Job ID = 10194912 sra ファイルのダウンロード中... Completed: 141933K bytes transferred in 8 seconds (131478K bits/sec), in 1 file. Completed: 138647K bytes transferred in 8 seconds (137700K bits/sec), in 1 file. Completed: 234567K bytes transferred in 12 seconds (149281K bits/sec), in 1 file. Completed: 230214K bytes transferred in 16 seconds (115507K bits/sec), in 1 file. Completed: 231333K bytes transferred in 16 seconds (117415K bits/sec), in 1 file. Completed: 227631K bytes transferred in 12 seconds (144994K bits/sec), in 1 file. 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 3255970 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319987.sra Written 3255970 spots total Written 3348292 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319986.sra Written 3348292 spots total Written 4984653 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319991.sra Written 4984653 spots total Written 4998890 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319989.sra Written 4998890 spots total Written 5128713 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319988.sra Written 5128713 spots total Written 5058826 spots for /home/okishinya/chipatlas/results/rn6/SRX2202907/SRR4319990.sra Written 5058826 spots total rm: cannot remove `[DSE]RX*': 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:53:52 26775344 reads; of these: 26775344 (100.00%) were unpaired; of these: 790184 (2.95%) aligned 0 times 17917078 (66.92%) aligned exactly 1 time 8068082 (30.13%) aligned >1 times 97.05% overall alignment rate Time searching: 00:53:56 Overall time: 00:53:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3012424 / 25985160 = 0.1159 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 @ Fri, 10 Nov 2017 23:28:18: # Command line: callpeak -t SRX2202907.bam -f BAM -g 2.15e9 -n SRX2202907.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202907.20 # format = BAM # ChIP-seq file = ['SRX2202907.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:28:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:28:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:28:18: # Command line: callpeak -t SRX2202907.bam -f BAM -g 2.15e9 -n SRX2202907.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202907.05 # format = BAM # ChIP-seq file = ['SRX2202907.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:28:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:28:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:28:18: # Command line: callpeak -t SRX2202907.bam -f BAM -g 2.15e9 -n SRX2202907.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202907.10 # format = BAM # ChIP-seq file = ['SRX2202907.bam'] # control file = None # effective genome size = 2.15e+09 # 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 # Paired-End mode is off INFO @ Fri, 10 Nov 2017 23:28:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:28:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:28:31: 1000000 INFO @ Fri, 10 Nov 2017 23:28:32: 1000000 INFO @ Fri, 10 Nov 2017 23:28:38: 1000000 INFO @ Fri, 10 Nov 2017 23:28:43: 2000000 INFO @ Fri, 10 Nov 2017 23:28:48: 2000000 INFO @ Fri, 10 Nov 2017 23:28:55: 3000000 INFO @ Fri, 10 Nov 2017 23:28:58: 2000000 INFO @ Fri, 10 Nov 2017 23:29:07: 3000000 INFO @ Fri, 10 Nov 2017 23:29:07: 4000000 INFO @ Fri, 10 Nov 2017 23:29:18: 3000000 INFO @ Fri, 10 Nov 2017 23:29:18: 5000000 INFO @ Fri, 10 Nov 2017 23:29:26: 4000000 INFO @ Fri, 10 Nov 2017 23:29:30: 6000000 INFO @ Fri, 10 Nov 2017 23:29:37: 4000000 INFO @ Fri, 10 Nov 2017 23:29:41: 7000000 INFO @ Fri, 10 Nov 2017 23:29:45: 5000000 INFO @ Fri, 10 Nov 2017 23:29:51: 5000000 INFO @ Fri, 10 Nov 2017 23:29:53: 8000000 INFO @ Fri, 10 Nov 2017 23:30:03: 6000000 INFO @ Fri, 10 Nov 2017 23:30:04: 6000000 INFO @ Fri, 10 Nov 2017 23:30:07: 9000000 INFO @ Fri, 10 Nov 2017 23:30:17: 7000000 INFO @ Fri, 10 Nov 2017 23:30:21: 10000000 INFO @ Fri, 10 Nov 2017 23:30:21: 7000000 INFO @ Fri, 10 Nov 2017 23:30:32: 8000000 INFO @ Fri, 10 Nov 2017 23:30:35: 11000000 INFO @ Fri, 10 Nov 2017 23:30:40: 8000000 INFO @ Fri, 10 Nov 2017 23:30:48: 9000000 INFO @ Fri, 10 Nov 2017 23:30:49: 12000000 INFO @ Fri, 10 Nov 2017 23:30:57: 9000000 INFO @ Fri, 10 Nov 2017 23:31:03: 13000000 INFO @ Fri, 10 Nov 2017 23:31:04: 10000000 INFO @ Fri, 10 Nov 2017 23:31:15: 10000000 INFO @ Fri, 10 Nov 2017 23:31:18: 14000000 INFO @ Fri, 10 Nov 2017 23:31:20: 11000000 INFO @ Fri, 10 Nov 2017 23:31:32: 11000000 INFO @ Fri, 10 Nov 2017 23:31:33: 15000000 INFO @ Fri, 10 Nov 2017 23:31:36: 12000000 INFO @ Fri, 10 Nov 2017 23:31:51: 12000000 INFO @ Fri, 10 Nov 2017 23:31:52: 16000000 INFO @ Fri, 10 Nov 2017 23:31:52: 13000000 INFO @ Fri, 10 Nov 2017 23:32:07: 14000000 INFO @ Fri, 10 Nov 2017 23:32:10: 13000000 INFO @ Fri, 10 Nov 2017 23:32:12: 17000000 INFO @ Fri, 10 Nov 2017 23:32:23: 15000000 INFO @ Fri, 10 Nov 2017 23:32:29: 14000000 INFO @ Fri, 10 Nov 2017 23:32:32: 18000000 INFO @ Fri, 10 Nov 2017 23:32:39: 16000000 INFO @ Fri, 10 Nov 2017 23:32:47: 15000000 INFO @ Fri, 10 Nov 2017 23:32:53: 19000000 INFO @ Fri, 10 Nov 2017 23:32:55: 17000000 INFO @ Fri, 10 Nov 2017 23:33:06: 16000000 INFO @ Fri, 10 Nov 2017 23:33:10: 18000000 INFO @ Fri, 10 Nov 2017 23:33:13: 20000000 INFO @ Fri, 10 Nov 2017 23:33:24: 17000000 INFO @ Fri, 10 Nov 2017 23:33:25: 19000000 INFO @ Fri, 10 Nov 2017 23:33:34: 21000000 INFO @ Fri, 10 Nov 2017 23:33:40: 20000000 INFO @ Fri, 10 Nov 2017 23:33:42: 18000000 INFO @ Fri, 10 Nov 2017 23:33:52: 22000000 INFO @ Fri, 10 Nov 2017 23:33:53: 21000000 INFO @ Fri, 10 Nov 2017 23:34:00: 19000000 INFO @ Fri, 10 Nov 2017 