Job ID = 10194880 sra ファイルのダウンロード中... Completed: 243035K bytes transferred in 8 seconds (234011K bits/sec), in 1 file. Completed: 243448K bytes transferred in 11 seconds (180781K bits/sec), in 1 file. Completed: 232129K bytes transferred in 10 seconds (189553K bits/sec), in 1 file. Completed: 229097K bytes transferred in 8 seconds (214297K bits/sec), in 1 file. Completed: 269885K bytes transferred in 11 seconds (192247K bits/sec), in 1 file. Completed: 272522K bytes transferred in 7 seconds (292890K 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 5174988 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319797.sra Written 5174988 spots total Written 5231302 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319796.sra Written 5231302 spots total Written 5450601 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319795.sra Written 5450601 spots total Written 5461558 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319794.sra Written 5461558 spots total Written 5938201 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319798.sra Written 5938201 spots total Written 5973119 spots for /home/okishinya/chipatlas/results/rn6/SRX2202875/SRR4319799.sra Written 5973119 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:41 33229769 reads; of these: 33229769 (100.00%) were unpaired; of these: 4579884 (13.78%) aligned 0 times 22350151 (67.26%) aligned exactly 1 time 6299734 (18.96%) aligned >1 times 86.22% overall alignment rate Time searching: 00:21:44 Overall time: 00:21:44 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 12 files... [bam_rmdupse_core] 5160598 / 28649885 = 0.1801 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 18:01:22: # Command line: callpeak -t SRX2202875.bam -f BAM -g 2.15e9 -n SRX2202875.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202875.05 # format = BAM # ChIP-seq file = ['SRX2202875.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 18:01:22: # Command line: callpeak -t SRX2202875.bam -f BAM -g 2.15e9 -n SRX2202875.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202875.20 # format = BAM # ChIP-seq file = ['SRX2202875.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 18:01:22: # Command line: callpeak -t SRX2202875.bam -f BAM -g 2.15e9 -n SRX2202875.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202875.10 # format = BAM # ChIP-seq file = ['SRX2202875.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 18:01:22: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:22: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:22: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:22: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:01:22: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:22: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:01:28: 1000000 INFO @ Fri, 10 Nov 2017 18:01:28: 1000000 INFO @ Fri, 10 Nov 2017 18:01:31: 1000000 INFO @ Fri, 10 Nov 2017 18:01:35: 2000000 INFO @ Fri, 10 Nov 2017 18:01:35: 2000000 INFO @ Fri, 10 Nov 2017 18:01:39: 2000000 INFO @ Fri, 10 Nov 2017 18:01:42: 3000000 INFO @ Fri, 10 Nov 2017 18:01:42: 3000000 INFO @ Fri, 10 Nov 2017 18:01:48: 3000000 INFO @ Fri, 10 Nov 2017 18:01:48: 4000000 INFO @ Fri, 10 Nov 2017 18:01:48: 4000000 INFO @ Fri, 10 Nov 2017 18:01:55: 5000000 INFO @ Fri, 10 Nov 2017 18:01:55: 5000000 INFO @ Fri, 10 Nov 2017 18:01:57: 4000000 INFO @ Fri, 10 Nov 2017 18:02:02: 6000000 INFO @ Fri, 10 Nov 2017 18:02:02: 6000000 INFO @ Fri, 10 Nov 2017 18:02:05: 5000000 INFO @ Fri, 10 Nov 2017 18:02:08: 7000000 INFO @ Fri, 10 Nov 2017 18:02:09: 7000000 INFO @ Fri, 10 Nov 2017 18:02:14: 6000000 INFO @ Fri, 10 Nov 2017 18:02:15: 8000000 INFO @ Fri, 10 Nov 2017 18:02:16: 8000000 INFO @ Fri, 10 Nov 2017 18:02:22: 9000000 INFO @ Fri, 10 Nov 2017 18:02:23: 7000000 INFO @ Fri, 10 Nov 2017 18:02:23: 9000000 INFO @ Fri, 10 Nov 2017 18:02:29: 10000000 INFO @ Fri, 10 Nov 2017 18:02:30: 10000000 INFO @ Fri, 10 Nov 2017 18:02:31: 8000000 INFO @ Fri, 10 Nov 2017 18:02:36: 11000000 INFO @ Fri, 10 Nov 2017 18:02:37: 11000000 INFO @ Fri, 10 Nov 2017 18:02:40: 9000000 INFO @ Fri, 10 Nov 2017 18:02:43: 12000000 INFO @ Fri, 10 Nov 2017 18:02:44: 12000000 INFO @ Fri, 10 Nov 2017 18:02:48: 10000000 INFO @ Fri, 10 Nov 2017 18:02:50: 13000000 INFO @ Fri, 10 Nov 2017 18:02:51: 13000000 INFO @ Fri, 10 Nov 2017 18:02:56: 14000000 INFO @ Fri, 10 Nov 2017 18:02:57: 11000000 INFO @ Fri, 10 Nov 2017 18:02:58: 14000000 INFO @ Fri, 10 Nov 2017 18:03:03: 15000000 INFO @ Fri, 10 Nov 2017 18:03:05: 15000000 INFO @ Fri, 10 Nov 2017 18:03:06: 12000000 INFO @ Fri, 10 Nov 2017 18:03:10: 16000000 INFO @ Fri, 10 Nov 2017 18:03:11: 16000000 INFO @ Fri, 10 Nov 2017 18:03:14: 13000000 INFO @ Fri, 10 Nov 2017 18:03:17: 17000000 INFO @ Fri, 10 Nov 2017 18:03:18: 17000000 INFO @ Fri, 10 Nov 2017 18:03:23: 14000000 INFO @ Fri, 10 Nov 2017 18:03:24: 18000000 INFO @ Fri, 10 Nov 2017 18:03:25: 18000000 INFO @ Fri, 10 Nov 2017 18:03:31: 19000000 INFO @ Fri, 10 Nov 2017 18:03:31: 15000000 INFO @ Fri, 10 Nov 2017 18:03:32: 19000000 INFO @ Fri, 10 Nov 2017 18:03:38: 20000000 INFO @ Fri, 10 Nov 2017 18:03:39: 20000000 INFO @ Fri, 10 Nov 2017 18:03:40: 16000000 INFO @ Fri, 10 Nov 2017 18:03:45: 21000000 INFO @ Fri, 10 Nov 2017 18:03:47: 21000000 INFO @ Fri, 10 Nov 2017 18:03:48: 