Job ID = 10194906 sra ファイルのダウンロード中... Completed: 341223K bytes transferred in 23 seconds (121267K bits/sec), in 1 file. Completed: 333766K bytes transferred in 20 seconds (131270K bits/sec), in 1 file. Completed: 560414K bytes transferred in 37 seconds (123175K bits/sec), in 1 file. Completed: 550346K bytes transferred in 30 seconds (148389K bits/sec), in 1 file. Completed: 553839K bytes transferred in 28 seconds (157048K bits/sec), in 1 file. Completed: 545655K bytes transferred in 29 seconds (151662K 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 7922329 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319951.sra Written 7922329 spots total Written 8138528 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319950.sra Written 8138528 spots total Written 12100162 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319953.sra Written 12100162 spots total Written 12095497 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319955.sra Written 12095497 spots total Written 12255653 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319954.sra Written 12255653 spots total Written 12403364 spots for /home/okishinya/chipatlas/results/rn6/SRX2202901/SRR4319952.sra Written 12403364 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: 00:00:00 Multiseed full-index search: 02:03:57 64915533 reads; of these: 64915533 (100.00%) were unpaired; of these: 2029350 (3.13%) aligned 0 times 43187170 (66.53%) aligned exactly 1 time 19699013 (30.35%) aligned >1 times 96.87% overall alignment rate Time searching: 02:04:00 Overall time: 02:04:00 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 28 files... [bam_rmdupse_core] 11818843 / 62886183 = 0.1879 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 00:32:14: # Command line: callpeak -t SRX2202901.bam -f BAM -g 2.15e9 -n SRX2202901.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202901.20 # format = BAM # ChIP-seq file = ['SRX2202901.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 00:32:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:32:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:32:14: # Command line: callpeak -t SRX2202901.bam -f BAM -g 2.15e9 -n SRX2202901.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202901.10 # format = BAM # ChIP-seq file = ['SRX2202901.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 00:32:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:32:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:32:14: # Command line: callpeak -t SRX2202901.bam -f BAM -g 2.15e9 -n SRX2202901.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202901.05 # format = BAM # ChIP-seq file = ['SRX2202901.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 00:32:14: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:32:14: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:32:24: 1000000 INFO @ Sat, 11 Nov 2017 00:32:28: 1000000 INFO @ Sat, 11 Nov 2017 00:32:34: 2000000 INFO @ Sat, 11 Nov 2017 00:32:35: 1000000 INFO @ Sat, 11 Nov 2017 00:32:43: 2000000 INFO @ Sat, 11 Nov 2017 00:32:44: 3000000 INFO @ Sat, 11 Nov 2017 00:32:54: 4000000 INFO @ Sat, 11 Nov 2017 00:32:55: 2000000 INFO @ Sat, 11 Nov 2017 00:32:58: 3000000 INFO @ Sat, 11 Nov 2017 00:33:03: 5000000 INFO @ Sat, 11 Nov 2017 00:33:12: 6000000 INFO @ Sat, 11 Nov 2017 00:33:13: 4000000 INFO @ Sat, 11 Nov 2017 00:33:16: 3000000 INFO @ Sat, 11 Nov 2017 00:33:22: 7000000 INFO @ Sat, 11 Nov 2017 00:33:27: 5000000 INFO @ Sat, 11 Nov 2017 00:33:32: 8000000 INFO @ Sat, 11 Nov 2017 00:33:37: 4000000 INFO @ Sat, 11 Nov 2017 00:33:42: 9000000 INFO @ Sat, 11 