Job ID = 1294933 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,268,681 reads read : 10,268,681 reads written : 10,268,681 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: 00:04:18 10268681 reads; of these: 10268681 (100.00%) were unpaired; of these: 628406 (6.12%) aligned 0 times 8210186 (79.95%) aligned exactly 1 time 1430089 (13.93%) aligned >1 times 93.88% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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_rmdupse_core] 485856 / 9640275 = 0.0504 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 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:59:07: 1000000 INFO @ Mon, 03 Jun 2019 10:59:08: 1000000 INFO @ Mon, 03 Jun 2019 10:59:08: 1000000 INFO @ Mon, 03 Jun 2019 10:59:20: 2000000 INFO @ Mon, 03 Jun 2019 10:59:21: 2000000 INFO @ Mon, 03 Jun 2019 10:59:21: 2000000 INFO @ Mon, 03 Jun 2019 10:59:35: 3000000 INFO @ Mon, 03 Jun 2019 10:59:35: 3000000 INFO @ Mon, 03 Jun 2019 10:59:36: 3000000 INFO @ Mon, 03 Jun 2019 10:59:49: 4000000 INFO @ Mon, 03 Jun 2019 10:59:49: 4000000 INFO @ Mon, 03 Jun 2019 10:59:50: 4000000 INFO @ Mon, 03 Jun 2019 11:00:02: 5000000 INFO @ Mon, 03 Jun 2019 11:00:02: 5000000 INFO @ Mon, 03 Jun 2019 11:00:03: 5000000 INFO @ Mon, 03 Jun 2019 11:00:15: 6000000 INFO @ Mon, 03 Jun 2019 11:00:15: 6000000 INFO @ Mon, 03 Jun 2019 11:00:17: 6000000 INFO @ Mon, 03 Jun 2019 11:00:28: 7000000 INFO @ Mon, 03 Jun 2019 11:00:28: 7000000 INFO @ Mon, 03 Jun 2019 11:00:30: 7000000 INFO @ Mon, 03 Jun 2019 11:00:40: 8000000 INFO @ Mon, 03 Jun 2019 11:00:41: 8000000 INFO @ Mon, 03 Jun 2019 11:00:43: 8000000 INFO @ Mon, 03 Jun 2019 11:00:53: 9000000 INFO @ Mon, 03 Jun 2019 11:00:54: 9000000 INFO @ Mon, 03 Jun 2019 11:00:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:55: #1 total tags in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:55: #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 11:00:56: #1 tags after filtering in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:56: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:00:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:56: #1 total tags in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:56: #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 11:00:56: 9000000 INFO @ Mon, 03 Jun 2019 11:00:57: #1 tags after filtering in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:57: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:00:57: #2 number of paired peaks: 488 WARNING @ Mon, 03 Jun 2019 11:00:57: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Mon, 03 Jun 2019 11:00:57: start model_add_line... INFO @ Mon, 03 Jun 2019 11:00:57: start X-correlation... INFO @ Mon, 03 Jun 2019 11:00:57: end of X-cor INFO @ Mon, 03 Jun 2019 11:00:57: #2 finished! INFO @ Mon, 03 Jun 2019 11:00:57: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:00:57: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20_model.r INFO @ Mon, 03 Jun 2019 11:00:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:00:58: #2 number of paired peaks: 488 WARNING @ Mon, 03 Jun 2019 11:00:58: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Mon, 03 Jun 2019 11:00:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:00:58: start X-correlation... INFO @ Mon, 03 Jun 2019 11:00:58: end of X-cor INFO @ Mon, 03 Jun 2019 11:00:58: #2 finished! INFO @ Mon, 03 Jun 2019 11:00:58: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:00:58: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05_model.r INFO @ Mon, 03 Jun 2019 11:00:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:00:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:59: #1 total tags in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:59: #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 11:00:59: #1 tags after filtering in treatment: 9154419 INFO @ Mon, 03 Jun 2019 11:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:59: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #2 number of paired peaks: 488 WARNING @ Mon, 03 Jun 2019 11:01:00: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Mon, 03 Jun 2019 11:01:00: start model_add_line... INFO @ Mon, 03 Jun 2019 11:01:00: start X-correlation... INFO @ Mon, 03 Jun 2019 11:01:00: end of X-cor INFO @ Mon, 03 Jun 2019 11:01:00: #2 finished! INFO @ Mon, 03 Jun 2019 11:01:00: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10_model.r INFO @ Mon, 03 Jun 2019 11:01:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:01:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:01:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.20_summits.bed INFO @ Mon, 03 Jun 2019 11:01:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.05_summits.bed INFO @ Mon, 03 Jun 2019 11:02:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5852 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287998/SRX287998.10_summits.bed INFO @ Mon, 03 Jun 2019 11:02:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3657 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。