Job ID = 9029783 sra ファイルのダウンロード中... Completed: 1213964K bytes transferred in 14 seconds (675315K 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 14324 0 14324 0 0 1930 0 --:--:-- 0:00:07 --:--:-- 14352 100 31058 0 31058 0 0 3921 0 --:--:-- 0:00:07 --:--:-- 20760 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 24910232 spots for /home/okishinya/chipatlas/results/dm3/SRX2055964/SRR4069196.sra Written 24910232 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: 00:12:40 24910232 reads; of these: 24910232 (100.00%) were unpaired; of these: 1038241 (4.17%) aligned 0 times 14863242 (59.67%) aligned exactly 1 time 9008749 (36.16%) aligned >1 times 95.83% overall alignment rate Time searching: 00:12:40 Overall time: 00:12:40 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] 3573314 / 23871991 = 0.1497 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 15:31:31: # Command line: callpeak -t SRX2055964.bam -f BAM -g dm -n SRX2055964.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055964.20 # format = BAM # ChIP-seq file = ['SRX2055964.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 15:31:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:31: # Command line: callpeak -t SRX2055964.bam -f BAM -g dm -n SRX2055964.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055964.05 # format = BAM # ChIP-seq file = ['SRX2055964.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 15:31:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:31: # Command line: callpeak -t SRX2055964.bam -f BAM -g dm -n SRX2055964.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055964.10 # format = BAM # ChIP-seq file = ['SRX2055964.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 15:31:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:31:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:31:39: 1000000 INFO @ Sat, 03 Jun 2017 15:31:39: 1000000 INFO @ Sat, 03 Jun 2017 15:31:40: 1000000 INFO @ Sat, 03 Jun 2017 15:31:46: 2000000 INFO @ Sat, 03 Jun 2017 15:31:46: 2000000 INFO @ Sat, 03 Jun 2017 15:31:49: 2000000 INFO @ Sat, 03 Jun 2017 15:31:53: 3000000 INFO @ Sat, 03 Jun 2017 15:31:53: 3000000 INFO @ Sat, 03 Jun 2017 15:31:57: 3000000 INFO @ Sat, 03 Jun 2017 15:32:01: 4000000 INFO @ Sat, 03 Jun 2017 15:32:01: 4000000 INFO @ Sat, 03 Jun 2017 15:32:06: 4000000 INFO @ Sat, 03 Jun 2017 15:32:08: 5000000 INFO @ Sat, 03 Jun 2017 15:32:08: 5000000 INFO @ Sat, 03 Jun 2017 15:32:15: 5000000 INFO @ Sat, 03 Jun 2017 15:32:15: 6000000 INFO @ Sat, 03 Jun 2017 15:32:15: 6000000 INFO @ Sat, 03 Jun 2017 15:32:23: 7000000 INFO @ Sat, 03 Jun 2017 15:32:23: 7000000 INFO @ Sat, 03 Jun 2017 15:32:24: 6000000 INFO @ Sat, 03 Jun 2017 15:32:30: 8000000 INFO @ Sat, 03 Jun 2017 15:32:31: 8000000 INFO @ Sat, 03 Jun 2017 15:32:33: 7000000 INFO @ Sat, 03 Jun 2017 15:32:38: 9000000 INFO @ Sat, 03 Jun 2017 15:32:39: 9000000 INFO @ Sat, 03 Jun 2017 15:32:42: 8000000 INFO @ Sat, 03 Jun 2017 15:32:46: 10000000 INFO @ Sat, 03 Jun 2017 15:32:47: 10000000 INFO @ Sat, 03 Jun 2017 15:32:51: 9000000 INFO @ Sat, 03 Jun 2017 15:32:53: 11000000 INFO @ Sat, 03 Jun 2017 15:32:55: 11000000 INFO @ Sat, 03 Jun 2017 15:33:00: 10000000 INFO @ Sat, 03 Jun 2017 15:33:01: 12000000 INFO @ Sat, 03 Jun 2017 15:33:03: 12000000 INFO @ Sat, 03 Jun 2017 15:33:08: 13000000 INFO @ Sat, 03 Jun 2017 15:33:09: 11000000 INFO @ Sat, 03 Jun 2017 15:33:12: 13000000 INFO @ Sat, 03 Jun 2017 15:33:16: 14000000 INFO @ Sat, 03 Jun 2017 15:33:17: 12000000 INFO @ Sat, 03 Jun 2017 15:33:19: 14000000 INFO @ Sat, 03 Jun 2017 15:33:24: 15000000 INFO @ Sat, 03 Jun 2017 15:33:26: 13000000 INFO @ Sat, 03 Jun 2017 15:33:27: 15000000 INFO @ Sat, 03 Jun 2017 15:33:31: 16000000 INFO @ Sat, 03 Jun 2017 15:33:35: 16000000 INFO @ Sat, 03 Jun 2017 15:33:35: 14000000 INFO @ Sat, 03 Jun 2017 15:33:39: 17000000 INFO @ Sat, 03 Jun 2017 15:33:43: 17000000 INFO @ Sat, 03 Jun 2017 15:33:44: 15000000 INFO @ Sat, 03 Jun 2017 15:33:47: 18000000 INFO @ Sat, 03 Jun 2017 15:33:51: 18000000 INFO @ Sat, 03 Jun 2017 15:33:53: 16000000 INFO @ Sat, 03 Jun 2017 15:33:54: 19000000 INFO @ Sat, 03 Jun 2017 15:33:58: 19000000 INFO @ Sat, 03 Jun 2017 15:34:01: 17000000 INFO @ Sat, 03 Jun 2017 15:34:01: 20000000 INFO @ Sat, 03 Jun 2017 15:34:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:34:04: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:34:04: #1 total tags in treatment: 20298677 INFO @ Sat, 03 Jun 2017 15:34:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:34:04: #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 15:34:05: 20000000 INFO @ Sat, 03 Jun 2017 15:34:07: #1 tags after filtering in treatment: 20293816 INFO @ Sat, 03 Jun 2017 15:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:34:07: #1 finished! INFO @ Sat, 03 Jun 2017 15:34:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:34:07: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:34:07: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:34:07: #1 total tags