Nov 2017 00:33:42: 6000000 INFO @ Sat, 11 Nov 2017 00:33:51: 10000000 INFO @ Sat, 11 Nov 2017 00:33:57: 7000000 INFO @ Sat, 11 Nov 2017 00:33:58: 5000000 INFO @ Sat, 11 Nov 2017 00:34:01: 11000000 INFO @ Sat, 11 Nov 2017 00:34:10: 12000000 INFO @ Sat, 11 Nov 2017 00:34:12: 8000000 INFO @ Sat, 11 Nov 2017 00:34:19: 6000000 INFO @ Sat, 11 Nov 2017 00:34:20: 13000000 INFO @ Sat, 11 Nov 2017 00:34:26: 9000000 INFO @ Sat, 11 Nov 2017 00:34:29: 14000000 INFO @ Sat, 11 Nov 2017 00:34:39: 15000000 INFO @ Sat, 11 Nov 2017 00:34:39: 10000000 INFO @ Sat, 11 Nov 2017 00:34:40: 7000000 INFO @ Sat, 11 Nov 2017 00:34:49: 16000000 INFO @ Sat, 11 Nov 2017 00:34:53: 11000000 INFO @ Sat, 11 Nov 2017 00:34:58: 17000000 INFO @ Sat, 11 Nov 2017 00:34:59: 8000000 INFO @ Sat, 11 Nov 2017 00:35:06: 12000000 INFO @ Sat, 11 Nov 2017 00:35:08: 18000000 INFO @ Sat, 11 Nov 2017 00:35:18: 19000000 INFO @ Sat, 11 Nov 2017 00:35:18: 9000000 INFO @ Sat, 11 Nov 2017 00:35:19: 13000000 INFO @ Sat, 11 Nov 2017 00:35:27: 20000000 INFO @ Sat, 11 Nov 2017 00:35:32: 14000000 INFO @ Sat, 11 Nov 2017 00:35:35: 10000000 INFO @ Sat, 11 Nov 2017 00:35:37: 21000000 INFO @ Sat, 11 Nov 2017 00:35:46: 15000000 INFO @ Sat, 11 Nov 2017 00:35:49: 22000000 INFO @ Sat, 11 Nov 2017 00:35:50: 11000000 INFO @ Sat, 11 Nov 2017 00:36:01: 16000000 INFO @ Sat, 11 Nov 2017 00:36:03: 23000000 INFO @ Sat, 11 Nov 2017 00:36:05: 12000000 INFO @ Sat, 11 Nov 2017 00:36:15: 17000000 INFO @ Sat, 11 Nov 2017 00:36:15: 24000000 INFO @ Sat, 11 Nov 2017 00:36:20: 13000000 INFO @ Sat, 11 Nov 2017 00:36:28: 25000000 INFO @ Sat, 11 Nov 2017 00:36:29: 18000000 INFO @ Sat, 11 Nov 2017 00:36:35: 14000000 INFO @ Sat, 11 Nov 2017 00:36:40: 26000000 INFO @ Sat, 11 Nov 2017 00:36:43: 19000000 INFO @ Sat, 11 Nov 2017 00:36:51: 15000000 INFO @ Sat, 11 Nov 2017 00:36:51: 27000000 INFO @ Sat, 11 Nov 2017 00:36:56: 20000000 INFO @ Sat, 11 Nov 2017 00:37:03: 28000000 INFO @ Sat, 11 Nov 2017 00:37:06: 16000000 INFO @ Sat, 11 Nov 2017 00:37:09: 21000000 INFO @ Sat, 11 Nov 2017 00:37:15: 29000000 INFO @ Sat, 11 Nov 2017 00:37:22: 17000000 INFO @ Sat, 11 Nov 2017 00:37:22: 22000000 INFO @ Sat, 11 Nov 2017 00:37:27: 30000000 INFO @ Sat, 11 Nov 2017 00:37:35: 23000000 INFO @ Sat, 11 Nov 2017 00:37:37: 18000000 INFO @ Sat, 11 Nov 2017 00:37:39: 31000000 INFO @ Sat, 11 Nov 2017 00:37:48: 24000000 INFO @ Sat, 11 Nov 2017 00:37:50: 32000000 INFO @ Sat, 11 Nov 2017 00:37:52: 19000000 INFO @ Sat, 11 Nov 2017 00:38:03: 25000000 INFO @ Sat, 11 Nov 2017 00:38:06: 33000000 INFO @ Sat, 11 Nov 2017 00:38:08: 20000000 INFO @ Sat, 11 Nov 2017 00:38:19: 26000000 INFO @ Sat, 11 Nov 2017 00:38:22: 34000000 INFO @ Sat, 11 Nov 2017 00:38:23: 21000000 INFO @ Sat, 11 Nov 2017 00:38:35: 27000000 INFO @ Sat, 11 Nov 2017 00:38:38: 22000000 INFO @ Sat, 11 Nov 2017 00:38:39: 35000000 INFO @ Sat, 11 Nov 2017 00:38:52: 28000000 INFO @ Sat, 11 Nov 2017 00:38:53: 23000000 INFO @ Sat, 11 Nov 2017 00:38:55: 36000000 INFO @ Sat, 11 Nov 2017 00:39:08: 29000000 INFO @ Sat, 11 Nov 2017 00:39:09: 24000000 INFO @ Sat, 11 Nov 2017 00:39:11: 37000000 INFO @ Sat, 11 Nov 2017 00:39:24: 25000000 INFO @ Sat, 11 Nov 2017 00:39:25: 30000000 INFO @ Sat, 11 Nov 2017 00:39:30: 38000000 INFO @ Sat, 11 Nov 2017 00:39:43: 26000000 INFO @ Sat, 11 Nov 2017 00:39:45: 31000000 INFO @ Sat, 11 Nov 2017 00:39:49: 39000000 INFO @ Sat, 11 Nov 2017 00:40:02: 27000000 INFO @ Sat, 11 Nov 2017 00:40:04: 32000000 INFO @ Sat, 11 Nov 2017 00:40:09: 40000000 INFO @ Sat, 11 Nov 2017 00:40:19: 28000000 INFO @ Sat, 11 Nov 2017 00:40:23: 33000000 INFO @ Sat, 11 Nov 2017 