Job ID = 1295144 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,881,276 reads read : 71,762,552 reads written : 35,881,276 reads 0-length : 35,881,276 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:15 35881276 reads; of these: 35881276 (100.00%) were unpaired; of these: 882638 (2.46%) aligned 0 times 30244406 (84.29%) aligned exactly 1 time 4754232 (13.25%) aligned >1 times 97.54% overall alignment rate Time searching: 00:16:15 Overall time: 00:16:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14302074 / 34998638 = 0.4086 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 @ Mon, 03 Jun 2019 12:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 12:54:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 12:54:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 12:54:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:44: 1000000 INFO @ Mon, 03 Jun 2019 12:54:45: 1000000 INFO @ Mon, 03 Jun 2019 12:54:45: 1000000 INFO @ Mon, 03 Jun 2019 12:54:56: 2000000 INFO @ Mon, 03 Jun 2019 12:54:56: 2000000 INFO @ Mon, 03 Jun 2019 12:54:59: 2000000 INFO @ Mon, 03 Jun 2019 12:55:06: 3000000 INFO @ Mon, 03 Jun 2019 12:55:06: 3000000 INFO @ Mon, 03 Jun 2019 12:55:10: 3000000 INFO @ Mon, 03 Jun 2019 12:55:16: 4000000 INFO @ Mon, 03 Jun 2019 12:55:16: 4000000 INFO @ Mon, 03 Jun 2019 12:55:21: 4000000 INFO @ Mon, 03 Jun 2019 12:55:25: 5000000 INFO @ Mon, 03 Jun 2019 12:55:26: 5000000 INFO @ Mon, 03 Jun 2019 12:55:31: 5000000 INFO @ Mon, 03 Jun 2019 12:55:35: 6000000 INFO @ Mon, 03 Jun 2019 12:55:36: 6000000 INFO @ Mon, 03 Jun 2019 12:55:42: 6000000 INFO @ Mon, 03 Jun 2019 12:55:44: 7000000 INFO @ Mon, 03 Jun 2019 12:55:46: 7000000 INFO @ Mon, 03 Jun 2019 12:55:52: 7000000 INFO @ Mon, 03 Jun 2019 12:55:53: 8000000 INFO @ Mon, 03 Jun 2019 12:55:55: 8000000 INFO @ Mon, 03 Jun 2019 12:56:02: 8000000 INFO @ Mon, 03 Jun 2019 12:56:02: 9000000 INFO @ Mon, 03 Jun 2019 12:56:05: 9000000 INFO @ Mon, 03 Jun 2019 12:56:12: 10000000 INFO @ Mon, 03 Jun 2019 12:56:13: 9000000 INFO @ Mon, 03 Jun 2019 12:56:15: 10000000 INFO @ Mon, 03 Jun 2019 12:56:21: 11000000 INFO @ Mon, 03 Jun 2019 12:56:23: 10000000 INFO @ Mon, 03 Jun 2019 12:56:24: 11000000 INFO @ Mon, 03 Jun 2019 12:56:30: 12000000 INFO @ Mon, 03 Jun 2019 12:56:33: 11000000 INFO @ Mon, 03 Jun 2019 12:56:34: 12000000 INFO @ Mon, 03 Jun 2019 12:56:39: 13000000 INFO @ Mon, 03 Jun 2019 12:56:43: 12000000 INFO @ Mon, 03 Jun 2019 12:56:43: 13000000 INFO @ Mon, 03 Jun 2019 12:56:48: 14000000 INFO @ Mon, 03 Jun 2019 12:56:53: 14000000 INFO @ Mon, 03 Jun 2019 12:56:53: 13000000 INFO @ Mon, 03 Jun 2019 12:56:57: 15000000 INFO @ Mon, 03 Jun 2019 12:57:03: 15000000 INFO @ Mon, 03 Jun 2019 12:57:05: 14000000 INFO @ Mon, 03 Jun 2019 12:57:06: 16000000 INFO @ Mon, 03 Jun 2019 12:57:12: 16000000 INFO @ Mon, 03 Jun 2019 12:57:15: 15000000 INFO @ Mon, 03 Jun 2019 12:57:15: 17000000 INFO @ Mon, 03 Jun 2019 12:57:22: 17000000 INFO @ Mon, 03 Jun 2019 12:57:25: 18000000 INFO @ Mon, 03 Jun 2019 12:57:25: 16000000 INFO @ Mon, 03 Jun 2019 12:57:31: 18000000 INFO @ Mon, 03 Jun 2019 12:57:34: 19000000 INFO @ Mon, 03 Jun 2019 12:57:35: 17000000 INFO @ Mon, 03 Jun 2019 12:57:41: 19000000 INFO @ Mon, 03 Jun 2019 12:57:43: 20000000 INFO @ Mon, 03 Jun 2019 12:57:45: 18000000 INFO @ Mon, 03 Jun 2019 12:57:49: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:57:49: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:57:49: #1 total tags in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:57:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:57:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:57:50: #1 tags after filtering in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:57:50: #1 finished! INFO @ Mon, 03 Jun 2019 12:57:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:57:51: 20000000 INFO @ Mon, 03 Jun 2019 12:57:52: #2 number of paired peaks: 3829 INFO @ Mon, 03 Jun 2019 12:57:52: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:52: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:52: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:52: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:52: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 12:57:52: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 12:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05_model.r INFO @ Mon, 03 Jun 2019 12:57:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:55: 19000000 INFO @ Mon, 03 Jun 2019 12:57:57: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:57:57: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:57:57: #1 total tags in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:57:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:57:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:57:58: #1 tags after filtering in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:57:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:57:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:58:00: #2 number of paired peaks: 3829 INFO @ Mon, 03 Jun 2019 12:58:00: start model_add_line... INFO @ Mon, 03 Jun 2019 12:58:00: start X-correlation... INFO @ Mon, 03 Jun 2019 12:58:00: end of X-cor INFO @ Mon, 03 Jun 2019 12:58:00: #2 finished! INFO @ Mon, 03 Jun 2019 12:58:00: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 12:58:00: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 12:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20_model.r INFO @ Mon, 03 Jun 2019 12:58:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:58:05: 20000000 INFO @ Mon, 03 Jun 2019 12:58:12: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 12:58:12: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 12:58:12: #1 total tags in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:58:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:58:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:58:12: #1 tags after filtering in treatment: 20696564 INFO @ Mon, 03 Jun 2019 12:58:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:58:12: #1 finished! INFO @ Mon, 03 Jun 2019 12:58:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:58:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:58:15: #2 number of paired peaks: 3829 INFO @ Mon, 03 Jun 2019 12:58:15: start model_add_line... INFO @ Mon, 03 Jun 2019 12:58:15: start X-correlation... INFO @ Mon, 03 Jun 2019 12:58:15: end of X-cor INFO @ Mon, 03 Jun 2019 12:58:15: #2 finished! INFO @ Mon, 03 Jun 2019 12:58:15: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 12:58:15: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 12:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10_model.r INFO @ Mon, 03 Jun 2019 12:58:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:59:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:59:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.05_summits.bed INFO @ Mon, 03 Jun 2019 12:59:28: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8649 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.20_summits.bed INFO @ Mon, 03 Jun 2019 12:59:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6730 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3279760/SRX3279760.10_summits.bed INFO @ Mon, 03 Jun 2019 12:59:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7811 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。