Job ID = 10320339 sra ファイルのダウンロード中... Completed: 734458K bytes transferred in 49 seconds (121460K 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 48394679 spots for /home/okishinya/chipatlas/results/dm3/SRX3166315/SRR6012933.sra Written 48394679 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 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: 00:20:30 48394679 reads; of these: 48394679 (100.00%) were unpaired; of these: 13292464 (27.47%) aligned 0 times 10727993 (22.17%) aligned exactly 1 time 24374222 (50.37%) aligned >1 times 72.53% overall alignment rate Time searching: 00:20:30 Overall time: 00:20:30 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 16 files... [bam_rmdupse_core] 10664109 / 35102215 = 0.3038 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 @ Thu, 11 Jan 2018 02:35:18: # Command line: callpeak -t SRX3166315.bam -f BAM -g dm -n SRX3166315.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3166315.05 # format = BAM # ChIP-seq file = ['SRX3166315.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 # Paired-End mode is off INFO @ Thu, 11 Jan 2018 02:35:18: # Command line: callpeak -t SRX3166315.bam -f BAM -g dm -n SRX3166315.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3166315.10 # format = BAM # ChIP-seq file = ['SRX3166315.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 # Paired-End mode is off INFO @ Thu, 11 Jan 2018 02:35:18: # Command line: callpeak -t SRX3166315.bam -f BAM -g dm -n SRX3166315.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3166315.20 # format = BAM # ChIP-seq file = ['SRX3166315.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 # Paired-End mode is off INFO @ Thu, 11 Jan 2018 02:35:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:35:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:35:18: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:35:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:35:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:35:18: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:35:24: 1000000 INFO @ Thu, 11 Jan 2018 02:35:25: 1000000 INFO @ Thu, 11 Jan 2018 02:35:25: 1000000 INFO @ Thu, 11 Jan 2018 02:35:30: 2000000 INFO @ Thu, 11 Jan 2018 02:35:31: 2000000 INFO @ Thu, 11 Jan 2018 02:35:31: 2000000 INFO @ Thu, 11 Jan 2018 02:35:36: 3000000 INFO @ Thu, 11 Jan 2018 02:35:38: 3000000 INFO @ Thu, 11 Jan 2018 02:35:38: 3000000 INFO @ Thu, 11 Jan 2018 02:35:42: 4000000 INFO @ Thu, 11 Jan 2018 02:35:45: 4000000 INFO @ Thu, 11 Jan 2018 02:35:45: 4000000 INFO @ Thu, 11 Jan 2018 02:35:48: 5000000 INFO @ Thu, 11 Jan 2018 02:35:52: 5000000 INFO @ Thu, 11 Jan 2018 02:35:52: 5000000 INFO @ Thu, 11 Jan 2018 02:35:54: 6000000 INFO @ Thu, 11 Jan 2018 02:35:58: 6000000 INFO @ Thu, 11 Jan 2018 02:35:59: 6000000 INFO @ Thu, 11 Jan 2018 02:36:00: 7000000 INFO @ Thu, 11 Jan 2018 02:36:05: 7000000 INFO @ Thu, 11 Jan 2018 02:36:06: 7000000 INFO @ Thu, 11 Jan 2018 02:36:06: 8000000 INFO @ Thu, 11 Jan 2018 02:36:12: 8000000 INFO @ Thu, 11 Jan 2018 02:36:12: 9000000 INFO @ Thu, 11 Jan 2018 02:36:12: 8000000 INFO @ Thu, 11 Jan 2018 02:36:19: 10000000 INFO @ Thu, 11 Jan 2018 02:36:19: 9000000 INFO @ Thu, 11 Jan 2018 02:36:19: 9000000 INFO @ Thu, 11 Jan 2018 02:36:25: 11000000 INFO @ Thu, 11 Jan 2018 02:36:26: 10000000 INFO @ Thu, 11 Jan 2018 02:36:27: 10000000 INFO @ Thu, 11 Jan 2018 02:36:31: 12000000 INFO @ Thu, 11 Jan 2018 02:36:32: 11000000 INFO @ Thu, 11 Jan 2018 02:36:33: 11000000 INFO @ Thu, 11 Jan 2018 02:36:37: 13000000 INFO @ Thu, 11 Jan 2018 02:36:39: 12000000 INFO @ Thu, 11 Jan 2018 02:36:40: 12000000 INFO @ Thu, 11 Jan 2018 02:36:43: 14000000 INFO @ Thu, 11 Jan 2018 02:36:46: 13000000 INFO @ Thu, 11 Jan 2018 02:36:48: 13000000 INFO @ Thu, 11 Jan 2018 02:36:49: 15000000 INFO @ Thu, 11 Jan 2018 02:36:53: 14000000 INFO @ Thu, 11 Jan 2018 02:36:55: 14000000 INFO @ Thu, 11 Jan 2018 02:36:55: 16000000 INFO @ Thu, 11 Jan 2018 02:37:00: 15000000 INFO @ Thu, 11 Jan 2018 02:37:01: 17000000 INFO @ Thu, 11 Jan 2018 02:37:02: 15000000 INFO @ Thu, 11 Jan 2018 02:37:07: 18000000 INFO @ Thu, 11 Jan 2018 02:37:07: 16000000 INFO @ Thu, 11 Jan 2018 02:37:09: 16000000 INFO @ Thu, 11 Jan 2018 02:37:13: 19000000 INFO @ Thu, 11 Jan 2018 02:37:14: 17000000 INFO @ Thu, 11 Jan 2018 02:37:16: 17000000 INFO @ Thu, 11 Jan 2018 02:37:19: 20000000 INFO @ Thu, 11 Jan 2018 02:37:21: 18000000 INFO @ Thu, 11 Jan 2018 02:37:23: 18000000 INFO @ Thu, 11 Jan 2018 02:37:25: 21000000 INFO @ Thu, 11 Jan 2018 02:37:28: 19000000 INFO @ Thu, 11 Jan 2018 02:37:30: 19000000 INFO @ Thu, 11 Jan 2018 02:37:31: 22000000 INFO @ Thu, 11 Jan 2018 02:37:35: 20000000 INFO @ Thu, 11 Jan 2018 02:37:37: 23000000 INFO @ Thu, 11 Jan 2018 02:37:37: 20000000 INFO @ Thu, 11 Jan 2018 02:37:42: 21000000 INFO @ Thu, 11 Jan 2018 02:37:43: 24000000 INFO @ Thu, 11 Jan 2018 02:37:45: 21000000 INFO @ Thu, 11 Jan 2018 02:37:46: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:37:46: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:37:46: #1 total tags in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:37:46: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:37:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:37:47: #1 tags after filtering in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:37:47: #1 