00:40:28: 41000000 INFO @ Sat, 11 Nov 2017 00:40:37: 29000000 INFO @ Sat, 11 Nov 2017 00:40:43: 34000000 INFO @ Sat, 11 Nov 2017 00:40:48: 42000000 INFO @ Sat, 11 Nov 2017 00:40:54: 30000000 INFO @ Sat, 11 Nov 2017 00:41:02: 35000000 INFO @ Sat, 11 Nov 2017 00:41:07: 43000000 INFO @ Sat, 11 Nov 2017 00:41:12: 31000000 INFO @ Sat, 11 Nov 2017 00:41:22: 36000000 INFO @ Sat, 11 Nov 2017 00:41:26: 44000000 INFO @ Sat, 11 Nov 2017 00:41:28: 32000000 INFO @ Sat, 11 Nov 2017 00:41:39: 37000000 INFO @ Sat, 11 Nov 2017 00:41:41: 33000000 INFO @ Sat, 11 Nov 2017 00:41:43: 45000000 INFO @ Sat, 11 Nov 2017 00:41:55: 34000000 INFO @ Sat, 11 Nov 2017 00:41:56: 38000000 INFO @ Sat, 11 Nov 2017 00:42:00: 46000000 INFO @ Sat, 11 Nov 2017 00:42:09: 35000000 INFO @ Sat, 11 Nov 2017 00:42:13: 39000000 INFO @ Sat, 11 Nov 2017 00:42:18: 47000000 INFO @ Sat, 11 Nov 2017 00:42:22: 36000000 INFO @ Sat, 11 Nov 2017 00:42:30: 40000000 INFO @ Sat, 11 Nov 2017 00:42:35: 48000000 INFO @ Sat, 11 Nov 2017 00:42:36: 37000000 INFO @ Sat, 11 Nov 2017 00:42:47: 41000000 INFO @ Sat, 11 Nov 2017 00:42:48: 38000000 INFO @ Sat, 11 Nov 2017 00:42:52: 49000000 INFO @ Sat, 11 Nov 2017 00:43:04: 42000000 INFO @ Sat, 11 Nov 2017 00:43:04: 39000000 INFO @ Sat, 11 Nov 2017 00:43:10: 50000000 INFO @ Sat, 11 Nov 2017 00:43:22: 40000000 INFO @ Sat, 11 Nov 2017 00:43:22: 43000000 INFO @ Sat, 11 Nov 2017 00:43:28: 51000000 INFO @ Sat, 11 Nov 2017 00:43:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:43:29: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:43:29: #1 total tags in treatment: 51067340 INFO @ Sat, 11 Nov 2017 00:43:29: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:43:29: #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 00:43:31: #1 tags after filtering in treatment: 51067291 INFO @ Sat, 11 Nov 2017 00:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:43:31: #1 finished! INFO @ Sat, 11 Nov 2017 00:43:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:43:36: 44000000 INFO @ Sat, 11 Nov 2017 00:43:38: #2 number of paired peaks: 24978 INFO @ Sat, 11 Nov 2017 00:43:38: start model_add_line... INFO @ Sat, 11 Nov 2017 00:43:38: 41000000 INFO @ Sat, 11 Nov 2017 00:43:39: start X-correlation... INFO @ Sat, 11 Nov 2017 00:43:39: end of X-cor INFO @ Sat, 11 Nov 2017 00:43:39: #2 finished! INFO @ Sat, 11 Nov 2017 00:43:39: #2 predicted fragment length is 113 bps INFO @ Sat, 11 Nov 2017 00:43:39: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 11 Nov 2017 00:43:39: #2.2 Generate R script for model : SRX2202901.20_model.r INFO @ Sat, 11 Nov 2017 00:43:39: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:43:48: 45000000 INFO @ Sat, 11 Nov 2017 00:43:55: 42000000 INFO @ Sat, 11 Nov 2017 00:44:05: 46000000 INFO @ Sat, 11 Nov 2017 00:44:11: 43000000 INFO @ Sat, 11 Nov 2017 00:44:21: 47000000 INFO @ Sat, 11 Nov 2017 00:44:30: 44000000 INFO @ Sat, 11 Nov 2017 00:44:40: 48000000 INFO @ Sat, 11 Nov 2017 00:44:49: 45000000 INFO @ Sat, 11 Nov 2017 00:44:58: 49000000 INFO @ Sat, 11 Nov 2017 00:45:05: 46000000 INFO @ Sat, 11 Nov 2017 00:45:13: 50000000 INFO @ Sat, 11 Nov 2017 00:45:20: 47000000 INFO @ Sat, 11 Nov 2017 00:45:29: 51000000 INFO @ Sat, 11 Nov 2017 00:45:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:45:31: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:45:31: #1 total tags in treatment: 51067340 INFO @ Sat, 11 Nov 2017 00:45:31: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:45:31: #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 00:45:33: #1 tags after filtering in treatment: 51067291 INFO @ Sat, 