Job ID = 11388794 sra ファイルのダウンロード中... Completed: 1199110K bytes transferred in 28 seconds (342504K 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... Read 47435884 spots for /home/okishinya/chipatlas/results/rn6/SRX2867572/SRR5627025.sra Written 47435884 spots for /home/okishinya/chipatlas/results/rn6/SRX2867572/SRR5627025.sra 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:52:32 47435884 reads; of these: 47435884 (100.00%) were unpaired; of these: 1604222 (3.38%) aligned 0 times 33384539 (70.38%) aligned exactly 1 time 12447123 (26.24%) aligned >1 times 96.62% overall alignment rate Time searching: 01:52:36 Overall time: 01:52:36 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 20 files... [bam_rmdupse_core] 6660029 / 45831662 = 0.1453 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, 13 Dec 2018 01:00:33: # Command line: callpeak -t SRX2867572.bam -f BAM -g 2.15e9 -n SRX2867572.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2867572.05 # format = BAM # ChIP-seq file = ['SRX2867572.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 @ Thu, 13 Dec 2018 01:00:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:33: # Command line: callpeak -t SRX2867572.bam -f BAM -g 2.15e9 -n SRX2867572.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2867572.10 # format = BAM # ChIP-seq file = ['SRX2867572.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 @ Thu, 13 Dec 2018 01:00:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:33: # Command line: callpeak -t SRX2867572.bam -f BAM -g 2.15e9 -n SRX2867572.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2867572.20 # format = BAM # ChIP-seq file = ['SRX2867572.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 @ Thu, 13 Dec 2018 01:00:33: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:00:33: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:00:46: 1000000 INFO @ Thu, 13 Dec 2018 01:00:47: 1000000 INFO @ Thu, 13 Dec 2018 01:00:48: 1000000 INFO @ Thu, 13 Dec 2018 01:00:58: 2000000 INFO @ Thu, 13 Dec 2018 01:01:01: 2000000 INFO @ Thu, 13 Dec 2018 01:01:03: 2000000 INFO @ Thu, 13 Dec 2018 01:01:09: 3000000 INFO @ Thu, 13 Dec 2018 01:01:13: 3000000 INFO @ Thu, 13 Dec 2018 01:01:20: 4000000 INFO @ Thu, 13 Dec 2018 01:01:23: 3000000 INFO @ Thu, 13 Dec 2018 01:01:25: 4000000 INFO @ Thu, 13 Dec 2018 01:01:30: 5000000 INFO @ Thu, 13 Dec 2018 01:01:36: 5000000 INFO @ Thu, 13 Dec 2018 01:01:41: 6000000 INFO @ Thu, 13 Dec 2018 01:01:42: 4000000 INFO @ Thu, 13 Dec 2018 01:01:48: 6000000 INFO @ Thu, 13 Dec 2018 01:02:02: 7000000 INFO @ Thu, 13 Dec 2018 01:02:02: 5000000 INFO @ Thu, 13 Dec 2018 01:02:02: 7000000 INFO @ Thu, 13 Dec 2018 01:02:12: 8000000 INFO @ Thu, 13 Dec 2018 01:02:23: 6000000 INFO @ Thu, 13 Dec 2018 01:02:23: 9000000 INFO @ Thu, 13 Dec 2018 01:02:23: 8000000 INFO @ Thu, 13 Dec 2018 01:02:34: 10000000 INFO @ Thu, 13 Dec 2018 01:02:40: 9000000 INFO @ Thu, 13 Dec 2018 01:02:40: 7000000 INFO @ Thu, 13 Dec 2018 01:02:45: 11000000 INFO @ Thu, 13 Dec 2018 01:02:52: 10000000 INFO @ Thu, 13 Dec 2018 01:02:56: 12000000 INFO @ Thu, 13 Dec 2018 01:03:02: 8000000 