Job ID = 1293308 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,567,533 reads read : 12,567,533 reads written : 12,567,533 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: 00:04:21 12567533 reads; of these: 12567533 (100.00%) were unpaired; of these: 937458 (7.46%) aligned 0 times 10858957 (86.40%) aligned exactly 1 time 771118 (6.14%) aligned >1 times 92.54% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 3647620 / 11630075 = 0.3136 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 @ Sun, 02 Jun 2019 23:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.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 @ Sun, 02 Jun 2019 23:02:07: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:07: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.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 @ Sun, 02 Jun 2019 23:02:07: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:07: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.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 @ Sun, 02 Jun 2019 23:02:07: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:02:07: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:02:22: 1000000 INFO @ Sun, 02 Jun 2019 23:02:23: 1000000 INFO @ Sun, 02 Jun 2019 23:02:23: 1000000 INFO @ Sun, 02 Jun 2019 23:02:36: 2000000 INFO @ Sun, 02 Jun 2019 23:02:39: 2000000 INFO @ Sun, 02 Jun 2019 23:02:39: 2000000 INFO @ Sun, 02 Jun 2019 23:02:49: 3000000 INFO @ Sun, 02 Jun 2019 23:02:53: 3000000 INFO @ Sun, 02 Jun 2019 23:02:54: 3000000 INFO @ Sun, 02 Jun 2019 23:03:02: 4000000 INFO @ Sun, 02 Jun 2019 23:03:07: 4000000 INFO @ Sun, 02 Jun 2019 23:03:09: 4000000 INFO @ Sun, 02 Jun 2019 23:03:16: 5000000 INFO @ Sun, 02 Jun 2019 23:03:19: 5000000 INFO @ Sun, 02 Jun 2019 23:03:24: 5000000 INFO @ Sun, 02 Jun 2019 23:03:29: 6000000 INFO @ Sun, 02 Jun 2019 23:03:32: 6000000 INFO @ Sun, 02 Jun 2019 23:03:39: 6000000 INFO @ Sun, 02 Jun 2019 23:03:43: 7000000 INFO @ Sun, 02 Jun 2019 23:03:47: 7000000 INFO @ Sun, 02 Jun 2019 23:03:56: 7000000 INFO @ Sun, 02 Jun 2019 23:03:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:03:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:03:58: #1 total tags in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:03:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:03:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:03:58: #1 tags after filtering in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:03:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:03:58: #1 finished! INFO @ Sun, 02 Jun 2019 23:03:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:03:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:03:59: #2 number of paired peaks: 4255 INFO @ Sun, 02 Jun 2019 23:03:59: start model_add_line... INFO @ Sun, 02 Jun 2019 23:03:59: start X-correlation... INFO @ Sun, 02 Jun 2019 23:03:59: end of X-cor INFO @ Sun, 02 Jun 2019 23:03:59: #2 finished! INFO @ Sun, 02 Jun 2019 23:03:59: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 23:03:59: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 23:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20_model.r INFO @ Sun, 02 Jun 2019 23:04:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:01: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:04:01: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:04:01: #1 total tags in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:04:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:04:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:04:01: #1 tags after filtering in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:04:01: #1 finished! INFO @ Sun, 02 Jun 2019 23:04:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:04:02: #2 number of paired peaks: 4255 INFO @ Sun, 02 Jun 2019 23:04:02: start model_add_line... INFO @ Sun, 02 Jun 2019 23:04:02: start X-correlation... INFO @ Sun, 02 Jun 2019 23:04:02: end of X-cor INFO @ Sun, 02 Jun 2019 23:04:02: #2 finished! INFO @ Sun, 02 Jun 2019 23:04:02: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 23:04:02: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 23:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05_model.r INFO @ Sun, 02 Jun 2019 23:04:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:10: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:04:10: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:04:10: #1 total tags in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:04:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:04:10: #1 tags after filtering in treatment: 7982455 INFO @ Sun, 02 Jun 2019 23:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:04:10: #1 finished! INFO @ Sun, 02 Jun 2019 23:04:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:04:11: #2 number of paired peaks: 4255 INFO @ Sun, 02 Jun 2019 23:04:11: start model_add_line... INFO @ Sun, 02 Jun 2019 23:04:11: start X-correlation... INFO @ Sun, 02 Jun 2019 23:04:12: end of X-cor INFO @ Sun, 02 Jun 2019 23:04:12: #2 finished! INFO @ Sun, 02 Jun 2019 23:04:12: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 23:04:12: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 02 Jun 2019 23:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10_model.r INFO @ Sun, 02 Jun 2019 23:04:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:04:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:04:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:04:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.20_summits.bed INFO @ Sun, 02 Jun 2019 23:05:00: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1772 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:05:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.05_summits.bed INFO @ Sun, 02 Jun 2019 23:05:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7414 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX101807/ERX101807.10_summits.bed INFO @ Sun, 02 Jun 2019 23:05:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4239 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。