Job ID = 4178492 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,193,733 reads read : 19,193,733 reads written : 19,193,733 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:55 19193733 reads; of these: 19193733 (100.00%) were unpaired; of these: 578135 (3.01%) aligned 0 times 13451381 (70.08%) aligned exactly 1 time 5164217 (26.91%) aligned >1 times 96.99% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 5094091 / 18615598 = 0.2736 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.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 @ Thu, 05 Dec 2019 12:43:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:43:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:43:45: 1000000 INFO @ Thu, 05 Dec 2019 12:43:51: 2000000 INFO @ Thu, 05 Dec 2019 12:43:58: 3000000 INFO @ Thu, 05 Dec 2019 12:44:05: 4000000 INFO @ Thu, 05 Dec 2019 12:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.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 @ Thu, 05 Dec 2019 12:44:08: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:08: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:11: 5000000 INFO @ Thu, 05 Dec 2019 12:44:15: 1000000 INFO @ Thu, 05 Dec 2019 12:44:18: 6000000 INFO @ Thu, 05 Dec 2019 12:44:21: 2000000 INFO @ Thu, 05 Dec 2019 12:44:24: 7000000 INFO @ Thu, 05 Dec 2019 12:44:27: 3000000 INFO @ Thu, 05 Dec 2019 12:44:31: 8000000 INFO @ Thu, 05 Dec 2019 12:44:34: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:44:37: 9000000 INFO @ Thu, 05 Dec 2019 12:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.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 @ Thu, 05 Dec 2019 12:44:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:44:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:44:40: 5000000 INFO @ Thu, 05 Dec 2019 12:44:43: 10000000 INFO @ Thu, 05 Dec 2019 12:44:44: 1000000 INFO @ Thu, 05 Dec 2019 12:44:47: 6000000 INFO @ Thu, 05 Dec 2019 12:44:49: 11000000 INFO @ Thu, 05 Dec 2019 12:44:50: 2000000 INFO @ Thu, 05 Dec 2019 12:44:53: 7000000 INFO @ Thu, 05 Dec 2019 12:44:55: 12000000 INFO @ Thu, 05 Dec 2019 12:44:55: 3000000 INFO @ Thu, 05 Dec 2019 12:44:59: 8000000 INFO @ Thu, 05 Dec 2019 12:45:00: 13000000 INFO @ Thu, 05 Dec 2019 12:45:01: 4000000 INFO @ Thu, 05 Dec 2019 12:45:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:03: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:03: #1 total tags in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:04: #1 tags after filtering in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:04: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:04: 9000000 INFO @ Thu, 05 Dec 2019 12:45:05: #2 number of paired peaks: 941 WARNING @ Thu, 05 Dec 2019 12:45:05: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:05: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:05: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:05: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:05: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:05: #2 predicted fragment length is 145 bps INFO @ Thu, 05 Dec 2019 12:45:05: #2 alternative fragment length(s) may be 20,145,251,272,295,315,489,522 bps INFO @ Thu, 05 Dec 2019 12:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05_model.r INFO @ Thu, 05 Dec 2019 12:45:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:07: 5000000 INFO @ Thu, 05 Dec 2019 12:45:10: 10000000 INFO @ Thu, 05 Dec 2019 12:45:13: 6000000 INFO @ Thu, 05 Dec 2019 12:45:15: 11000000 INFO @ Thu, 05 Dec 2019 12:45:19: 7000000 INFO @ Thu, 05 Dec 2019 12:45:20: 12000000 INFO @ Thu, 05 Dec 2019 12:45:24: 8000000 INFO @ Thu, 05 Dec 2019 12:45:26: 13000000 INFO @ Thu, 05 Dec 2019 12:45:28: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:28: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:28: #1 total tags in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:28: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:29: #1 tags after filtering in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:29: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:29: #2 number of paired peaks: 941 WARNING @ Thu, 05 Dec 2019 12:45:29: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:29: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:30: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:30: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:30: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:30: #2 predicted fragment length is 145 bps INFO @ Thu, 05 Dec 2019 12:45:30: #2 alternative fragment length(s) may be 20,145,251,272,295,315,489,522 bps INFO @ Thu, 05 Dec 2019 12:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10_model.r INFO @ Thu, 05 Dec 2019 12:45:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:45:30: 9000000 INFO @ Thu, 05 Dec 2019 12:45:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:36: 10000000 INFO @ Thu, 05 Dec 2019 12:45:41: 11000000 INFO @ Thu, 05 Dec 2019 12:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.05_summits.bed INFO @ Thu, 05 Dec 2019 12:45:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2288 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:45:47: 12000000 INFO @ Thu, 05 Dec 2019 12:45:52: 13000000 INFO @ Thu, 05 Dec 2019 12:45:55: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:45:55: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:45:55: #1 total tags in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:55: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:45:55: #1 tags after filtering in treatment: 13521507 INFO @ Thu, 05 Dec 2019 12:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:45:55: #1 finished! INFO @ Thu, 05 Dec 2019 12:45:55: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:45:55: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:45:56: #2 number of paired peaks: 941 WARNING @ Thu, 05 Dec 2019 12:45:56: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Thu, 05 Dec 2019 12:45:56: start model_add_line... INFO @ Thu, 05 Dec 2019 12:45:56: start X-correlation... INFO @ Thu, 05 Dec 2019 12:45:56: end of X-cor INFO @ Thu, 05 Dec 2019 12:45:56: #2 finished! INFO @ Thu, 05 Dec 2019 12:45:56: #2 predicted fragment length is 145 bps INFO @ Thu, 05 Dec 2019 12:45:56: #2 alternative fragment length(s) may be 20,145,251,272,295,315,489,522 bps INFO @ Thu, 05 Dec 2019 12:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20_model.r INFO @ Thu, 05 Dec 2019 12:45:56: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.10_summits.bed INFO @ Thu, 05 Dec 2019 12:46:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1149 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:46:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5535392/SRX5535392.20_summits.bed INFO @ Thu, 05 Dec 2019 12:46:37: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。