INFO @ Thu, 13 Dec 2018 01:03:05: 11000000 INFO @ Thu, 13 Dec 2018 01:03:07: 13000000 INFO @ Thu, 13 Dec 2018 01:03:17: 12000000 INFO @ Thu, 13 Dec 2018 01:03:18: 14000000 INFO @ Thu, 13 Dec 2018 01:03:24: 9000000 INFO @ Thu, 13 Dec 2018 01:03:30: 13000000 INFO @ Thu, 13 Dec 2018 01:03:30: 15000000 INFO @ Thu, 13 Dec 2018 01:03:41: 10000000 INFO @ Thu, 13 Dec 2018 01:03:47: 14000000 INFO @ Thu, 13 Dec 2018 01:03:49: 16000000 INFO @ Thu, 13 Dec 2018 01:03:52: 11000000 INFO @ Thu, 13 Dec 2018 01:04:03: 12000000 INFO @ Thu, 13 Dec 2018 01:04:05: 17000000 INFO @ Thu, 13 Dec 2018 01:04:06: 15000000 INFO @ Thu, 13 Dec 2018 01:04:17: 13000000 INFO @ Thu, 13 Dec 2018 01:04:17: 18000000 INFO @ Thu, 13 Dec 2018 01:04:21: 16000000 INFO @ Thu, 13 Dec 2018 01:04:29: 19000000 INFO @ Thu, 13 Dec 2018 01:04:32: 14000000 INFO @ Thu, 13 Dec 2018 01:04:35: 17000000 INFO @ Thu, 13 Dec 2018 01:04:42: 20000000 INFO @ Thu, 13 Dec 2018 01:04:45: 15000000 INFO @ Thu, 13 Dec 2018 01:04:48: 18000000 INFO @ Thu, 13 Dec 2018 01:04:53: 21000000 INFO @ Thu, 13 Dec 2018 01:04:56: 16000000 INFO @ Thu, 13 Dec 2018 01:05:00: 19000000 INFO @ Thu, 13 Dec 2018 01:05:10: 22000000 INFO @ Thu, 13 Dec 2018 01:05:15: 17000000 INFO @ Thu, 13 Dec 2018 01:05:21: 20000000 INFO @ Thu, 13 Dec 2018 01:05:32: 23000000 INFO @ Thu, 13 Dec 2018 01:05:35: 18000000 INFO @ Thu, 13 Dec 2018 01:05:41: 21000000 INFO @ Thu, 13 Dec 2018 01:05:53: 22000000 INFO @ Thu, 13 Dec 2018 01:05:54: 24000000 INFO @ Thu, 13 Dec 2018 01:05:57: 19000000 INFO @ Thu, 13 Dec 2018 01:06:06: 23000000 INFO @ Thu, 13 Dec 2018 01:06:16: 25000000 INFO @ Thu, 13 Dec 2018 01:06:17: 20000000 INFO @ Thu, 13 Dec 2018 01:06:19: 24000000 INFO @ Thu, 13 Dec 2018 01:06:29: 26000000 INFO @ Thu, 13 Dec 2018 01:06:32: 21000000 INFO @ Thu, 13 Dec 2018 01:06:32: 25000000 INFO @ Thu, 13 Dec 2018 01:06:45: 26000000 INFO @ Thu, 13 Dec 2018 01:06:47: 22000000 INFO @ Thu, 13 Dec 2018 01:06:49: 27000000 INFO @ Thu, 13 Dec 2018 01:06:59: 27000000 INFO @ Thu, 13 Dec 2018 01:07:04: 23000000 INFO @ Thu, 13 Dec 2018 01:07:06: 28000000 INFO @ Thu, 13 Dec 2018 01:07:15: 28000000 INFO @ Thu, 13 Dec 2018 01:07:20: 24000000 INFO @ Thu, 13 Dec 2018 01:07:21: 29000000 INFO @ Thu, 13 Dec 2018 01:07:28: 29000000 INFO @ Thu, 13 Dec 2018 01:07:36: 25000000 INFO @ Thu, 13 Dec 2018 01:07:37: 30000000 INFO @ Thu, 13 Dec 2018 01:07:49: 30000000 INFO @ Thu, 13 Dec 2018 01:07:55: 31000000 INFO @ Thu, 13 Dec 2018 01:08:00: 26000000 INFO @ Thu, 13 Dec 2018 01:08:05: 31000000 INFO @ Thu, 13 Dec 2018 01:08:12: 32000000 INFO @ Thu, 13 Dec 2018 01:08:21: 27000000 INFO @ Thu, 13 Dec 2018 01:08:23: 32000000 INFO @ Thu, 13 Dec 2018 01:08:31: 33000000 INFO @ Thu, 13 Dec 2018 01:08:37: 28000000 INFO @ Thu, 13 Dec 2018 01:08:39: 33000000 INFO @ Thu, 13 Dec 2018 01:08:51: 34000000 INFO @ Thu, 13 Dec 2018 01:08:54: 34000000 INFO @ Thu, 13 Dec 2018 01:08:56: 29000000 INFO @ Thu, 13 Dec 2018 01:09:09: 35000000 INFO @ Thu, 13 Dec 2018 01:09:14: 35000000 INFO @ Thu, 13 Dec 2018 01:09:19: 30000000 INFO @ Thu, 13 Dec 2018 01:09:26: 36000000 INFO @ Thu, 13 Dec 2018 01:09:29: 36000000 