finished! INFO @ Thu, 11 Jan 2018 02:37:47: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:37:48: 22000000 INFO @ Thu, 11 Jan 2018 02:37:49: #2 number of paired peaks: 1927 INFO @ Thu, 11 Jan 2018 02:37:49: start model_add_line... INFO @ Thu, 11 Jan 2018 02:37:49: start X-correlation... INFO @ Thu, 11 Jan 2018 02:37:49: end of X-cor INFO @ Thu, 11 Jan 2018 02:37:49: #2 finished! INFO @ Thu, 11 Jan 2018 02:37:49: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:37:49: #2 alternative fragment length(s) may be 2,56 bps INFO @ Thu, 11 Jan 2018 02:37:49: #2.2 Generate R script for model : SRX3166315.05_model.r WARNING @ Thu, 11 Jan 2018 02:37:49: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:37:49: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Thu, 11 Jan 2018 02:37:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:37:49: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:37:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:37:52: 22000000 INFO @ Thu, 11 Jan 2018 02:37:55: 23000000 INFO @ Thu, 11 Jan 2018 02:37:59: 23000000 INFO @ Thu, 11 Jan 2018 02:38:02: 24000000 INFO @ Thu, 11 Jan 2018 02:38:05: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:38:05: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:38:05: #1 total tags in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:38:05: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:38:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:38:06: 24000000 INFO @ Thu, 11 Jan 2018 02:38:06: #1 tags after filtering in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:38:06: #1 finished! INFO @ Thu, 11 Jan 2018 02:38:06: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:38:08: #2 number of paired peaks: 1927 INFO @ Thu, 11 Jan 2018 02:38:08: start model_add_line... INFO @ Thu, 11 Jan 2018 02:38:08: start X-correlation... INFO @ Thu, 11 Jan 2018 02:38:08: end of X-cor INFO @ Thu, 11 Jan 2018 02:38:08: #2 finished! INFO @ Thu, 11 Jan 2018 02:38:08: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:38:08: #2 alternative fragment length(s) may be 2,56 bps INFO @ Thu, 11 Jan 2018 02:38:08: #2.2 Generate R script for model : SRX3166315.10_model.r WARNING @ Thu, 11 Jan 2018 02:38:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:38:08: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Thu, 11 Jan 2018 02:38:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:38:08: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:38:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:38:09: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:38:09: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:38:09: #1 total tags in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:38:09: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:38:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:38:09: #1 tags after filtering in treatment: 24438106 INFO @ Thu, 11 Jan 2018 02:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:38:09: #1 finished! INFO @ Thu, 11 Jan 2018 02:38:09: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:38:11: #2 number of paired peaks: 1927 INFO @ Thu, 11 Jan 2018 02:38:11: start model_add_line... INFO @ Thu, 11 Jan 2018 02:38:12: start X-correlation... INFO @ Thu, 11 Jan 2018 02:38:12: end of X-cor INFO @ Thu, 11 Jan 2018 02:38:12: #2 finished! INFO @ Thu, 11 Jan 2018 02:38:12: #2 predicted fragment length is 56 bps INFO @ Thu, 11 Jan 2018 02:38:12: #2 alternative fragment length(s) may be 2,56 bps INFO @ Thu, 11 Jan 2018 02:38:12: #2.2 Generate R script for model : SRX3166315.20_model.r WARNING @ Thu, 11 Jan 2018 02:38:12: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:38:12: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Thu, 11 Jan 2018 02:38:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:38:12: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:38:33: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:38:54: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:38:58: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:38:59: #4 Write output xls file... SRX3166315.05_peaks.xls INFO @ Thu, 11 Jan 2018 02:39:00: #4 Write peak in narrowPeak format file... SRX3166315.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:39:00: #4 Write summits bed file... SRX3166315.05_summits.bed INFO @ Thu, 11 Jan 2018 02:39:00: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (18990 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:39:21: #4 Write output xls file... SRX3166315.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:39:21: #4 Write peak in narrowPeak format file... SRX3166315.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:39:21: #4 Write summits bed file... SRX3166315.10_summits.bed INFO @ Thu, 11 Jan 2018 02:39:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8673 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:39:24: #4 Write output xls file... SRX3166315.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:39:24: #4 Write peak in narrowPeak format file... SRX3166315.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:39:24: #4 Write summits bed file... SRX3166315.20_summits.bed INFO @ Thu, 11 Jan 2018 02:39:24: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (2124 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。