Job ID = 1295808 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,336,771 reads read : 14,336,771 reads written : 14,336,771 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: 00:04:44 14336771 reads; of these: 14336771 (100.00%) were unpaired; of these: 1057152 (7.37%) aligned 0 times 10382835 (72.42%) aligned exactly 1 time 2896784 (20.21%) aligned >1 times 92.63% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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] 6059535 / 13279619 = 0.4563 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 15:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.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 15:51:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.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 15:51:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.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 15:51:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:11: 1000000 INFO @ Mon, 03 Jun 2019 15:51:11: 1000000 INFO @ Mon, 03 Jun 2019 15:51:13: 1000000 INFO @ Mon, 03 Jun 2019 15:51:19: 2000000 INFO @ Mon, 03 Jun 2019 15:51:19: 2000000 INFO @ Mon, 03 Jun 2019 15:51:21: 2000000 INFO @ Mon, 03 Jun 2019 15:51:26: 3000000 INFO @ Mon, 03 Jun 2019 15:51:26: 3000000 INFO @ Mon, 03 Jun 2019 15:51:29: 3000000 INFO @ Mon, 03 Jun 2019 15:51:33: 4000000 INFO @ Mon, 03 Jun 2019 15:51:34: 4000000 INFO @ Mon, 03 Jun 2019 15:51:37: 4000000 INFO @ Mon, 03 Jun 2019 15:51:41: 5000000 INFO @ Mon, 03 Jun 2019 15:51:41: 5000000 INFO @ Mon, 03 Jun 2019 15:51:45: 5000000 INFO @ Mon, 03 Jun 2019 15:51:48: 6000000 INFO @ Mon, 03 Jun 2019 15:51:49: 6000000 INFO @ Mon, 03 Jun 2019 15:51:53: 6000000 INFO @ Mon, 03 Jun 2019 15:51:55: 7000000 INFO @ Mon, 03 Jun 2019 15:51:57: 7000000 INFO @ Mon, 03 Jun 2019 15:51:57: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:57: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:57: #1 total tags in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:51:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:57: #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 15:51:57: #1 tags after filtering in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:57: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:58: #2 number of paired peaks: 2619 INFO @ Mon, 03 Jun 2019 15:51:58: start model_add_line... INFO @ Mon, 03 Jun 2019 15:51:58: start X-correlation... INFO @ Mon, 03 Jun 2019 15:51:58: end of X-cor INFO @ Mon, 03 Jun 2019 15:51:58: #2 finished! INFO @ Mon, 03 Jun 2019 15:51:58: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:51:58: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05_model.r INFO @ Mon, 03 Jun 2019 15:51:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:51:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:51:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:51:58: #1 total tags in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:51:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:51:58: #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 15:51:59: #1 tags after filtering in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:51:59: #1 finished! INFO @ Mon, 03 Jun 2019 15:51:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:51:59: #2 number of paired peaks: 2619 INFO @ Mon, 03 Jun 2019 15:51:59: start model_add_line... INFO @ Mon, 03 Jun 2019 15:52:00: start X-correlation... INFO @ Mon, 03 Jun 2019 15:52:00: end of X-cor INFO @ Mon, 03 Jun 2019 15:52:00: #2 finished! INFO @ Mon, 03 Jun 2019 15:52:00: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:52:00: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20_model.r INFO @ Mon, 03 Jun 2019 15:52:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:52:02: 7000000 INFO @ Mon, 03 Jun 2019 15:52:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:52:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:52:03: #1 total tags in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:52:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:52:03: #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 15:52:04: #1 tags after filtering in treatment: 7220084 INFO @ Mon, 03 Jun 2019 15:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:52:04: #1 finished! INFO @ Mon, 03 Jun 2019 15:52:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:52:04: #2 number of paired peaks: 2619 INFO @ Mon, 03 Jun 2019 15:52:04: start model_add_line... INFO @ Mon, 03 Jun 2019 15:52:05: start X-correlation... INFO @ Mon, 03 Jun 2019 15:52:05: end of X-cor INFO @ Mon, 03 Jun 2019 15:52:05: #2 finished! INFO @ Mon, 03 Jun 2019 15:52:05: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:52:05: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10_model.r INFO @ Mon, 03 Jun 2019 15:52:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:52:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.05_summits.bed INFO @ Mon, 03 Jun 2019 15:52:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4951 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.20_summits.bed INFO @ Mon, 03 Jun 2019 15:52:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2329 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563528/SRX4563528.10_summits.bed INFO @ Mon, 03 Jun 2019 15:52:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3543 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。