Job ID = 9371942 sra ファイルのダウンロード中... Completed: 2507851K bytes transferred in 106 seconds (193601K bits/sec), in 1 file, 2 directories. 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 87596775 spots for /home/okishinya/chipatlas/results/dm3/SRX2692976/SRR5398175.sra Written 87596775 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: 04:19:35 87596775 reads; of these: 87596775 (100.00%) were unpaired; of these: 17742395 (20.25%) aligned 0 times 11895901 (13.58%) aligned exactly 1 time 57958479 (66.17%) aligned >1 times 79.75% overall alignment rate Time searching: 04:19:35 Overall time: 04:19:35 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 32 files... [bam_rmdupse_core] 45773069 / 69854380 = 0.6553 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, 04 Aug 2017 19:52:40: # Command line: callpeak -t SRX2692976.bam -f BAM -g dm -n SRX2692976.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2692976.05 # format = BAM # ChIP-seq file = ['SRX2692976.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 @ Fri, 04 Aug 2017 19:52:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:52:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:52:40: # Command line: callpeak -t SRX2692976.bam -f BAM -g dm -n SRX2692976.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2692976.20 # format = BAM # ChIP-seq file = ['SRX2692976.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 @ Fri, 04 Aug 2017 19:52:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:52:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:52:40: # Command line: callpeak -t SRX2692976.bam -f BAM -g dm -n SRX2692976.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2692976.10 # format = BAM # ChIP-seq file = ['SRX2692976.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 @ Fri, 04 Aug 2017 19:52:40: #1 read tag files... INFO @ Fri, 04 Aug 2017 19:52:40: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 19:52:59: 1000000 INFO @ Fri, 04 Aug 2017 19:53:04: 1000000 INFO @ Fri, 04 Aug 2017 19:53:06: 1000000 INFO @ Fri, 04 Aug 2017 19:53:15: 2000000 INFO @ Fri, 04 Aug 2017 19:53:27: 2000000 INFO @ Fri, 04 Aug 2017 19:53:29: 2000000 INFO @ Fri, 04 Aug 2017 19:53:32: 3000000 INFO @ Fri, 04 Aug 2017 19:53:50: 4000000 INFO @ Fri, 04 Aug 2017 19:53:52: 3000000 INFO @ Fri, 04 Aug 2017 19:53:52: 3000000 INFO @ Fri, 04 Aug 2017 19:54:05: 5000000 INFO @ Fri, 04 Aug 2017 19:54:09: 4000000 INFO @ Fri, 04 Aug 2017 19:54:17: 4000000 INFO @ Fri, 04 Aug 2017 19:54:21: 6000000 INFO @ Fri, 04 Aug 2017 19:54:27: 5000000 INFO @ Fri, 04 Aug 2017 19:54:39: 7000000 INFO @ Fri, 04 Aug 2017 19:54:40: 5000000 INFO @ Fri, 04 Aug 2017 19:54:48: 6000000 INFO @ Fri, 04 Aug 2017 19:54:55: 8000000 INFO @ Fri, 04 Aug 2017 19:55:03: 6000000 INFO @ Fri, 04 Aug 2017 19:55:09: 9000000 INFO @ Fri, 04 Aug 2017 19:55:09: 7000000 INFO @ Fri, 04 Aug 2017 19:55:23: 10000000 INFO @ Fri, 04 Aug 2017 19:55:24: 7000000 INFO @ Fri, 04 Aug 2017 19:55:30: 8000000 INFO @ Fri, 04 Aug 2017 19:55:42: 11000000 INFO @ Fri, 04 Aug 2017 19:55:42: 8000000 INFO @ Fri, 04 Aug 2017 19:55:51: 9000000 INFO @ Fri, 04 Aug 2017 19:56:04: 12000000 INFO @ Fri, 04 Aug 2017 19:56:05: 9000000 INFO @ Fri, 04 Aug 2017 19:56:11: 10000000 INFO @ Fri, 04 Aug 2017 19:56:26: 13000000 INFO @ Fri, 04 Aug 2017 19:56:31: 10000000 INFO @ Fri, 04 Aug 2017 19:56:33: 11000000 INFO @ Fri, 04 Aug 2017 19:56:48: 14000000 INFO @ Fri, 04 Aug 2017 19:56:53: 12000000 INFO @ Fri, 04 Aug 2017 19:56:55: 11000000 INFO @ Fri, 04 Aug 2017 19:57:12: 15000000 INFO @ Fri, 04 Aug 2017 19:57:15: 13000000 INFO @ Fri, 04 Aug 2017 19:57:19: 12000000 INFO @ Fri, 04 Aug 2017 19:57:36: 14000000 INFO @ Fri, 04 Aug 2017 19:57:36: 16000000 INFO @ Fri, 04 Aug 2017 19:57:43: 13000000 INFO @ Fri, 04 Aug 2017 19:57:55: 15000000 INFO @ Fri, 04 Aug 2017 19:58:00: 17000000 INFO @ Fri, 04 Aug 2017 19:58:06: 14000000 INFO @ Fri, 04 Aug 2017 19:58:13: 16000000 INFO @ Fri, 04 Aug 2017 19:58:21: 18000000 INFO @ Fri, 04 Aug 2017 19:58:27: 15000000 INFO @ Fri, 04 Aug 2017 19:58:33: 17000000 INFO @ Fri, 04 Aug 2017 19:58:43: 19000000 INFO @ Fri, 04 Aug 2017 19:58:47: 16000000 INFO @ Fri, 04 Aug 2017 19:58:51: 18000000 INFO @ Fri, 04 Aug 2017 19:59:05: 20000000 INFO @ Fri, 04 Aug 2017 19:59:09: 17000000 INFO @ Fri, 04 Aug 2017 19:59:09: 19000000 INFO @ Fri, 04 Aug 2017 19:59:27: 21000000 INFO @ Fri, 04 Aug 2017 19:59:27: 20000000 INFO @ Fri, 04 Aug 2017 19:59:31: 18000000 INFO @ Fri, 04 Aug 2017 19:59:45: 21000000 INFO @ Fri, 04 Aug 2017 19:59:49: 22000000 INFO @ Fri, 04 Aug 2017 19:59:53: 19000000 INFO @ Fri, 04 Aug 2017 20:00:03: 22000000 INFO @ Fri, 04 Aug 2017 20:00:11: 23000000 INFO @ Fri, 04 Aug 2017 20:00:14: 20000000 INFO @ Fri, 04 Aug 2017 20:00:22: 23000000 INFO @ Fri, 04 Aug 2017 20:00:32: 24000000 INFO @ Fri, 04 Aug 2017 20:00:33: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 20:00:33: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 20:00:33: #1 total tags in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:00:33: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:00:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:00:34: #1 tags