INFO @ Thu, 13 Dec 2018 01:09:41: 31000000 INFO @ Thu, 13 Dec 2018 01:09:42: 37000000 INFO @ Thu, 13 Dec 2018 01:09:46: 37000000 INFO @ Thu, 13 Dec 2018 01:10:02: 38000000 INFO @ Thu, 13 Dec 2018 01:10:04: 32000000 INFO @ Thu, 13 Dec 2018 01:10:07: 38000000 INFO @ Thu, 13 Dec 2018 01:10:12: 39000000 INFO @ Thu, 13 Dec 2018 01:10:15: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:10:15: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:10:15: #1 total tags in treatment: 39171633 INFO @ Thu, 13 Dec 2018 01:10:15: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:10:16: #1 tags after filtering in treatment: 39171560 INFO @ Thu, 13 Dec 2018 01:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:10:16: #1 finished! INFO @ Thu, 13 Dec 2018 01:10:16: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:10:19: 33000000 INFO @ Thu, 13 Dec 2018 01:10:21: #2 number of paired peaks: 6857 INFO @ Thu, 13 Dec 2018 01:10:21: start model_add_line... INFO @ Thu, 13 Dec 2018 01:10:22: start X-correlation... INFO @ Thu, 13 Dec 2018 01:10:22: end of X-cor INFO @ Thu, 13 Dec 2018 01:10:22: #2 finished! INFO @ Thu, 13 Dec 2018 01:10:22: #2 predicted fragment length is 77 bps INFO @ Thu, 13 Dec 2018 01:10:22: #2 alternative fragment length(s) may be 77,557 bps INFO @ Thu, 13 Dec 2018 01:10:22: #2.2 Generate R script for model : SRX2867572.20_model.r WARNING @ Thu, 13 Dec 2018 01:10:22: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:10:22: #2 You may need to consider one of the other alternative d(s): 77,557 WARNING @ Thu, 13 Dec 2018 01:10:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:10:22: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:10:31: 39000000 INFO @ Thu, 13 Dec 2018 01:10:33: 34000000 INFO @ Thu, 13 Dec 2018 01:10:35: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:10:35: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:10:35: #1 total tags in treatment: 39171633 INFO @ Thu, 13 Dec 2018 01:10:35: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:10:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:10:37: #1 tags after filtering in treatment: 39171560 INFO @ Thu, 13 Dec 2018 01:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:10:37: #1 finished! INFO @ Thu, 13 Dec 2018 01:10:37: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:10:42: #2 number of paired peaks: 6857 INFO @ Thu, 13 Dec 2018 01:10:42: start model_add_line... INFO @ Thu, 13 Dec 2018 01:10:42: start X-correlation... INFO @ Thu, 13 Dec 2018 01:10:42: end of X-cor INFO @ Thu, 13 Dec 2018 01:10:42: #2 finished! INFO @ Thu, 13 Dec 2018 01:10:42: #2 predicted fragment length is 77 bps INFO @ Thu, 13 Dec 2018 01:10:42: #2 alternative fragment length(s) may be 77,557 bps INFO @ Thu, 13 Dec 2018 01:10:42: #2.2 Generate R script for model : SRX2867572.05_model.r WARNING @ Thu, 13 Dec 2018 01:10:42: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:10:42: #2 You may need to consider one of the other alternative d(s): 77,557 WARNING @ Thu, 13 Dec 2018 01:10:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:10:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:10:50: 