Job ID = 10194874 sra ファイルのダウンロード中... Completed: 244994K bytes transferred in 8 seconds (243901K bits/sec), in 1 file. Completed: 245953K bytes transferred in 8 seconds (246335K bits/sec), in 1 file. Completed: 233471K bytes transferred in 9 seconds (210134K bits/sec), in 1 file. Completed: 230427K bytes transferred in 10 seconds (178866K bits/sec), in 1 file. Completed: 264981K bytes transferred in 11 seconds (192261K bits/sec), in 1 file. Completed: 267941K bytes transferred in 10 seconds (214721K 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 5192118 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319767.sra Written 5192118 spots total Written 5250431 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319766.sra Written 5250431 spots total Written 5497189 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319764.sra Written 5497189 spots total Written 5499107 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319765.sra Written 5499107 spots total Written 5819239 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319768.sra Written 5819239 spots total Written 5862230 spots for /home/okishinya/chipatlas/results/rn6/SRX2202870/SRR4319769.sra Written 5862230 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: 00:00:01 Multiseed full-index search: 00:23:12 33120314 reads; of these: 33120314 (100.00%) were unpaired; of these: 1159504 (3.50%) aligned 0 times 25127293 (75.87%) aligned exactly 1 time 6833517 (20.63%) aligned >1 times 96.50% overall alignment rate Time searching: 00:23:16 Overall time: 00:23:16 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 16 files... [bam_rmdupse_core] 3399983 / 31960810 = 0.1064 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, 10 Nov 2017 18:01:47: # Command line: callpeak -t SRX2202870.bam -f BAM -g 2.15e9 -n SRX2202870.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202870.10 # format = BAM # ChIP-seq file = ['SRX2202870.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 @ Fri, 10 Nov 2017 18:01:47: # Command line: callpeak -t SRX2202870.bam -f BAM -g 2.15e9 -n SRX2202870.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202870.05 # format = BAM # ChIP-seq file = ['SRX2202870.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 @ Fri, 10 Nov 2017 18:01:47: # Command line: callpeak -t SRX2202870.bam -f BAM -g 2.15e9 -n SRX2202870.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202870.20 # format = BAM # ChIP-seq file = ['SRX2202870.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 @ Fri, 10 Nov 2017 18:01:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:54: 1000000 INFO @ Fri, 10 Nov 2017 18:01:54: 1000000 INFO @ Fri, 10 Nov 2017 18:01:54: 1000000 INFO @ Fri, 10 Nov 2017 18:02:01: 2000000 INFO @ Fri, 10 Nov 2017 18:02:01: 2000000 INFO @ Fri, 10 Nov 2017 18:02:01: 2000000 INFO @ Fri, 10 Nov 2017 18:02:08: 3000000 INFO @ Fri, 10 Nov 2017 18:02:08: 3000000 INFO @ Fri, 10 Nov 2017 18:02:08: 3000000 INFO @ Fri, 10 Nov 2017 18:02:15: 4000000 INFO @ Fri, 10 Nov 2017 18:02:15: 4000000 INFO @ Fri, 10 Nov 2017 18:02:15: 4000000 INFO @ Fri, 10 Nov 2017 18:02:22: 5000000 INFO @ Fri, 10 Nov 2017 18:02:22: 5000000 INFO @ Fri, 10 Nov 2017 18:02:23: 5000000 INFO @ Fri, 10 Nov 2017 18:02:29: 6000000 INFO @ Fri, 10 Nov 2017 18:02:29: 6000000 INFO @ Fri, 10 Nov 2017 18:02:30: 6000000 INFO @ Fri, 10 Nov 2017 18:02:36: 7000000 INFO @ Fri, 10 Nov 2017 18:02:36: 7000000 INFO @ Fri, 10 Nov 2017 18:02:37: 7000000 INFO @ Fri, 10 Nov 2017 18:02:43: 8000000 INFO @ Fri, 10 Nov 2017 18:02:43: 8000000 INFO @ Fri, 10 Nov 2017 18:02:44: 8000000 INFO @ Fri, 10 Nov 2017 18:02:50: 9000000 INFO @ Fri, 10 Nov 2017 18:02:50: 9000000 INFO @ Fri, 10 Nov 2017 18:02:51: 9000000 INFO @ Fri, 10 Nov 2017 18:02:58: 10000000 INFO @ Fri, 10 Nov 2017 18:02:58: 10000000 INFO @ Fri, 10 Nov 2017 18:02:58: 10000000 INFO @ Fri, 10 Nov 2017 18:03:05: 11000000 INFO @ Fri, 10 Nov 2017 18:03:05: 11000000 INFO @ Fri, 10 Nov 2017 18:03:05: 11000000 INFO @ Fri, 10 Nov 2017 18:03:12: 12000000 INFO @ Fri, 10 Nov 2017 18:03:12: 12000000 INFO @ Fri, 10 Nov 2017 18:03:13: 12000000 INFO @ Fri, 10 Nov 2017 18:03:19: 13000000 INFO @ Fri, 10 Nov 2017 18:03:19: 13000000 INFO @ Fri, 10 Nov 2017 18:03:20: 13000000 INFO @ Fri, 10 Nov 2017 18:03:26: 14000000 INFO @ Fri, 10 Nov 2017 18:03:26: 14000000 INFO @ Fri, 10 Nov 2017 18:03:27: 14000000 INFO @ Fri, 10 Nov 2017 18:03:33: 15000000 INFO @ Fri, 10 Nov 2017 18:03:33: 15000000 INFO @ Fri, 10 Nov 2017 18:03:34: 15000000 INFO @ Fri, 10 Nov 2017 18:03:40: 16000000 INFO @ Fri, 10 Nov 2017 18:03:40: 16000000 INFO @ Fri, 10 Nov 2017 18:03:42: 16000000 INFO @ Fri, 10 Nov 2017 18:03:47: 17000000 INFO @ Fri, 10 Nov 2017 18:03:47: 17000000 INFO @ Fri, 10 Nov 2017 18:03:49: 17000000 INFO @ Fri, 10 Nov 2017 18:03:54: 18000000 INFO @ Fri, 10 Nov 2017 18:03:54: 18000000 INFO @ Fri, 10 Nov 2017 18:03:56: 18000000 INFO @ Fri, 10 Nov 2017 18:04:00: 19000000 INFO @ Fri, 10 Nov 2017 18:04:00: 19000000 INFO @ Fri, 10 Nov 2017 18:04:04: 19000000 INFO @ Fri, 10 Nov 2017 18:04:07: 20000000 INFO @ Fri, 10 Nov 2017 18:04:07: 20000000 INFO @ Fri, 10 Nov 2017 18:04:11: 20000000 INFO @ Fri, 10 Nov 2017 18:04:14: 21000000 INFO @ Fri, 10 Nov 2017 18:04:14: 21000000 INFO @ Fri, 10 Nov 2017 18:04:18: 21000000 INFO @ Fri, 10 Nov 2017 18:04:21: 22000000 INFO @ Fri, 10 Nov 2017 18:04:21: 22000000 INFO @ Fri, 10 Nov 2017 18:04:25: 22000000 INFO @ Fri, 10 Nov 2017 18:04:28: 23000000 INFO @ Fri, 10 Nov 2017 18:04:28: 23000000 INFO @ Fri, 10 Nov 2017 18:04:31: 23000000 INFO @ Fri, 10 Nov 2017 18:04:35: 24000000 INFO @ Fri, 10 Nov 2017 18:04:35: 24000000 INFO @ Fri, 10 Nov 2017 18:04:38: 24000000 INFO @ Fri, 10 Nov 2017 18:04:43: 25000000 INFO @ Fri, 10 Nov 2017 18:04:43: 25000000 INFO @ Fri, 10 Nov 2017 18:04:45: 25000000 INFO @ Fri, 10 Nov 2017 18:04:50: 26000000 INFO @ Fri, 10 Nov 2017 18:04:50: 26000000 INFO @ Fri, 10 Nov 2017 18:04:52: 26000000 INFO @ Fri, 10 Nov 2017 18:04:57: 27000000 INFO @ Fri, 10 Nov 2017 18:04:57: 27000000 INFO @ Fri, 10 Nov 2017 18:04:58: 27000000 INFO @ Fri, 10 Nov 2017 18:05:04: 28000000 INFO @ Fri, 10 Nov 2017 18:05:04: 28000000 INFO @ Fri, 10 Nov 2017 18:05:05: 28000000 INFO @ Fri, 10 Nov 2017 18:05:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:05:08: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:05:08: #1 total tags in treatment: 28560827 INFO @ Fri, 10 Nov 2017 18:05:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:05:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:05:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:05:08: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:05:08: #1 total tags in treatment: 28560827 INFO @ Fri, 10 Nov 2017 18:05:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:05:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:05:09: #1 tags after filtering in treatment: 28560709 INFO @ Fri, 10 Nov 2017 18:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:05:09: #1 finished! INFO @ Fri, 10 Nov 2017 18:05:09: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:05:09: #1 tags after filtering in treatment: 28560709 INFO @ Fri, 10 Nov 2017 18:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:05:09: #1 finished! INFO @ Fri, 10 Nov 2017 18:05:09: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:05:09: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:05:09: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:05:09: #1 total tags in treatment: 28560827 INFO @ Fri, 10 Nov 2017 18:05:09: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:05:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:05:10: #1 tags after filtering in treatment: 28560709 INFO @ Fri, 10 Nov 2017 18:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:05:10: #1 finished! INFO @ Fri, 10 Nov 2017 18:05:10: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:05:13: #2 number of paired peaks: 51726 INFO @ Fri, 10 Nov 2017 18:05:13: start model_add_line... INFO @ Fri, 10 Nov 2017 18:05:14: #2 number of paired peaks: 51726 INFO @ Fri, 10 Nov 2017 18:05:14: start model_add_line... INFO @ Fri, 10 Nov 2017 18:05:14: start X-correlation... INFO @ Fri, 10 Nov 2017 18:05:14: end of X-cor INFO @ Fri, 10 Nov 2017 18:05:14: #2 finished! INFO @ Fri, 10 Nov 2017 18:05:14: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:05:14: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:05:14: #2.2 Generate R script for model : SRX2202870.10_model.r INFO @ Fri, 10 Nov 2017 18:05:14: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:05:14: start X-correlation... INFO @ Fri, 10 Nov 2017 18:05:14: end of X-cor INFO @ Fri, 10 Nov 2017 18:05:14: #2 finished! INFO @ Fri, 10 Nov 2017 18:05:14: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:05:14: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:05:14: #2.2 Generate R script for model : SRX2202870.05_model.r INFO @ Fri, 10 Nov 2017 18:05:14: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:05:15: #2 number of paired peaks: 51726 INFO @ Fri, 10 Nov 2017 18:05:15: start model_add_line... INFO @ Fri, 10 Nov 2017 18:05:15: start X-correlation... INFO @ Fri, 10 Nov 2017 18:05:15: end of X-cor INFO @ Fri, 10 Nov 2017 18:05:15: #2 finished! INFO @ Fri, 10 Nov 2017 18:05:15: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:05:15: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:05:15: #2.2 Generate R script for model : SRX2202870.20_model.r INFO @ Fri, 10 Nov 2017 18:05:15: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:06:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:06:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:06:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:07:06: #4 Write output xls file... SRX2202870.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:07:06: #4 Write peak in narrowPeak format file... SRX2202870.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:07:06: #4 Write summits bed file... SRX2202870.20_summits.bed INFO @ Fri, 10 Nov 2017 18:07:06: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (7757 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:07:08: #4 Write output xls file... SRX2202870.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:07:08: #4 Write peak in narrowPeak format file... SRX2202870.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:07:08: #4 Write summits bed file... SRX2202870.10_summits.bed INFO @ Fri, 10 Nov 2017 18:07:09: Done! pass1 - making usageList (86 chroms): 4 millis pass2 - checking and writing primary data (16145 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:07:10: #4 Write output xls file... SRX2202870.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:07:10: #4 Write peak in narrowPeak format file... SRX2202870.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:07:10: #4 Write summits bed file... SRX2202870.05_summits.bed INFO @ Fri, 10 Nov 2017 18:07:10: Done! pass1 - making usageList (106 chroms): 5 millis pass2 - checking and writing primary data (25374 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。