Job ID = 1294226 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,998,952 reads read : 28,998,952 reads written : 28,998,952 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: 00:07:12 28998952 reads; of these: 28998952 (100.00%) were unpaired; of these: 1868495 (6.44%) aligned 0 times 24971007 (86.11%) aligned exactly 1 time 2159450 (7.45%) aligned >1 times 93.56% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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 12 files... [bam_rmdupse_core] 12451167 / 27130457 = 0.4589 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 05:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.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 05:51:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:51:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.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 05:51:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:51:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.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 05:51:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:51:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:51:32: 1000000 INFO @ Mon, 03 Jun 2019 05:51:32: 1000000 INFO @ Mon, 03 Jun 2019 05:51:33: 1000000 INFO @ Mon, 03 Jun 2019 05:51:41: 2000000 INFO @ Mon, 03 Jun 2019 05:51:43: 2000000 INFO @ Mon, 03 Jun 2019 05:51:43: 2000000 INFO @ Mon, 03 Jun 2019 05:51:51: 3000000 INFO @ Mon, 03 Jun 2019 05:51:53: 3000000 INFO @ Mon, 03 Jun 2019 05:51:55: 3000000 INFO @ Mon, 03 Jun 2019 05:52:00: 4000000 INFO @ Mon, 03 Jun 2019 05:52:03: 4000000 INFO @ Mon, 03 Jun 2019 05:52:05: 4000000 INFO @ Mon, 03 Jun 2019 05:52:08: 5000000 INFO @ Mon, 03 Jun 2019 05:52:12: 5000000 INFO @ Mon, 03 Jun 2019 05:52:14: 5000000 INFO @ Mon, 03 Jun 2019 05:52:18: 6000000 INFO @ Mon, 03 Jun 2019 05:52:22: 6000000 INFO @ Mon, 03 Jun 2019 05:52:24: 6000000 INFO @ Mon, 03 Jun 2019 05:52:27: 7000000 INFO @ Mon, 03 Jun 2019 05:52:32: 7000000 INFO @ Mon, 03 Jun 2019 05:52:35: 7000000 INFO @ Mon, 03 Jun 2019 05:52:36: 8000000 INFO @ Mon, 03 Jun 2019 05:52:41: 8000000 INFO @ Mon, 03 Jun 2019 05:52:44: 8000000 INFO @ Mon, 03 Jun 2019 05:52:44: 9000000 INFO @ Mon, 03 Jun 2019 05:52:51: 9000000 INFO @ Mon, 03 Jun 2019 05:52:54: 10000000 INFO @ Mon, 03 Jun 2019 05:52:55: 9000000 INFO @ Mon, 03 Jun 2019 05:53:01: 10000000 INFO @ Mon, 03 Jun 2019 05:53:03: 11000000 INFO @ Mon, 03 Jun 2019 05:53:06: 10000000 INFO @ Mon, 03 Jun 2019 05:53:10: 11000000 INFO @ Mon, 03 Jun 2019 05:53:12: 12000000 INFO @ Mon, 03 Jun 2019 05:53:15: 11000000 INFO @ Mon, 03 Jun 2019 05:53:20: 12000000 INFO @ Mon, 03 Jun 2019 05:53:20: 13000000 INFO @ Mon, 03 Jun 2019 05:53:25: 12000000 INFO @ Mon, 03 Jun 2019 05:53:29: 14000000 INFO @ Mon, 03 Jun 2019 05:53:30: 13000000 INFO @ Mon, 03 Jun 2019 05:53:35: 13000000 INFO @ Mon, 03 Jun 2019 05:53:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:53:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:53:35: #1 total tags in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:53:35: #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 05:53:36: #1 tags after filtering in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:53:36: #1 finished! INFO @ Mon, 03 Jun 2019 05:53:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:53:38: #2 number of paired peaks: 5899 INFO @ Mon, 03 Jun 2019 05:53:38: start model_add_line... INFO @ Mon, 03 Jun 2019 05:53:38: start X-correlation... INFO @ Mon, 03 Jun 2019 05:53:38: end of X-cor INFO @ Mon, 03 Jun 2019 05:53:38: #2 finished! INFO @ Mon, 03 Jun 2019 05:53:38: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 05:53:38: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 05:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10_model.r INFO @ Mon, 03 Jun 2019 05:53:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:53:39: 14000000 INFO @ Mon, 03 Jun 2019 05:53:45: 14000000 INFO @ Mon, 03 Jun 2019 05:53:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:53:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:53:45: #1 total tags in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:53:45: #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 05:53:46: #1 tags after filtering in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:53:46: #1 finished! INFO @ Mon, 03 Jun 2019 05:53:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:53:48: #2 number of paired peaks: 5899 INFO @ Mon, 03 Jun 2019 05:53:48: start model_add_line... INFO @ Mon, 03 Jun 2019 05:53:48: start X-correlation... INFO @ Mon, 03 Jun 2019 05:53:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:53:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:53:48: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 05:53:48: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 05:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20_model.r INFO @ Mon, 03 Jun 2019 05:53:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:53:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:53:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:53:51: #1 total tags in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:53:51: #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 05:53:51: #1 tags after filtering in treatment: 14679290 INFO @ Mon, 03 Jun 2019 05:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:53:51: #1 finished! INFO @ Mon, 03 Jun 2019 05:53:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:53:53: #2 number of paired peaks: 5899 INFO @ Mon, 03 Jun 2019 05:53:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:53:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:53:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:53:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:53:53: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 05:53:53: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 05:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05_model.r INFO @ Mon, 03 Jun 2019 05:53:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:54:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:54:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:54:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.10_summits.bed INFO @ Mon, 03 Jun 2019 05:54:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7423 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:55:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:55:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:55:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.20_summits.bed INFO @ Mon, 03 Jun 2019 05:55:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5254 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201903/SRX201903.05_summits.bed INFO @ Mon, 03 Jun 2019 05:55:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9825 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。