in treatment: 20298677 INFO @ Sat, 03 Jun 2017 15:34:07: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:34:07: #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 15:34:08: 18000000 INFO @ Sat, 03 Jun 2017 15:34:11: #1 tags after filtering in treatment: 20293816 INFO @ Sat, 03 Jun 2017 15:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:34:11: #1 finished! INFO @ Sat, 03 Jun 2017 15:34:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:34:11: #2 number of paired peaks: 640 WARNING @ Sat, 03 Jun 2017 15:34:11: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 03 Jun 2017 15:34:11: start model_add_line... INFO @ Sat, 03 Jun 2017 15:34:14: #2 number of paired peaks: 640 WARNING @ Sat, 03 Jun 2017 15:34:14: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 03 Jun 2017 15:34:14: start model_add_line... INFO @ Sat, 03 Jun 2017 15:34:15: 19000000 INFO @ Sat, 03 Jun 2017 15:34:20: start X-correlation... INFO @ Sat, 03 Jun 2017 15:34:20: end of X-cor INFO @ Sat, 03 Jun 2017 15:34:20: #2 finished! INFO @ Sat, 03 Jun 2017 15:34:20: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:34:20: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:34:20: #2.2 Generate R script for model : SRX2055964.20_model.r WARNING @ Sat, 03 Jun 2017 15:34:20: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:34:20: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:34:20: #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 15:34:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:34:21: 20000000 INFO @ Sat, 03 Jun 2017 15:34:23: start X-correlation... INFO @ Sat, 03 Jun 2017 15:34:23: end of X-cor INFO @ Sat, 03 Jun 2017 15:34:23: #2 finished! INFO @ Sat, 03 Jun 2017 15:34:23: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:34:23: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:34:23: #2.2 Generate R script for model : SRX2055964.10_model.r WARNING @ Sat, 03 Jun 2017 15:34:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:34:23: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:34:23: #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 15:34:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:34:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:34:24: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:34:24: #1 total tags in treatment: 20298677 INFO @ Sat, 03 Jun 2017 15:34:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:34:24: #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 15:34:28: #1 tags after filtering in treatment: 20293816 INFO @ Sat, 03 Jun 2017 15:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:34:28: #1 finished! INFO @ Sat, 03 Jun 2017 15:34:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:34:32: #2 number of paired peaks: 640 WARNING @ Sat, 03 Jun 2017 15:34:32: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Sat, 03 Jun 2017 15:34:32: start model_add_line... INFO @ Sat, 03 Jun 2017 15:34:40: start X-correlation... INFO @ Sat, 03 Jun 2017 15:34:40: end of X-cor INFO @ Sat, 03 Jun 2017 15:34:40: #2 finished! INFO @ Sat, 03 Jun 2017 15:34:40: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 15:34:40: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 15:34:40: #2.2 Generate R script for model : SRX2055964.05_model.r WARNING @ Sat, 03 Jun 2017 15:34:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:34:40: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 15:34:40: #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 15:34:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:36:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:36:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:36:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:37:23: #4 Write output xls file... SRX2055964.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:37:23: #4 Write peak in narrowPeak format file... SRX2055964.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:37:23: #4 Write summits bed file... SRX2055964.10_summits.bed INFO @ Sat, 03 Jun 2017 15:37:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2998 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:37:25: #4 Write output xls file... SRX2055964.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:37:25: #4 Write peak in narrowPeak format file... SRX2055964.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:37:25: #4 Write summits bed file... SRX2055964.20_summits.bed INFO @ Sat, 03 Jun 2017 15:37:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1626 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:37:42: #4 Write output xls file... SRX2055964.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:37:42: #4 Write peak in narrowPeak format file... SRX2055964.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:37:42: #4 Write summits bed file... SRX2055964.05_summits.bed INFO @ Sat, 03 Jun 2017 15:37:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4445 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。