Job ID = 1294074 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,989,589 reads read : 32,989,589 reads written : 32,989,589 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: 00:08:07 32989589 reads; of these: 32989589 (100.00%) were unpaired; of these: 2198092 (6.66%) aligned 0 times 26539367 (80.45%) aligned exactly 1 time 4252130 (12.89%) aligned >1 times 93.34% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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 8 files... [bam_rmdupse_core] 13968223 / 30791497 = 0.4536 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 04:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.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 04:55:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:55:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.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 04:55:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:55:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.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 04:55:45: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:55:45: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:55:52: 1000000 INFO @ Mon, 03 Jun 2019 04:55:54: 1000000 INFO @ Mon, 03 Jun 2019 04:55:54: 1000000 INFO @ Mon, 03 Jun 2019 04:55:58: 2000000 INFO @ Mon, 03 Jun 2019 04:56:04: 2000000 INFO @ Mon, 03 Jun 2019 04:56:04: 2000000 INFO @ Mon, 03 Jun 2019 04:56:05: 3000000 INFO @ Mon, 03 Jun 2019 04:56:12: 4000000 INFO @ Mon, 03 Jun 2019 04:56:13: 3000000 INFO @ Mon, 03 Jun 2019 04:56:13: 3000000 INFO @ Mon, 03 Jun 2019 04:56:18: 5000000 INFO @ Mon, 03 Jun 2019 04:56:22: 4000000 INFO @ Mon, 03 Jun 2019 04:56:22: 4000000 INFO @ Mon, 03 Jun 2019 04:56:25: 6000000 INFO @ Mon, 03 Jun 2019 04:56:31: 7000000 INFO @ Mon, 03 Jun 2019 04:56:31: 5000000 INFO @ Mon, 03 Jun 2019 04:56:32: 5000000 INFO @ Mon, 03 Jun 2019 04:56:38: 8000000 INFO @ Mon, 03 Jun 2019 04:56:41: 6000000 INFO @ Mon, 03 Jun 2019 04:56:41: 6000000 INFO @ Mon, 03 Jun 2019 04:56:45: 9000000 INFO @ Mon, 03 Jun 2019 04:56:50: 7000000 INFO @ Mon, 03 Jun 2019 04:56:50: 7000000 INFO @ Mon, 03 Jun 2019 04:56:51: 10000000 INFO @ Mon, 03 Jun 2019 04:56:58: 11000000 INFO @ Mon, 03 Jun 2019 04:56:59: 8000000 INFO @ Mon, 03 Jun 2019 04:56:59: 8000000 INFO @ Mon, 03 Jun 2019 04:57:05: 12000000 INFO @ Mon, 03 Jun 2019 04:57:09: 9000000 INFO @ Mon, 03 Jun 2019 04:57:09: 9000000 INFO @ Mon, 03 Jun 2019 04:57:12: 13000000 INFO @ Mon, 03 Jun 2019 04:57:19: 10000000 INFO @ Mon, 03 Jun 2019 04:57:19: 10000000 INFO @ Mon, 03 Jun 2019 04:57:19: 14000000 INFO @ Mon, 03 Jun 2019 04:57:26: 15000000 INFO @ Mon, 03 Jun 2019 04:57:28: 11000000 INFO @ Mon, 03 Jun 2019 04:57:28: 11000000 INFO @ Mon, 03 Jun 2019 04:57:33: 16000000 INFO @ Mon, 03 Jun 2019 04:57:38: 12000000 INFO @ Mon, 03 Jun 2019 04:57:38: 12000000 INFO @ Mon, 03 Jun 2019 04:57:39: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:57:39: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:57:39: #1 total tags in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:57:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:57:39: #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 04:57:39: #1 tags after filtering in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:57:39: #1 finished! INFO @ Mon, 03 Jun 2019 04:57:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:57:41: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 04:57:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:57:41: start X-correlation... INFO @ Mon, 03 Jun 2019 04:57:41: end of X-cor INFO @ Mon, 03 Jun 2019 04:57:41: #2 finished! INFO @ Mon, 03 Jun 2019 04:57:41: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:57:41: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05_model.r INFO @ Mon, 03 Jun 2019 04:57:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:57:47: 13000000 INFO @ Mon, 03 Jun 2019 04:57:47: 13000000 INFO @ Mon, 03 Jun 2019 04:57:57: 14000000 INFO @ Mon, 03 Jun 2019 04:57:57: 14000000 INFO @ Mon, 03 Jun 2019 04:58:06: 15000000 INFO @ Mon, 03 Jun 2019 04:58:06: 15000000 INFO @ Mon, 03 Jun 2019 04:58:15: 16000000 INFO @ Mon, 03 Jun 2019 04:58:15: 16000000 INFO @ Mon, 03 Jun 2019 04:58:23: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:58:23: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:58:23: #1 total tags in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:58:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:58:23: #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 04:58:23: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:58:23: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:58:23: #1 total tags in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:58:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:58:23: #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 04:58:23: #1 tags after filtering in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:58:23: #1 finished! INFO @ Mon, 03 Jun 2019 04:58:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:58:23: #1 tags after filtering in treatment: 16823274 INFO @ Mon, 03 Jun 2019 04:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:58:23: #1 finished! INFO @ Mon, 03 Jun 2019 04:58:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:58:25: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 04:58:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:58:25: #2 number of paired peaks: 1465 INFO @ Mon, 03 Jun 2019 04:58:25: start model_add_line... INFO @ Mon, 03 Jun 2019 04:58:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:58:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:58:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:58:25: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:58:25: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:58:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20_model.r INFO @ Mon, 03 Jun 2019 04:58:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:58:25: start X-correlation... INFO @ Mon, 03 Jun 2019 04:58:25: end of X-cor INFO @ Mon, 03 Jun 2019 04:58:25: #2 finished! INFO @ Mon, 03 Jun 2019 04:58:25: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:58:25: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:58:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10_model.r INFO @ Mon, 03 Jun 2019 04:58:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:58:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:58:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:58:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:58:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.05_summits.bed INFO @ Mon, 03 Jun 2019 04:58:52: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11076 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:59:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:59:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.20_summits.bed INFO @ Mon, 03 Jun 2019 04:59:36: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3953 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181432/SRX181432.10_summits.bed INFO @ Mon, 03 Jun 2019 04:59:37: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7904 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。