Job ID = 9033405 sra ファイルのダウンロード中... Completed: 568717K bytes transferred in 12 seconds (362712K 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 --:--:-- 0 101 5455 0 5455 0 0 772 0 --:--:-- 0:00:07 --:--:-- 7534 100 36038 0 36038 0 0 4473 0 --:--:-- 0:00:08 --:--:-- 20964 100 58135 0 58135 0 0 6931 0 --:--:-- 0:00:08 --:--:-- 28344 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 18749323 spots for /home/okishinya/chipatlas/results/dm3/SRX969927/SRR1931643.sra Written 18749323 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: 00:07:58 18749323 reads; of these: 18749323 (100.00%) were unpaired; of these: 788181 (4.20%) aligned 0 times 13024230 (69.47%) aligned exactly 1 time 4936912 (26.33%) aligned >1 times 95.80% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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] 2223728 / 17961142 = 0.1238 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, 04 Jun 2017 00:26:45: # Command line: callpeak -t SRX969927.bam -f BAM -g dm -n SRX969927.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969927.10 # format = BAM # ChIP-seq file = ['SRX969927.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 @ Sun, 04 Jun 2017 00:26:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:26:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:26:45: # Command line: callpeak -t SRX969927.bam -f BAM -g dm -n SRX969927.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969927.20 # format = BAM # ChIP-seq file = ['SRX969927.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 @ Sun, 04 Jun 2017 00:26:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:26:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:26:45: # Command line: callpeak -t SRX969927.bam -f BAM -g dm -n SRX969927.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969927.05 # format = BAM # ChIP-seq file = ['SRX969927.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 @ Sun, 04 Jun 2017 00:26:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:26:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:26:51: 1000000 INFO @ Sun, 04 Jun 2017 00:26:51: 1000000 INFO @ Sun, 04 Jun 2017 00:26:51: 1000000 INFO @ Sun, 04 Jun 2017 00:26:58: 2000000 INFO @ Sun, 04 Jun 2017 00:26:58: 2000000 INFO @ Sun, 04 Jun 2017 00:26:58: 2000000 INFO @ Sun, 04 Jun 2017 00:27:04: 3000000 INFO @ Sun, 04 Jun 2017 00:27:05: 3000000 INFO @ Sun, 04 Jun 2017 00:27:05: 3000000 INFO @ Sun, 04 Jun 2017 00:27:11: 4000000 INFO @ Sun, 04 Jun 2017 00:27:12: 4000000 INFO @ Sun, 04 Jun 2017 00:27:12: 4000000 INFO @ Sun, 04 Jun 2017 00:27:17: 5000000 INFO @ Sun, 04 Jun 2017 00:27:19: 5000000 INFO @ Sun, 04 Jun 2017 00:27:19: 5000000 INFO @ Sun, 04 Jun 2017 00:27:23: 6000000 INFO @ Sun, 04 Jun 2017 00:27:25: 6000000 INFO @ Sun, 04 Jun 2017 00:27:25: 6000000 INFO @ Sun, 04 Jun 2017 00:27:30: 7000000 INFO @ Sun, 04 Jun 2017 00:27:32: 7000000 INFO @ Sun, 04 Jun 2017 00:27:32: 7000000 INFO @ Sun, 04 Jun 2017 00:27:36: 8000000 INFO @ Sun, 04 Jun 2017 00:27:39: 8000000 INFO @ Sun, 04 Jun 2017 00:27:39: 8000000 INFO @ Sun, 04 Jun 2017 00:27:43: 9000000 INFO @ Sun, 04 Jun 2017 00:27:46: 9000000 INFO @ Sun, 04 Jun 2017 00:27:46: 9000000 INFO @ Sun, 04 Jun 2017 00:27:49: 10000000 INFO @ Sun, 04 Jun 2017 00:27:53: 10000000 INFO @ Sun, 04 Jun 2017 00:27:53: 10000000 INFO @ Sun, 04 Jun 2017 00:27:55: 11000000 INFO @ Sun, 04 Jun 2017 00:27:59: 11000000 INFO @ Sun, 04 Jun 2017 00:27:59: 11000000 INFO @ Sun, 04 Jun 2017 00:28:02: 12000000 INFO @ Sun, 04 Jun 2017 00:28:06: 12000000 INFO @ Sun, 04 Jun 2017 00:28:06: 12000000 INFO @ Sun, 04 Jun 2017 00:28:08: 13000000 INFO @ Sun, 04 Jun 2017 00:28:13: 13000000 INFO @ Sun, 04 Jun 2017 00:28:13: 13000000 INFO @ Sun, 04 Jun 2017 00:28:14: 14000000 INFO @ Sun, 04 Jun 2017 00:28:20: 14000000 INFO @ Sun, 04 Jun 2017 00:28:20: 14000000 INFO @ Sun, 04 Jun 2017 00:28:21: 15000000 INFO @ Sun, 04 Jun 2017 00:28:25: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:28:25: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:28:25: #1 total tags in treatment: 15737414 INFO @ Sun, 04 Jun 2017 00:28:25: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:28:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:28:27: 15000000 INFO @ Sun, 04 Jun 2017 00:28:27: 15000000 INFO @ Sun, 04 Jun 2017 00:28:29: #1 tags after filtering in treatment: 15733790 INFO @ Sun, 04 Jun 2017 00:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:28:29: #1 finished! INFO @ Sun, 04 Jun 2017 00:28:29: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:28:32: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:28:32: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:28:32: #1 total tags in treatment: 15737414 INFO @ Sun, 04 Jun 2017 