dec 2019 01:08:30: 14000000 INFO @ Thu, 12 Dec 2019 01:08:36: 15000000 INFO @ Thu, 12 Dec 2019 01:08:38: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:08:38: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:08:38: #1 total tags in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:08:38: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:08:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:08:38: #1 tags after filtering in treatment: 15310393 INFO @ Thu, 12 Dec 2019 01:08:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:08:38: #1 finished! INFO @ Thu, 12 Dec 2019 01:08:38: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:08:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.10_summits.bed INFO @ Thu, 12 Dec 2019 01:08:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4694 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:08:39: #2 number of paired peaks: 758 WARNING @ Thu, 12 Dec 2019 01:08:39: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Thu, 12 Dec 2019 01:08:39: start model_add_line... INFO @ Thu, 12 Dec 2019 01:08:40: start X-correlation... INFO @ Thu, 12 Dec 2019 01:08:40: end of X-cor INFO @ Thu, 12 Dec 2019 01:08:40: #2 finished! INFO @ Thu, 12 Dec 2019 01:08:40: #2 predicted fragment length is 217 bps INFO @ Thu, 12 Dec 2019 01:08:40: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 12 Dec 2019 01:08:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20_model.r INFO @ Thu, 12 Dec 2019 01:08:40: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:09:12: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:09:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:09:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:09:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681831/SRX681831.20_summits.bed INFO @ Thu, 12 Dec 2019 01:09:29: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2545 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。