Job ID = 10194853 sra ファイルのダウンロード中... Completed: 1008101K bytes transferred in 10 seconds (805609K 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 50313451 spots for /home/okishinya/chipatlas/results/rn6/SRX1977142/SRR3952274.sra Written 50313451 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:35:37 50313451 reads; of these: 50313451 (100.00%) were unpaired; of these: 9017308 (17.92%) aligned 0 times 22426018 (44.57%) aligned exactly 1 time 18870125 (37.51%) aligned >1 times 82.08% overall alignment rate Time searching: 01:35:40 Overall time: 01:35:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 3568670 / 41296143 = 0.0864 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, 11 Nov 2017 04:39:02: # Command line: callpeak -t SRX1977142.bam -f BAM -g 2.15e9 -n SRX1977142.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977142.10 # format = BAM # ChIP-seq file = ['SRX1977142.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 @ Sat, 11 Nov 2017 04:39:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:39:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:39:02: # Command line: callpeak -t SRX1977142.bam -f BAM -g 2.15e9 -n SRX1977142.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977142.20 # format = BAM # ChIP-seq file = ['SRX1977142.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 @ Sat, 11 Nov 2017 04:39:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:39:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:39:02: # Command line: callpeak -t SRX1977142.bam -f BAM -g 2.15e9 -n SRX1977142.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977142.05 # format = BAM # ChIP-seq file = ['SRX1977142.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 @ Sat, 11 Nov 2017 04:39:02: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:39:02: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:39:09: 1000000 INFO @ Sat, 11 Nov 2017 04:39:09: 1000000 INFO @ Sat, 11 Nov 2017 04:39:09: 1000000 INFO @ Sat, 11 Nov 2017 04:39:15: 2000000 INFO @ Sat, 11 Nov 2017 04:39:15: 2000000 INFO @ Sat, 11 Nov 2017 04:39:16: 2000000 INFO @ Sat, 11 Nov 2017 04:39:21: 3000000 INFO @ Sat, 11 Nov 2017 04:39:22: 3000000 INFO @ Sat, 11 Nov 2017 04:39:22: 3000000 INFO @ Sat, 11 Nov 2017 04:39:27: 4000000 INFO @ Sat, 11 Nov 2017 04:39:28: 4000000 INFO @ Sat, 11 Nov 2017 04:39:29: 4000000 INFO @ Sat, 11 Nov 2017 04:39:34: 5000000 INFO @ Sat, 11 Nov 2017 04:39:34: 5000000 INFO @ Sat, 11 Nov 2017 04:39:36: 5000000 INFO @ Sat, 11 Nov 2017 04:39:40: 6000000 INFO @ Sat, 11 Nov 2017 04:39:40: 6000000 INFO @ Sat, 11 Nov 2017 04:39:43: 6000000 INFO @ Sat, 11 Nov 2017 04:39:46: 7000000 INFO @ Sat, 11 Nov 2017 04:39:48: 7000000 INFO @ Sat, 11 Nov 2017 04:39:49: 7000000 INFO @ Sat, 11 Nov 2017 04:39:52: 8000000 INFO @ Sat, 11 Nov 2017 04:39:54: 8000000 INFO @ Sat, 11 Nov 2017 04:39:56: 8000000 INFO @ Sat, 11 Nov 2017 04:39:59: 9000000 INFO @ Sat, 11 Nov 2017 04:40:01: 9000000 INFO @ Sat, 11 Nov 2017 04:40:02: 9000000 INFO @ Sat, 11 Nov 2017 04:40:05: 10000000 INFO @ Sat, 11 Nov 2017 04:40:07: 10000000 INFO @ Sat, 11 Nov 2017 04:40:08: 10000000 INFO @ Sat, 11 Nov 2017 04:40:11: 11000000 INFO @ Sat, 11 Nov 2017 04:40:13: 11000000 INFO @ Sat, 11 Nov 2017 04:40:15: 11000000 INFO @ Sat, 11 Nov 2017 04:40:18: 12000000 INFO @ Sat, 11 Nov 2017 04:40:20: 12000000 INFO @ Sat, 11 Nov 2017 04:40:21: 12000000 INFO @ Sat, 11 Nov 2017 04:40:24: 13000000 INFO @ Sat, 11 Nov 2017 04:40:26: 13000000 INFO @ Sat, 11 Nov 2017 04:40:28: 13000000 INFO @ Sat, 11 Nov 2017 04:40:29: 14000000 INFO @ Sat, 11 Nov 2017 04:40:33: 14000000 INFO @ Sat, 11 Nov 2017 04:40:34: 14000000 INFO @ Sat, 11 Nov 2017 04:40:35: 15000000 INFO @ Sat, 11 Nov 2017 04:40:39: 15000000 INFO @ Sat, 11 Nov 2017 04:40:41: 15000000 INFO @ Sat, 11 Nov 2017 04:40:41: 16000000 INFO @ Sat, 11 Nov 2017 04:40:46: 16000000 INFO @ Sat, 11 Nov 2017 04:40:47: 17000000 INFO @ Sat, 11 Nov 2017 04:40:48: 16000000 INFO @ Sat, 11 Nov 2017 04:40:53: 17000000 INFO @ Sat, 11 Nov 2017 04:40:55: 17000000 INFO @ Sat, 11 Nov 2017 04:40:55: 18000000 INFO @ Sat, 11 Nov 2017 04:40:59: 18000000 INFO @ Sat, 11 Nov 2017 04:41:01: 18000000 INFO @ Sat, 11 Nov 2017 04:41:02: 19000000 INFO @ Sat, 11 Nov 2017 04:41:05: 19000000 INFO @ Sat, 11 Nov 2017 04:41:08: 19000000 INFO @ Sat, 11 Nov 2017 04:41:10: 20000000 INFO @ Sat, 11 Nov 2017 04:41:11: 20000000 INFO @ Sat, 11 Nov 2017 04:41:14: 20000000 INFO @ Sat, 11 Nov 2017 04:41:16: 21000000 INFO @ Sat, 11 Nov 2017 04:41:17: 21000000 INFO @ Sat, 11 Nov 2017 04:41:20: 21000000 INFO @ Sat, 11 Nov 2017 04:41:23: 22000000 INFO @ Sat, 11 Nov 2017 04:41:23: 22000000 INFO @ Sat, 11 Nov 2017 04:41:27: 22000000 INFO @ Sat, 11 Nov 2017 04:41:29: 23000000 INFO @ Sat, 11 Nov 2017 04:41:31: 23000000 INFO @ Sat, 11 Nov 2017 04:41:33: 23000000 INFO @ Sat, 11 Nov 2017 04:41:35: 24000000 INFO @ Sat, 11 Nov 2017 04:41:37: 24000000 INFO @ Sat, 11 Nov 2017 04:41:40: 24000000 INFO @ Sat, 11 Nov 2017 04:41:41: 25000000 INFO @ Sat, 11 Nov 2017 04:41:44: 25000000 INFO @ Sat, 11 Nov 2017 04:41:47: 25000000 INFO @ Sat, 11 Nov 2017 04:41:48: 26000000 INFO @ Sat, 11 Nov 2017 04:41:51: 26000000 INFO @ Sat, 11 Nov 2017 04:41:54: 27000000 INFO @ Sat, 11 Nov 2017 04:41:54: 26000000 INFO @ Sat, 11 Nov 2017 04:41:57: 27000000 INFO @ Sat, 11 Nov 2017 04:42:00: 28000000 INFO @ Sat, 11 Nov 2017 04:42:01: 27000000 INFO @ Sat, 11 Nov 2017 04:42:04: 28000000 INFO @ Sat, 11 Nov 2017 04:42:06: 29000000 INFO @ Sat, 11 Nov 2017 04:42:07: 28000000 INFO @ Sat, 11 Nov 2017 04:42:10: 29000000 INFO @ Sat, 11 Nov 2017 04:42:12: 30000000 INFO @ Sat, 11 Nov 2017 04:42:14: 29000000 INFO @ Sat, 11 Nov 2017 04:42:17: 30000000 INFO @ Sat, 11 Nov 2017 04:42:18: 31000000 INFO @ Sat, 11 Nov 2017 04:42:20: 30000000 INFO @ Sat, 11 Nov 2017 04:42:24: 31000000 INFO @ Sat, 11 Nov 2017 04:42:24: 32000000 INFO @ Sat, 11 Nov 2017 04:42:27: 31000000 INFO @ Sat, 11 Nov 2017 04:42:30: 32000000 INFO @ Sat, 11 Nov 2017 04:42:30: 33000000 INFO @ Sat, 11 Nov 2017 04:42:33: 32000000 INFO @ Sat, 11 Nov 2017 04:42:37: 34000000 INFO @ Sat, 11 Nov 2017 04:42:37: 33000000 INFO @ Sat, 11 Nov 2017 04:42:40: 33000000 INFO @ Sat, 11 Nov 2017 04:42:43: 35000000 INFO @ Sat, 11 Nov 2017 04:42:43: 34000000 INFO @ Sat, 11 Nov 2017 04:42:47: 34000000 INFO @ Sat, 11 Nov 2017 04:42:49: 35000000 INFO @ Sat, 11 Nov 2017 04:42:50: 36000000 INFO @ Sat, 11 Nov 2017 04:42:54: 35000000 INFO @ Sat, 11 Nov 2017 04:42:55: 36000000 INFO @ Sat, 11 Nov 2017 04:42:57: 37000000 INFO @ Sat, 11 Nov 2017 04:43:00: 36000000 INFO @ Sat, 11 Nov 2017 04:43:02: 37000000 INFO @ Sat, 11 Nov 2017 04:43:02: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:43:02: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:43:02: #1 total tags in treatment: 37727473 INFO @ Sat, 11 Nov 2017 04:43:02: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:43:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 04:43:04: #1 tags after filtering in treatment: 37727408 INFO @ Sat, 11 Nov 2017 04:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:43:04: #1 finished! INFO @ Sat, 11 Nov 2017 04:43:04: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:43:06: 37000000 INFO @ Sat, 11 Nov 2017 04:43:06: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:43:06: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:43:06: #1 total tags in treatment: 37727473 INFO @ Sat, 11 Nov 2017 04:43:06: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:43:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 04:43:07: #1 tags after filtering in treatment: 37727408 INFO @ Sat, 11 Nov 2017 04:43:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:43:07: #1 finished! INFO @ Sat, 11 Nov 2017 04:43:07: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:43:09: #2 number of paired peaks: 38423 INFO @ Sat, 11 Nov 2017 04:43:09: start model_add_line... INFO @ Sat, 11 Nov 2017 04:43:10: start X-correlation... INFO @ Sat, 11 Nov 2017 04:43:10: end of X-cor INFO @ Sat, 11 Nov 2017 04:43:10: #2 finished! INFO @ Sat, 11 Nov 2017 04:43:10: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 04:43:10: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 04:43:10: #2.2 Generate R script for model : SRX1977142.10_model.r INFO @ Sat, 11 Nov 2017 04:43:10: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:43:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:43:11: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 04:43:11: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 04:43:11: #1 total tags in treatment: 37727473 INFO @ Sat, 11 Nov 2017 04:43:11: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:43:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 04:43:12: #1 tags after filtering in treatment: 37727408 INFO @ Sat, 11 Nov 2017 04:43:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:43:12: #1 finished! INFO @ Sat, 11 Nov 2017 04:43:12: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:43:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:43:13: #2 number of paired peaks: 38423 INFO @ Sat, 11 Nov 2017 04:43:13: start model_add_line... INFO @ Sat, 11 Nov 2017 04:43:13: start X-correlation... INFO @ Sat, 11 Nov 2017 04:43:13: end of X-cor INFO @ Sat, 11 Nov 2017 04:43:13: #2 finished! INFO @ Sat, 11 Nov 2017 04:43:13: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 04:43:13: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 04:43:13: #2.2 Generate R script for model : SRX1977142.20_model.r INFO @ Sat, 11 Nov 2017 04:43:13: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:43:17: #2 number of paired peaks: 38423 INFO @ Sat, 11 Nov 2017 04:43:17: start model_add_line... INFO @ Sat, 11 Nov 2017 04:43:18: start X-correlation... INFO @ Sat, 11 Nov 2017 04:43:18: end of X-cor INFO @ Sat, 11 Nov 2017 04:43:18: #2 finished! INFO @ Sat, 11 Nov 2017 04:43:18: #2 predicted fragment length is 136 bps INFO @ Sat, 11 Nov 2017 04:43:18: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 11 Nov 2017 04:43:18: #2.2 Generate R script for model : SRX1977142.05_model.r INFO @ Sat, 11 Nov 2017 04:43:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:43:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:44:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:44:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:44:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:45:50: #4 Write output xls file... SRX1977142.20_peaks.xls INFO @ Sat, 11 Nov 2017 04:45:50: #4 Write peak in narrowPeak format file... SRX1977142.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:45:50: #4 Write summits bed file... SRX1977142.20_summits.bed INFO @ Sat, 11 Nov 2017 04:45:50: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (4975 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:45:56: #4 Write output xls file... SRX1977142.10_peaks.xls INFO @ Sat, 11 Nov 2017 04:45:57: #4 Write peak in narrowPeak format file... SRX1977142.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:45:57: #4 Write summits bed file... SRX1977142.10_summits.bed INFO @ Sat, 11 Nov 2017 04:45:57: Done! pass1 - making usageList (142 chroms): 5 millis pass2 - checking and writing primary data (24556 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:45:58: #4 Write output xls file... SRX1977142.05_peaks.xls INFO @ Sat, 11 Nov 2017 04:45:59: #4 Write peak in narrowPeak format file... SRX1977142.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:46:00: #4 Write summits bed file... SRX1977142.05_summits.bed INFO @ Sat, 11 Nov 2017 04:46:00: Done! pass1 - making usageList (229 chroms): 14 millis pass2 - checking and writing primary data (77381 records, 4 fields): 94 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。