Job ID = 9029216 sra ファイルのダウンロード中... Completed: 454785K bytes transferred in 9 seconds (399218K 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 --:--:-- 0:00:07 --:--:-- 0 101 5455 0 5455 0 0 716 0 --:--:-- 0:00:07 --:--:-- 4603 100 31694 0 31694 0 0 3682 0 --:--:-- 0:00:08 --:--:-- 14531 100 53835 0 53835 0 0 6022 0 --:--:-- 0:00:08 --:--:-- 21414 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 21493747 spots for /home/okishinya/chipatlas/results/dm3/SRX1433356/SRR2919821.sra Written 21493747 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: 00:09:21 21493747 reads; of these: 21493747 (100.00%) were unpaired; of these: 481902 (2.24%) aligned 0 times 16067995 (74.76%) aligned exactly 1 time 4943850 (23.00%) aligned >1 times 97.76% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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] 2976914 / 21011845 = 0.1417 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 13:07:26: # Command line: callpeak -t SRX1433356.bam -f BAM -g dm -n SRX1433356.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433356.20 # format = BAM # ChIP-seq file = ['SRX1433356.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 13:07:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:26: # Command line: callpeak -t SRX1433356.bam -f BAM -g dm -n SRX1433356.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433356.05 # format = BAM # ChIP-seq file = ['SRX1433356.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 13:07:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:26: # Command line: callpeak -t SRX1433356.bam -f BAM -g dm -n SRX1433356.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433356.10 # format = BAM # ChIP-seq file = ['SRX1433356.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 13:07:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:32: 1000000 INFO @ Sat, 03 Jun 2017 13:07:33: 1000000 INFO @ Sat, 03 Jun 2017 13:07:33: 1000000 INFO @ Sat, 03 Jun 2017 13:07:38: 2000000 INFO @ Sat, 03 Jun 2017 13:07:39: 2000000 INFO @ Sat, 03 Jun 2017 13:07:40: 2000000 INFO @ Sat, 03 Jun 2017 13:07:43: 3000000 INFO @ Sat, 03 Jun 2017 13:07:46: 3000000 INFO @ Sat, 03 Jun 2017 13:07:48: 3000000 INFO @ Sat, 03 Jun 2017 13:07:49: 4000000 INFO @ Sat, 03 Jun 2017 13:07:53: 4000000 INFO @ Sat, 03 Jun 2017 13:07:55: 5000000 INFO @ Sat, 03 Jun 2017 13:07:55: 4000000 INFO @ Sat, 03 Jun 2017 13:08:00: 5000000 INFO @ Sat, 03 Jun 2017 13:08:01: 6000000 INFO @ Sat, 03 Jun 2017 13:08:02: 5000000 INFO @ Sat, 03 Jun 2017 13:08:07: 7000000 INFO @ Sat, 03 Jun 2017 13:08:07: 6000000 INFO @ Sat, 03 Jun 2017 13:08:10: 6000000 INFO @ Sat, 03 Jun 2017 13:08:12: 8000000 INFO @ Sat, 03 Jun 2017 13:08:13: 7000000 INFO @ Sat, 03 Jun 2017 13:08:17: 7000000 INFO @ Sat, 03 Jun 2017 13:08:18: 9000000 INFO @ Sat, 03 Jun 2017 13:08:20: 8000000 INFO @ Sat, 03 Jun 2017 13:08:24: 10000000 INFO @ Sat, 03 Jun 2017 13:08:25: 8000000 INFO @ Sat, 03 Jun 2017 13:08:27: 9000000 INFO @ Sat, 03 Jun 2017 13:08:29: 11000000 INFO @ Sat, 03 Jun 2017 13:08:32: 9000000 INFO @ Sat, 03 Jun 2017 13:08:34: 10000000 INFO @ Sat, 03 Jun 2017 13:08:35: 12000000 INFO @ Sat, 03 Jun 2017 13:08:39: 10000000 INFO @ Sat, 03 Jun 2017 13:08:41: 11000000 INFO @ Sat, 03 Jun 2017 13:08:41: 13000000 INFO @ Sat, 03 Jun 2017 13:08:47: 11000000 INFO @ Sat, 03 Jun 2017 13:08:47: 14000000 INFO @ Sat, 03 Jun 2017 13:08:47: 12000000 INFO @ Sat, 03 Jun 2017 13:08:53: 15000000 INFO @ Sat, 03 Jun 2017 13:08:54: 12000000 INFO @ Sat, 03 Jun 2017 13:08:54: 13000000 INFO @ Sat, 03 Jun 2017 13:08:58: 16000000 INFO @ Sat, 03 Jun 2017 13:09:01: 14000000 INFO @ Sat, 03 Jun 2017 13:09:01: 13000000 INFO @ Sat, 03 Jun 2017 13:09:04: 17000000 INFO @ Sat, 03 Jun 2017 13:09:09: 15000000 INFO @ Sat, 03 Jun 2017 13:09:10: 14000000 INFO @ Sat, 03 Jun 2017 13:09:12: 18000000 INFO @ Sat, 03 Jun 2017 13:09:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:13: #1 total tags in treatment: 18034931 INFO @ Sat, 03 Jun 2017 13:09:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:13: #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 13:09:16: #1 tags after filtering in treatment: 18030613 INFO @ Sat, 03 Jun 2017 13:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:16: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:17: 16000000 INFO @ Sat, 03 Jun 2017 13:09:19: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 13:09:19: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:19: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:20: 15000000 INFO @ Sat, 03 Jun 2017 