after filtering in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 20:00:34: #1 finished! INFO @ Fri, 04 Aug 2017 20:00:34: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:00:35: 21000000 INFO @ Fri, 04 Aug 2017 20:00:37: #2 number of paired peaks: 3554 INFO @ Fri, 04 Aug 2017 20:00:37: start model_add_line... INFO @ Fri, 04 Aug 2017 20:00:38: start X-correlation... INFO @ Fri, 04 Aug 2017 20:00:38: end of X-cor INFO @ Fri, 04 Aug 2017 20:00:38: #2 finished! INFO @ Fri, 04 Aug 2017 20:00:38: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 20:00:38: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 04 Aug 2017 20:00:38: #2.2 Generate R script for model : SRX2692976.05_model.r WARNING @ Fri, 04 Aug 2017 20:00:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 20:00:38: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 04 Aug 2017 20:00:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 20:00:38: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:00:39: 24000000 INFO @ Fri, 04 Aug 2017 20:00:40: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 20:00:40: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 20:00:40: #1 total tags in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:00:40: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:00:41: #1 tags after filtering in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 20:00:41: #1 finished! INFO @ Fri, 04 Aug 2017 20:00:41: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:00:44: #2 number of paired peaks: 3554 INFO @ Fri, 04 Aug 2017 20:00:44: start model_add_line... INFO @ Fri, 04 Aug 2017 20:00:45: start X-correlation... INFO @ Fri, 04 Aug 2017 20:00:45: end of X-cor INFO @ Fri, 04 Aug 2017 20:00:45: #2 finished! INFO @ Fri, 04 Aug 2017 20:00:45: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 20:00:45: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 04 Aug 2017 20:00:45: #2.2 Generate R script for model : SRX2692976.10_model.r WARNING @ Fri, 04 Aug 2017 20:00:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 20:00:45: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 04 Aug 2017 20:00:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 20:00:45: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:00:53: 22000000 INFO @ Fri, 04 Aug 2017 20:01:10: 23000000 INFO @ Fri, 04 Aug 2017 20:01:32: 24000000 INFO @ Fri, 04 Aug 2017 20:01:33: #1 tag size is determined as 75 bps INFO @ Fri, 04 Aug 2017 20:01:33: #1 tag size = 75 INFO @ Fri, 04 Aug 2017 20:01:33: #1 total tags in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:01:33: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:01:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:01:34: #1 tags after filtering in treatment: 24081311 INFO @ Fri, 04 Aug 2017 20:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 20:01:34: #1 finished! INFO @ Fri, 04 Aug 2017 20:01:34: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:01:37: #2 number of paired peaks: 3554 INFO @ Fri, 04 Aug 2017 20:01:37: start model_add_line... INFO @ Fri, 04 Aug 2017 20:01:37: start X-correlation... INFO @ Fri, 04 Aug 2017 20:01:37: end of X-cor INFO @ Fri, 04 Aug 2017 20:01:37: #2 finished! INFO @ Fri, 04 Aug 2017 20:01:37: #2 predicted fragment length is 52 bps INFO @ Fri, 04 Aug 2017 20:01:37: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 04 Aug 2017 20:01:37: #2.2 Generate R script for model : SRX2692976.20_model.r WARNING @ Fri, 04 Aug 2017 20:01:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 20:01:37: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 04 Aug 2017 20:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 20:01:37: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:01:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:01:48: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:02:20: #4 Write output xls file... SRX2692976.05_peaks.xls INFO @ Fri, 04 Aug 2017 20:02:20: #4 Write peak in narrowPeak format file... SRX2692976.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:02:20: #4 Write summits bed file... SRX2692976.05_summits.bed INFO @ Fri, 04 Aug 2017 20:02:20: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (19649 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write output xls file... SRX2692976.10_peaks.xls INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write peak in narrowPeak format file... SRX2692976.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:02:23: #4 Write summits bed file... SRX2692976.10_summits.bed INFO @ Fri, 04 Aug 2017 20:02:24: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (14044 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:02:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:03:20: #4 Write output xls file... SRX2692976.20_peaks.xls INFO @ Fri, 04 Aug 2017 20:03:20: #4 Write peak in narrowPeak format file... SRX2692976.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:03:20: #4 Write summits bed file... SRX2692976.20_summits.bed INFO @ Fri, 04 Aug 2017 20:03:20: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (7434 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。