Job ID = 9029251 sra ファイルのダウンロード中... Completed: 1105230K bytes transferred in 16 seconds (555043K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1044 0 --:--:-- 0:00:07 --:--:-- 9926 100 38317 0 38317 0 0 4598 0 --:--:-- 0:00:08 --:--:-- 21660 100 108k 0 108k 0 0 11867 0 --:--:-- 0:00:09 --:--:-- 40027 100 118k 0 118k 0 0 12728 0 --:--:-- 0:00:09 --:--:-- 41222 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 56185355 spots for /home/okishinya/chipatlas/results/dm3/SRX1433400/SRR2919816.sra Written 56185355 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:20:37 56185355 reads; of these: 56185355 (100.00%) were unpaired; of these: 5963134 (10.61%) aligned 0 times 35846974 (63.80%) aligned exactly 1 time 14375247 (25.59%) aligned >1 times 89.39% overall alignment rate Time searching: 00:20:37 Overall time: 00:20:37 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 24 files... [bam_rmdupse_core] 28555915 / 50222221 = 0.5686 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, 03 Jun 2017 13:26:01: # Command line: callpeak -t SRX1433400.bam -f BAM -g dm -n SRX1433400.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433400.10 # format = BAM # ChIP-seq file = ['SRX1433400.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 INFO @ Sat, 03 Jun 2017 13:26:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:26:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:26:01: # Command line: callpeak -t SRX1433400.bam -f BAM -g dm -n SRX1433400.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433400.20 # format = BAM # ChIP-seq file = ['SRX1433400.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 INFO @ Sat, 03 Jun 2017 13:26:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:26:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:26:01: # Command line: callpeak -t SRX1433400.bam -f BAM -g dm -n SRX1433400.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433400.05 # format = BAM # ChIP-seq file = ['SRX1433400.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 INFO @ Sat, 03 Jun 2017 13:26:01: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:26:01: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:26:07: 1000000 INFO @ Sat, 03 Jun 2017 13:26:08: 1000000 INFO @ Sat, 03 Jun 2017 13:26:08: 1000000 INFO @ Sat, 03 Jun 2017 13:26:13: 2000000 INFO @ Sat, 03 Jun 2017 13:26:14: 2000000 INFO @ Sat, 03 Jun 2017 13:26:14: 2000000 INFO @ Sat, 03 Jun 2017 13:26:20: 3000000 INFO @ Sat, 03 Jun 2017 13:26:20: 3000000 INFO @ Sat, 03 Jun 2017 13:26:20: 3000000 INFO @ Sat, 03 Jun 2017 13:26:26: 4000000 INFO @ Sat, 03 Jun 2017 13:26:26: 4000000 INFO @ Sat, 03 Jun 2017 13:26:26: 4000000 INFO @ Sat, 03 Jun 2017 13:26:32: 5000000 INFO @ Sat, 03 Jun 2017 13:26:32: 5000000 INFO @ Sat, 03 Jun 2017 13:26:32: 5000000 INFO @ Sat, 03 Jun 2017 13:26:38: 6000000 INFO @ Sat, 03 Jun 2017 13:26:39: 6000000 INFO @ Sat, 03 Jun 2017 13:26:39: 6000000 INFO @ Sat, 03 Jun 2017 13:26:43: 7000000 INFO @ Sat, 03 Jun 2017 13:26:45: 7000000 INFO @ Sat, 03 Jun 2017 13:26:45: 7000000 INFO @ Sat, 03 Jun 2017 13:26:49: 8000000 INFO @ Sat, 03 Jun 2017 13:26:51: 8000000 INFO @ Sat, 03 Jun 2017 13:26:51: 8000000 INFO @ Sat, 03 Jun 2017 13:26:56: 9000000 INFO @ Sat, 03 Jun 2017 13:26:57: 9000000 INFO @ Sat, 03 Jun 2017 13:26:57: 9000000 INFO @ Sat, 03 Jun 2017 13:27:03: 10000000 INFO @ Sat, 03 Jun 2017 13:27:03: 10000000 INFO @ Sat, 03 Jun 2017 13:27:04: 10000000 INFO @ Sat, 03 Jun 2017 13:27:09: 11000000 INFO @ Sat, 03 Jun 2017 13:27:09: 11000000 INFO @ Sat, 03 Jun 2017 13:27:11: 11000000 INFO @ Sat, 03 Jun 2017 13:27:15: 12000000 INFO @ Sat, 03 Jun 2017 13:27:16: 12000000 INFO @ Sat, 03 Jun 2017 13:27:18: 12000000 INFO @ Sat, 03 Jun 2017 13:27:21: 13000000 INFO @ Sat, 03 Jun 2017 13:27:22: 13000000 INFO @ Sat, 03 Jun 2017 13:27:26: 13000000 INFO @ Sat, 03 Jun 2017 13:27:27: 14000000 INFO @ Sat, 03 Jun 2017 13:27:29: 14000000 INFO @ Sat, 03 Jun 2017 13:27:32: 15000000 INFO @ Sat, 03 Jun 2017 13:27:32: 14000000 INFO @ Sat, 03 Jun 2017 13:27:35: 15000000 INFO @ Sat, 03 Jun 2017 13:27:38: 16000000 INFO @ Sat, 03 Jun 2017 13:27:39: 15000000 INFO @ Sat, 03 Jun 2017 13:27:42: 16000000 INFO @ Sat, 03 Jun 2017 13:27:45: 17000000 INFO @ Sat, 03 Jun 2017 13:27:47: 16000000 INFO @ Sat, 03 Jun 2017 13:27:49: 17000000 INFO @ Sat, 03 Jun 2017 13:27:52: 18000000 INFO @ Sat, 03 Jun 2017 13:27:56: 17000000 INFO @ Sat, 03 Jun 2017 13:27:57: 18000000 INFO @ Sat, 03 Jun 2017 13:27:59: 19000000 INFO @ Sat, 03 Jun 2017 13:28:03: 18000000 INFO @ Sat, 03 Jun 2017 13:28:03: 19000000 INFO @ Sat, 03 Jun 2017 13:28:05: 20000000 INFO @ Sat, 03 Jun 2017 13:28:10: 20000000 INFO @ Sat, 03 Jun 2017 13:28:11: 19000000 INFO @ Sat, 03 Jun 2017 13:28:11: 21000000 INFO @ Sat, 03 Jun 2017 13:28:15: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:28:15: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:28:15: #1 total tags in treatment: 21666306 INFO @ Sat, 03 Jun 2017 13:28:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:28:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:28:16: 21000000 INFO @ Sat, 03 Jun 2017 13:28:17: 20000000 INFO @ Sat, 03 Jun 2017 13:28:19: #1 tags after filtering in treatment: 21658379 INFO @ Sat, 03 Jun 2017 13:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:28:19: #1 finished! INFO @ Sat, 03 Jun 2017 13:28:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:28:21: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:28:21: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:28:21: #1 total tags in treatment: 21666306 INFO @ Sat, 03 Jun 2017 13:28:21: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:28:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:28:23: #2 number of paired peaks: 712 WARNING @ Sat, 03 Jun 2017 13:28:23: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 03 Jun 2017 13:28:23: start model_add_line... INFO @ Sat, 03 Jun 2017 13:28:24: 21000000 INFO @ Sat, 03 Jun 2017 13:28:25: #1 tags after filtering in treatment: 21658379 INFO @ Sat, 03 Jun 2017 13:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:28:25: #1 finished! INFO @ Sat, 03 Jun 2017 13:28:25: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:28:28: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 13:28:28: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 13:28:28: #1 total tags in treatment: 21666306 INFO @ Sat, 03 Jun 2017 13:28:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:28:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:28:29: #2 number of paired peaks: 712 WARNING @ Sat, 03 Jun 2017 13:28:29: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 03 Jun 2017 13:28:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:28:33: #1 tags after filtering in treatment: 21658379 INFO @ Sat, 03 Jun 2017 13:28:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:28:33: #1 finished! INFO @ Sat, 03 Jun 2017 13:28:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:28:33: start X-correlation... INFO @ Sat, 03 Jun 2017 13:28:33: end of X-cor INFO @ Sat, 03 Jun 2017 13:28:33: #2 finished! INFO @ Sat, 03 Jun 2017 13:28:33: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 13:28:33: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sat, 03 Jun 2017 13:28:33: #2.2 Generate R script for model : SRX1433400.10_model.r WARNING @ Sat, 03 Jun 2017 13:28:33: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:28:33: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sat, 03 Jun 2017 13:28:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:28:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:28:36: #2 number of paired peaks: 712 WARNING @ Sat, 03 Jun 2017 13:28:36: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Sat, 03 Jun 2017 13:28:36: start model_add_line... INFO @ Sat, 03 Jun 2017 13:28:39: start X-correlation... INFO @ Sat, 03 Jun 2017 13:28:39: end of X-cor INFO @ Sat, 03 Jun 2017 13:28:39: #2 finished! INFO @ Sat, 03 Jun 2017 13:28:39: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 13:28:39: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sat, 03 Jun 2017 13:28:39: #2.2 Generate R script for model : SRX1433400.05_model.r WARNING @ Sat, 03 Jun 2017 13:28:39: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:28:39: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sat, 03 Jun 2017 13:28:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:28:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:28:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:28:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:28:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:28:49: #2 predicted fragment length is 65 bps INFO @ Sat, 03 Jun 2017 13:28:49: #2 alternative fragment length(s) may be 4,65 bps INFO @ Sat, 03 Jun 2017 13:28:49: #2.2 Generate R script for model : SRX1433400.20_model.r WARNING @ Sat, 03 Jun 2017 13:28:49: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:28:49: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Sat, 03 Jun 2017 13:28:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:28:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:30:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:30:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:30:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:31:46: #4 Write output xls file... SRX1433400.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:31:46: #4 Write peak in narrowPeak format file... SRX1433400.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:31:46: #4 Write summits bed file... SRX1433400.10_summits.bed INFO @ Sat, 03 Jun 2017 13:31:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3729 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:31:50: #4 Write output xls file... SRX1433400.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:31:50: #4 Write peak in narrowPeak format file... SRX1433400.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:31:50: #4 Write summits bed file... SRX1433400.20_summits.bed INFO @ Sat, 03 Jun 2017 13:31:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2175 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:31:54: #4 Write output xls file... SRX1433400.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:31:54: #4 Write peak in narrowPeak format file... SRX1433400.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:31:54: #4 Write summits bed file... SRX1433400.05_summits.bed INFO @ Sat, 03 Jun 2017 13:31:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5990 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。