13:09:22: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:22: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:22: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:22: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:09:22: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:09:22: #2.2 Generate R script for model : SRX1433356.10_model.r WARNING @ Sat, 03 Jun 2017 13:09:22: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:22: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:09:22: #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 13:09:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:25: 17000000 INFO @ Sat, 03 Jun 2017 13:09:29: 16000000 INFO @ Sat, 03 Jun 2017 13:09:33: 18000000 INFO @ Sat, 03 Jun 2017 13:09:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:34: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:34: #1 total tags in treatment: 18034931 INFO @ Sat, 03 Jun 2017 13:09:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:34: #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 13:09:38: #1 tags after filtering in treatment: 18030613 INFO @ Sat, 03 Jun 2017 13:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:38: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:38: 17000000 INFO @ Sat, 03 Jun 2017 13:09:41: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 13:09:41: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:41: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:44: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:44: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:44: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:44: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:09:44: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:09:44: #2.2 Generate R script for model : SRX1433356.05_model.r WARNING @ Sat, 03 Jun 2017 13:09:44: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:44: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:09:44: #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 13:09:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:47: 18000000 INFO @ Sat, 03 Jun 2017 13:09:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:48: #1 total tags in treatment: 18034931 INFO @ Sat, 03 Jun 2017 13:09:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:48: #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 13:09:51: #1 tags after filtering in treatment: 18030613 INFO @ Sat, 03 Jun 2017 13:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:54: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 13:09:54: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:54: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:57: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:57: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:57: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:57: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 13:09:57: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Jun 2017 13:09:57: #2.2 Generate R script for model : SRX1433356.20_model.r WARNING @ Sat, 03 Jun 2017 13:09:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:57: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Jun 2017 13:09:57: #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 13:09:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:10:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:02: #4 Write output xls file... SRX1433356.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:02: #4 Write peak in narrowPeak format file... SRX1433356.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:02: #4 Write summits bed file... SRX1433356.10_summits.bed INFO @ Sat, 03 Jun 2017 13:12:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write output xls file... SRX1433356.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write peak in narrowPeak format file... SRX1433356.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:29: #4 Write summits bed file... SRX1433356.05_summits.bed INFO @ Sat, 03 Jun 2017 13:12:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1862 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:49: #4 Write output xls file... SRX1433356.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:49: #4 Write peak in narrowPeak format file... SRX1433356.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:50: #4 Write summits bed file... SRX1433356.20_summits.bed INFO @ Sat, 03 Jun 2017 13:12:50: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (910 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。