35000000 INFO @ Thu, 13 Dec 2018 01:11:05: 36000000 INFO @ Thu, 13 Dec 2018 01:11:19: 37000000 INFO @ Thu, 13 Dec 2018 01:11:33: 38000000 INFO @ Thu, 13 Dec 2018 01:11:47: 39000000 INFO @ Thu, 13 Dec 2018 01:11:49: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:11:49: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:11:49: #1 total tags in treatment: 39171633 INFO @ Thu, 13 Dec 2018 01:11:49: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:11:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:11:51: #1 tags after filtering in treatment: 39171560 INFO @ Thu, 13 Dec 2018 01:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:11:51: #1 finished! INFO @ Thu, 13 Dec 2018 01:11:51: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:11:55: #2 number of paired peaks: 6857 INFO @ Thu, 13 Dec 2018 01:11:55: start model_add_line... INFO @ Thu, 13 Dec 2018 01:11:56: start X-correlation... INFO @ Thu, 13 Dec 2018 01:11:56: end of X-cor INFO @ Thu, 13 Dec 2018 01:11:56: #2 finished! INFO @ Thu, 13 Dec 2018 01:11:56: #2 predicted fragment length is 77 bps INFO @ Thu, 13 Dec 2018 01:11:56: #2 alternative fragment length(s) may be 77,557 bps INFO @ Thu, 13 Dec 2018 01:11:56: #2.2 Generate R script for model : SRX2867572.10_model.r WARNING @ Thu, 13 Dec 2018 01:11:56: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:11:56: #2 You may need to consider one of the other alternative d(s): 77,557 WARNING @ Thu, 13 Dec 2018 01:11:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:11:56: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:12:19: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:12:38: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:13:30: #4 Write output xls file... SRX2867572.20_peaks.xls INFO @ Thu, 13 Dec 2018 01:13:30: #4 Write peak in narrowPeak format file... SRX2867572.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:13:30: #4 Write summits bed file... SRX2867572.20_summits.bed INFO @ Thu, 13 Dec 2018 01:13:30: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (620 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:13:50: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:13:52: #4 Write output xls file... SRX2867572.05_peaks.xls INFO @ Thu, 13 Dec 2018 01:13:52: #4 Write peak in narrowPeak format file... SRX2867572.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:13:52: #4 Write summits bed file... SRX2867572.05_summits.bed INFO @ Thu, 13 Dec 2018 01:13:52: Done! pass1 - making usageList (69 chroms): 2 millis pass2 - checking and writing primary data (2789 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:14:55: #4 Write output xls file... SRX2867572.10_peaks.xls INFO @ Thu, 13 Dec 2018 01:14:55: #4 Write peak in narrowPeak format file... SRX2867572.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:14:55: #4 Write summits bed file... SRX2867572.10_summits.bed INFO @ Thu, 13 Dec 2018 01:14:55: Done! pass1 - making usageList (53 chroms): 3 millis pass2 - checking and writing primary data (1335 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。