23:34:06: 22000000 INFO @ Fri, 10 Nov 2017 23:34:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:34:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:34:06: #1 total tags in treatment: 22972736 INFO @ Fri, 10 Nov 2017 23:34:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:34:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:34:07: #1 tags after filtering in treatment: 22972622 INFO @ Fri, 10 Nov 2017 23:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:34:07: #1 finished! INFO @ Fri, 10 Nov 2017 23:34:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:34:11: #2 number of paired peaks: 15338 INFO @ Fri, 10 Nov 2017 23:34:11: start model_add_line... INFO @ Fri, 10 Nov 2017 23:34:11: start X-correlation... INFO @ Fri, 10 Nov 2017 23:34:11: end of X-cor INFO @ Fri, 10 Nov 2017 23:34:11: #2 finished! INFO @ Fri, 10 Nov 2017 23:34:11: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Nov 2017 23:34:11: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Nov 2017 23:34:11: #2.2 Generate R script for model : SRX2202907.05_model.r WARNING @ Fri, 10 Nov 2017 23:34:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:34:11: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Nov 2017 23:34:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:34:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:34:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:34:16: 20000000 INFO @ Fri, 10 Nov 2017 23:34:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:34:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:34:18: #1 total tags in treatment: 22972736 INFO @ Fri, 10 Nov 2017 23:34:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:34:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:34:19: #1 tags after filtering in treatment: 22972622 INFO @ Fri, 10 Nov 2017 23:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:34:19: #1 finished! INFO @ Fri, 10 Nov 2017 23:34:19: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:34:22: #2 number of paired peaks: 15338 INFO @ Fri, 10 Nov 2017 23:34:22: start model_add_line... INFO @ Fri, 10 Nov 2017 23:34:23: start X-correlation... INFO @ Fri, 10 Nov 2017 23:34:23: end of X-cor INFO @ Fri, 10 Nov 2017 23:34:23: #2 finished! INFO @ Fri, 10 Nov 2017 23:34:23: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Nov 2017 23:34:23: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Nov 2017 23:34:23: #2.2 Generate R script for model : SRX2202907.10_model.r WARNING @ Fri, 10 Nov 2017 23:34:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:34:23: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Nov 2017 23:34:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:34:23: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:34:33: 21000000 INFO @ Fri, 10 Nov 2017 23:34:50: 22000000 INFO @ Fri, 10 Nov 2017 23:35:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:35:07: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:35:07: #1 total tags in treatment: 22972736 INFO @ Fri, 10 Nov 2017 23:35:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:35:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:35:08: #1 tags after filtering in treatment: 22972622 INFO @ Fri, 10 Nov 2017 23:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:35:08: #1 finished! INFO @ Fri, 10 Nov 2017 23:35:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:35:11: #2 number of paired peaks: 15338 INFO @ Fri, 10 Nov 2017 23:35:11: start model_add_line... INFO @ Fri, 10 Nov 2017 23:35:11: start X-correlation... INFO @ Fri, 10 Nov 2017 23:35:11: end of X-cor INFO @ Fri, 10 Nov 2017 23:35:11: #2 finished! INFO @ Fri, 10 Nov 2017 23:35:11: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Nov 2017 23:35:11: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Nov 2017 23:35:11: #2.2 Generate R script for model : SRX2202907.20_model.r WARNING @ Fri, 10 Nov 2017 23:35:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:35:11: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Nov 2017 23:35:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:35:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:35:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:35:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:36:05: #4 Write output xls file... SRX2202907.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:36:05: #4 Write peak in narrowPeak format file... SRX2202907.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:36:05: #4 Write summits bed file... SRX2202907.05_summits.bed INFO @ Fri, 10 Nov 2017 23:36:05: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (2175 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:36:18: #4 Write output xls file... SRX2202907.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:36:18: #4 Write peak in narrowPeak format file... SRX2202907.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:36:18: #4 Write summits bed file... SRX2202907.10_summits.bed INFO @ Fri, 10 Nov 2017 23:36:18: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1135 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:36:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:37:08: #4 Write output xls file... SRX2202907.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:37:08: #4 Write peak in narrowPeak format file... SRX2202907.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:37:08: #4 Write summits bed file... SRX2202907.20_summits.bed INFO @ Fri, 10 Nov 2017 23:37:08: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (590 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。