11 Nov 2017 00:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:45:33: #1 finished! INFO @ Sat, 11 Nov 2017 00:45:33: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:45:34: 48000000 INFO @ Sat, 11 Nov 2017 00:45:39: #2 number of paired peaks: 24978 INFO @ Sat, 11 Nov 2017 00:45:39: start model_add_line... INFO @ Sat, 11 Nov 2017 00:45:40: start X-correlation... INFO @ Sat, 11 Nov 2017 00:45:40: end of X-cor INFO @ Sat, 11 Nov 2017 00:45:40: #2 finished! INFO @ Sat, 11 Nov 2017 00:45:40: #2 predicted fragment length is 113 bps INFO @ Sat, 11 Nov 2017 00:45:40: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 11 Nov 2017 00:45:40: #2.2 Generate R script for model : SRX2202901.10_model.r INFO @ Sat, 11 Nov 2017 00:45:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:45:51: 49000000 INFO @ Sat, 11 Nov 2017 00:46:08: 50000000 INFO @ Sat, 11 Nov 2017 00:46:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:46:26: 51000000 INFO @ Sat, 11 Nov 2017 00:46:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:46:27: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:46:27: #1 total tags in treatment: 51067340 INFO @ Sat, 11 Nov 2017 00:46:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:46:27: #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 00:46:29: #1 tags after filtering in treatment: 51067291 INFO @ Sat, 11 Nov 2017 00:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:46:29: #1 finished! INFO @ Sat, 11 Nov 2017 00:46:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:46:36: #2 number of paired peaks: 24978 INFO @ Sat, 11 Nov 2017 00:46:36: start model_add_line... INFO @ Sat, 11 Nov 2017 00:46:37: start X-correlation... INFO @ Sat, 11 Nov 2017 00:46:37: end of X-cor INFO @ Sat, 11 Nov 2017 00:46:37: #2 finished! INFO @ Sat, 11 Nov 2017 00:46:37: #2 predicted fragment length is 113 bps INFO @ Sat, 11 Nov 2017 00:46:37: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 11 Nov 2017 00:46:37: #2.2 Generate R script for model : SRX2202901.05_model.r INFO @ Sat, 11 Nov 2017 00:46:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:48:01: #4 Write output xls file... SRX2202901.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:48:01: #4 Write peak in narrowPeak format file... SRX2202901.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:48:01: #4 Write summits bed file... SRX2202901.20_summits.bed INFO @ Sat, 11 Nov 2017 00:48:01: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (2937 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:48:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:49:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:49:47: #4 Write output xls file... SRX2202901.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:49:47: #4 Write peak in narrowPeak format file... SRX2202901.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:49:47: #4 Write summits bed file... SRX2202901.10_summits.bed INFO @ Sat, 11 Nov 2017 00:49:47: Done! pass1 - making usageList (84 chroms): 4 millis pass2 - checking and writing primary data (12146 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:50:42: #4 Write output xls file... SRX2202901.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:50:43: #4 Write peak in narrowPeak format file... SRX2202901.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:50:43: #4 Write summits bed file... SRX2202901.05_summits.bed INFO @ Sat, 11 Nov 2017 00:50:43: Done! pass1 - making usageList (111 chroms): 7 millis pass2 - checking and writing primary data (21697 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。