17000000 INFO @ Fri, 10 Nov 2017 18:03:52: 22000000 INFO @ Fri, 10 Nov 2017 18:03:54: 22000000 INFO @ Fri, 10 Nov 2017 18:03:57: 18000000 INFO @ Fri, 10 Nov 2017 18:03:59: 23000000 INFO @ Fri, 10 Nov 2017 18:04:01: 23000000 INFO @ Fri, 10 Nov 2017 18:04:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:04:03: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:04:03: #1 total tags in treatment: 23489287 INFO @ Fri, 10 Nov 2017 18:04:03: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:04:03: #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 18:04:03: #1 tags after filtering in treatment: 23489139 INFO @ Fri, 10 Nov 2017 18:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:04:03: #1 finished! INFO @ Fri, 10 Nov 2017 18:04:03: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:04:05: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:04:05: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:04:05: #1 total tags in treatment: 23489287 INFO @ Fri, 10 Nov 2017 18:04:05: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:04:05: #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 18:04:05: #1 tags after filtering in treatment: 23489139 INFO @ Fri, 10 Nov 2017 18:04:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:04:05: #1 finished! INFO @ Fri, 10 Nov 2017 18:04:05: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:04:06: 19000000 INFO @ Fri, 10 Nov 2017 18:04:07: #2 number of paired peaks: 46301 INFO @ Fri, 10 Nov 2017 18:04:07: start model_add_line... INFO @ Fri, 10 Nov 2017 18:04:08: start X-correlation... INFO @ Fri, 10 Nov 2017 18:04:08: end of X-cor INFO @ Fri, 10 Nov 2017 18:04:08: #2 finished! INFO @ Fri, 10 Nov 2017 18:04:08: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:04:08: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:04:08: #2.2 Generate R script for model : SRX2202875.20_model.r INFO @ Fri, 10 Nov 2017 18:04:08: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:04:09: #2 number of paired peaks: 46301 INFO @ Fri, 10 Nov 2017 18:04:09: start model_add_line... INFO @ Fri, 10 Nov 2017 18:04:10: start X-correlation... INFO @ Fri, 10 Nov 2017 18:04:10: end of X-cor INFO @ Fri, 10 Nov 2017 18:04:10: #2 finished! INFO @ Fri, 10 Nov 2017 18:04:10: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:04:10: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:04:10: #2.2 Generate R script for model : SRX2202875.05_model.r INFO @ Fri, 10 Nov 2017 18:04:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:04:14: 20000000 INFO @ Fri, 10 Nov 2017 18:04:23: 21000000 INFO @ Fri, 10 Nov 2017 18:04:32: 22000000 INFO @ Fri, 10 Nov 2017 18:04:41: 23000000 INFO @ Fri, 10 Nov 2017 18:04:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:04:45: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:04:45: #1 total tags in treatment: 23489287 INFO @ Fri, 10 Nov 2017 18:04:45: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:04:45: #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 18:04:46: #1 tags after filtering in treatment: 23489139 INFO @ Fri, 10 Nov 2017 18:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:04:46: #1 finished! INFO @ Fri, 10 Nov 2017 18:04:46: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:04:50: #2 number of paired peaks: 46301 INFO @ Fri, 10 Nov 2017 18:04:50: start model_add_line... INFO @ Fri, 10 Nov 2017 18:04:50: start X-correlation... INFO @ Fri, 10 Nov 2017 18:04:50: end of X-cor INFO @ Fri, 10 Nov 2017 18:04:50: #2 finished! INFO @ Fri, 10 Nov 2017 18:04:50: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Nov 2017 18:04:50: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Nov 2017 18:04:50: #2.2 Generate R script for model : SRX2202875.10_model.r INFO @ Fri, 10 Nov 2017 18:04:50: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:05:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:05:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:05:45: #4 Write output xls file... SRX2202875.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:05:45: #4 Write peak in narrowPeak format file... SRX2202875.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:05:45: #4 Write summits bed file... SRX2202875.20_summits.bed INFO @ Fri, 10 Nov 2017 18:05:45: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (1132 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:05:46: #4 Write output xls file... SRX2202875.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:05:46: #4 Write peak in narrowPeak format file... SRX2202875.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:05:46: #4 Write summits bed file... SRX2202875.05_summits.bed INFO @ Fri, 10 Nov 2017 18:05:46: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (16499 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:05:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:06:31: #4 Write output xls file... SRX2202875.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:06:31: #4 Write peak in narrowPeak format file... SRX2202875.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:06:31: #4 Write summits bed file... SRX2202875.10_summits.bed INFO @ Fri, 10 Nov 2017 18:06:31: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (6707 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。