Job ID = 9029786 sra ファイルのダウンロード中... Completed: 1259594K bytes transferred in 17 seconds (602496K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 21558 0 21558 0 0 2760 0 --:--:-- 0:00:07 --:--:-- 15464 100 31057 0 31057 0 0 3739 0 --:--:-- 0:00:08 --:--:-- 16423 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 25880670 spots for /home/okishinya/chipatlas/results/dm3/SRX2055966/SRR4069198.sra Written 25880670 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: 00:13:16 25880670 reads; of these: 25880670 (100.00%) were unpaired; of these: 1081955 (4.18%) aligned 0 times 15442897 (59.67%) aligned exactly 1 time 9355818 (36.15%) aligned >1 times 95.82% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 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] 3917913 / 24798715 = 0.1580 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 15:32:38: # Command line: callpeak -t SRX2055966.bam -f BAM -g dm -n SRX2055966.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055966.10 # format = BAM # ChIP-seq file = ['SRX2055966.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 15:32:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:32:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:32:38: # Command line: callpeak -t SRX2055966.bam -f BAM -g dm -n SRX2055966.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055966.20 # format = BAM # ChIP-seq file = ['SRX2055966.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 15:32:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:32:38: # Command line: callpeak -t SRX2055966.bam -f BAM -g dm -n SRX2055966.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055966.05 # format = BAM # ChIP-seq file = ['SRX2055966.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 15:32:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:32:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:32:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:32:45: 1000000 INFO @ Sat, 03 Jun 2017 15:32:45: 1000000 INFO @ Sat, 03 Jun 2017 15:32:45: 1000000 INFO @ Sat, 03 Jun 2017 15:32:51: 2000000 INFO @ Sat, 03 Jun 2017 15:32:51: 2000000 INFO @ Sat, 03 Jun 2017 15:32:51: 2000000 INFO @ Sat, 03 Jun 2017 15:32:58: 3000000 INFO @ Sat, 03 Jun 2017 15:32:58: 3000000 INFO @ Sat, 03 Jun 2017 15:32:58: 3000000 INFO @ Sat, 03 Jun 2017 15:33:06: 4000000 INFO @ Sat, 03 Jun 2017 15:33:06: 4000000 INFO @ Sat, 03 Jun 2017 15:33:06: 4000000 INFO @ Sat, 03 Jun 2017 15:33:13: 5000000 INFO @ Sat, 03 Jun 2017 15:33:13: 5000000 INFO @ Sat, 03 Jun 2017 15:33:13: 5000000 INFO @ Sat, 03 Jun 2017 15:33:19: 6000000 INFO @ Sat, 03 Jun 2017 15:33:19: 6000000 INFO @ Sat, 03 Jun 2017 15:33:20: 6000000 INFO @ Sat, 03 Jun 2017 15:33:26: 7000000 INFO @ Sat, 03 Jun 2017 15:33:26: 7000000 INFO @ Sat, 03 Jun 2017 15:33:26: 7000000 INFO @ Sat, 03 Jun 2017 15:33:33: 8000000 INFO @ Sat, 03 Jun 2017 15:33:33: 8000000 INFO @ Sat, 03 Jun 2017 15:33:33: 8000000 INFO @ Sat, 03 Jun 2017 15:33:39: 9000000 INFO @ Sat, 03 Jun 2017 15:33:39: 9000000 INFO @ Sat, 03 Jun 2017 15:33:40: 9000000 INFO @ Sat, 03 Jun 2017 15:33:45: 10000000 INFO @ Sat, 03 Jun 2017 15:33:46: 10000000 INFO @ Sat, 03 Jun 2017 15:33:46: 10000000 INFO @ Sat, 03 Jun 2017 15:33:52: 11000000 INFO @ Sat, 03 Jun 2017 15:33:52: 11000000 INFO @ Sat, 03 Jun 2017 15:33:53: 11000000 INFO @ Sat, 03 Jun 2017 15:33:59: 12000000 INFO @ Sat, 03 Jun 2017 15:34:00: 12000000 INFO @ Sat, 03 Jun 2017 15:34:01: 12000000 INFO @ Sat, 03 Jun 2017 15:34:07: 13000000 INFO @ Sat, 03 Jun 2017 15:34:07: 13000000 INFO @ Sat, 03 Jun 2017 15:34:08: 13000000 INFO @ Sat, 03 Jun 2017 15:34:14: 14000000 INFO @ Sat, 03 Jun 2017 15:34:15: 14000000 INFO @ Sat, 03 Jun 2017 15:34:16: 14000000 INFO @ Sat, 03 Jun 2017 15:34:22: 15000000 INFO @ Sat, 03 Jun 2017 15:34:22: 15000000 INFO @ Sat, 03 Jun 2017 15:34:24: 15000000 INFO @ Sat, 03 Jun 2017 15:34:29: 16000000 INFO @ Sat, 03 Jun 2017 15:34:30: 16000000 INFO @ Sat, 03 Jun 2017 15:34:31: 16000000 INFO @ Sat, 03 Jun 2017 15:34:37: 17000000 INFO @ Sat, 03 Jun 2017 15:34:37: 17000000 INFO @ Sat, 03 Jun 2017 15:34:39: 17000000 INFO @ Sat, 03 Jun 2017 15:34:43: 18000000 INFO @ Sat, 03 Jun 2017 15:34:44: 18000000 INFO @ Sat, 03 Jun 2017 15:34:46: 18000000 INFO @ Sat, 03 Jun 2017 15:34:50: 19000000 INFO @ Sat, 03 Jun 2017 15:34:51: 19000000 INFO @ Sat, 03 Jun 2017 15:34:53: 19000000 INFO @ Sat, 03 Jun 2017 15:34:57: 20000000 INFO @ Sat, 03 Jun 2017 15:34:58: 20000000 INFO @ Sat, 03 Jun 2017 15:35:00: 20000000 INFO @ Sat, 03 Jun 2017 15:35:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:35:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:35:03: #1 total tags in treatment: 20880802 INFO @ Sat, 03 Jun 2017 15:35:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:35:03: #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 15:35:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:35:04: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:35:04: #1 total tags in treatment: 20880802 INFO @ Sat, 03 Jun 2017 15:35:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:35:04: #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 15:35:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:35:06: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:35:06: #1 total tags in treatment: 20880802 INFO @ Sat, 03 Jun 2017 15:35:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:35:06: #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 15:35:07: #1 tags after filtering in treatment: 20875732 INFO @ Sat, 03 Jun 2017 15:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:35:07: #1 finished! INFO @ Sat, 03 Jun 2017 15:35:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:35:09: #1 tags after filtering in treatment: 20875732 INFO @ Sat, 03 Jun 2017 15:35:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:35:09: #1 finished! INFO @ Sat, 03 Jun 2017 15:35:09: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:35:10: #2 number of paired peaks: 662 WARNING @ Sat, 03 Jun 2017 15:35:10: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 03 Jun 2017 15:35:10: start model_add_line... INFO @ Sat, 03 Jun 2017 15:35:11: #1 tags after filtering in treatment: 20875732 INFO @ Sat, 03 Jun 2017 15:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:35:11: #1 finished! INFO @ Sat, 03 Jun 2017 15:35:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:35:13: #2 number of paired peaks: 662 WARNING @ Sat, 03 Jun 2017 15:35:13: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 03 Jun 2017 15:35:13: start model_add_line... INFO @ Sat, 03 Jun 2017 15:35:15: #2 number of paired peaks: 662 WARNING @ Sat, 03 Jun 2017 15:35:15: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 03 Jun 2017 15:35:15: start model_add_line... INFO @ Sat, 03 Jun 2017 15:35:19: start X-correlation... INFO @ Sat, 03 Jun 2017 15:35:19: end of X-cor INFO @ Sat, 03 Jun 2017 15:35:19: #2 finished! INFO @ Sat, 03 Jun 2017 15:35:19: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:35:19: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:35:19: #2.2 Generate R script for model : SRX2055966.20_model.r WARNING @ Sat, 03 Jun 2017 15:35:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:35:19: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:35:19: #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 15:35:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:35:22: start X-correlation... INFO @ Sat, 03 Jun 2017 15:35:22: end of X-cor INFO @ Sat, 03 Jun 2017 15:35:22: #2 finished! INFO @ Sat, 03 Jun 2017 15:35:22: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:35:22: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:35:22: #2.2 Generate R script for model : SRX2055966.05_model.r WARNING @ Sat, 03 Jun 2017 15:35:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:35:22: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:35:22: #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 15:35:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:35:24: start X-correlation... INFO @ Sat, 03 Jun 2017 15:35:24: end of X-cor INFO @ Sat, 03 Jun 2017 15:35:24: #2 finished! INFO @ Sat, 03 Jun 2017 15:35:24: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Jun 2017 15:35:24: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sat, 03 Jun 2017 15:35:24: #2.2 Generate R script for model : SRX2055966.10_model.r WARNING @ Sat, 03 Jun 2017 15:35:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:35:24: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sat, 03 Jun 2017 15:35:24: #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 15:35:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:35:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:36:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:37:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:37:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:38:13: #4 Write output xls file... SRX2055966.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:38:13: #4 Write peak in narrowPeak format file... SRX2055966.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:38:13: #4 Write summits bed file... SRX2055966.20_summits.bed INFO @ Sat, 03 Jun 2017 15:38:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1521 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:38:22: #4 Write output xls file... SRX2055966.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:38:22: #4 Write peak in narrowPeak format file... SRX2055966.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:38:22: #4 Write summits bed file... SRX2055966.05_summits.bed INFO @ Sat, 03 Jun 2017 15:38:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4371 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:38:26: #4 Write output xls file... SRX2055966.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:38:26: #4 Write peak in narrowPeak format file... SRX2055966.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:38:26: #4 Write summits bed file... SRX2055966.10_summits.bed INFO @ Sat, 03 Jun 2017 15:38:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2938 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。