00:28:32: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:28:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:28:32: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:28:32: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:28:32: #1 total tags in treatment: 15737414 INFO @ Sun, 04 Jun 2017 00:28:32: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:28:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:28:32: #2 number of paired peaks: 247 WARNING @ Sun, 04 Jun 2017 00:28:32: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Sun, 04 Jun 2017 00:28:32: start model_add_line... INFO @ Sun, 04 Jun 2017 00:28:34: start X-correlation... INFO @ Sun, 04 Jun 2017 00:28:34: end of X-cor INFO @ Sun, 04 Jun 2017 00:28:34: #2 finished! INFO @ Sun, 04 Jun 2017 00:28:34: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 00:28:34: #2 alternative fragment length(s) may be 46 bps INFO @ Sun, 04 Jun 2017 00:28:34: #2.2 Generate R script for model : SRX969927.10_model.r WARNING @ Sun, 04 Jun 2017 00:28:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:28:34: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sun, 04 Jun 2017 00:28:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:28:34: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:28:35: #1 tags after filtering in treatment: 15733790 INFO @ Sun, 04 Jun 2017 00:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:28:35: #1 finished! INFO @ Sun, 04 Jun 2017 00:28:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:28:35: #1 tags after filtering in treatment: 15733790 INFO @ Sun, 04 Jun 2017 00:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:28:35: #1 finished! INFO @ Sun, 04 Jun 2017 00:28:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:28:37: #2 number of paired peaks: 247 WARNING @ Sun, 04 Jun 2017 00:28:37: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Sun, 04 Jun 2017 00:28:37: start model_add_line... INFO @ Sun, 04 Jun 2017 00:28:37: #2 number of paired peaks: 247 WARNING @ Sun, 04 Jun 2017 00:28:37: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Sun, 04 Jun 2017 00:28:37: start model_add_line... INFO @ Sun, 04 Jun 2017 00:28:39: start X-correlation... INFO @ Sun, 04 Jun 2017 00:28:39: end of X-cor INFO @ Sun, 04 Jun 2017 00:28:39: #2 finished! INFO @ Sun, 04 Jun 2017 00:28:39: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 00:28:39: #2 alternative fragment length(s) may be 46 bps INFO @ Sun, 04 Jun 2017 00:28:39: #2.2 Generate R script for model : SRX969927.05_model.r WARNING @ Sun, 04 Jun 2017 00:28:39: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:28:39: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sun, 04 Jun 2017 00:28:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:28:39: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:28:39: start X-correlation... INFO @ Sun, 04 Jun 2017 00:28:39: end of X-cor INFO @ Sun, 04 Jun 2017 00:28:39: #2 finished! INFO @ Sun, 04 Jun 2017 00:28:39: #2 predicted fragment length is 46 bps INFO @ Sun, 04 Jun 2017 00:28:39: #2 alternative fragment length(s) may be 46 bps INFO @ Sun, 04 Jun 2017 00:28:39: #2.2 Generate R script for model : SRX969927.20_model.r WARNING @ Sun, 04 Jun 2017 00:28:39: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:28:39: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sun, 04 Jun 2017 00:28:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:28:39: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:56: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:30:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:30:06: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:30:54: #4 Write output xls file... SRX969927.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:30:54: #4 Write peak in narrowPeak format file... SRX969927.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:30:54: #4 Write summits bed file... SRX969927.10_summits.bed INFO @ Sun, 04 Jun 2017 00:30:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:03: #4 Write output xls file... SRX969927.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:03: #4 Write peak in narrowPeak format file... SRX969927.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:03: #4 Write summits bed file... SRX969927.05_summits.bed INFO @ Sun, 04 Jun 2017 00:31:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1583 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:09: #4 Write output xls file... SRX969927.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:09: #4 Write peak in narrowPeak format file... SRX969927.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:09: #4 Write summits bed file... SRX969927.20_summits.bed INFO @ Sun, 04 Jun 2017 00:31:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1063 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。