Job ID = 1295530 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,791,523 reads read : 29,791,523 reads written : 29,791,523 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: 00:08:43 29791523 reads; of these: 29791523 (100.00%) were unpaired; of these: 8021536 (26.93%) aligned 0 times 16255279 (54.56%) aligned exactly 1 time 5514708 (18.51%) aligned >1 times 73.07% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 13256054 / 21769987 = 0.6089 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 14:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.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 14:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.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 14:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.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 14:25:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:25:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:26:06: 1000000 INFO @ Mon, 03 Jun 2019 14:26:06: 1000000 INFO @ Mon, 03 Jun 2019 14:26:06: 1000000 INFO @ Mon, 03 Jun 2019 14:26:16: 2000000 INFO @ Mon, 03 Jun 2019 14:26:16: 2000000 INFO @ Mon, 03 Jun 2019 14:26:16: 2000000 INFO @ Mon, 03 Jun 2019 14:26:24: 3000000 INFO @ Mon, 03 Jun 2019 14:26:25: 3000000 INFO @ Mon, 03 Jun 2019 14:26:26: 3000000 INFO @ Mon, 03 Jun 2019 14:26:34: 4000000 INFO @ Mon, 03 Jun 2019 14:26:34: 4000000 INFO @ Mon, 03 Jun 2019 14:26:37: 4000000 INFO @ Mon, 03 Jun 2019 14:26:43: 5000000 INFO @ Mon, 03 Jun 2019 14:26:43: 5000000 INFO @ Mon, 03 Jun 2019 14:26:47: 5000000 INFO @ Mon, 03 Jun 2019 14:26:51: 6000000 INFO @ Mon, 03 Jun 2019 14:26:52: 6000000 INFO @ Mon, 03 Jun 2019 14:26:57: 6000000 INFO @ Mon, 03 Jun 2019 14:27:00: 7000000 INFO @ Mon, 03 Jun 2019 14:27:02: 7000000 INFO @ Mon, 03 Jun 2019 14:27:06: 7000000 INFO @ Mon, 03 Jun 2019 14:27:09: 8000000 INFO @ Mon, 03 Jun 2019 14:27:12: 8000000 INFO @ Mon, 03 Jun 2019 14:27:14: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:27:14: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:27:14: #1 total tags in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:27:14: #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 14:27:14: #1 tags after filtering in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:27:14: #1 finished! INFO @ Mon, 03 Jun 2019 14:27:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:27:15: #2 number of paired peaks: 1224 INFO @ Mon, 03 Jun 2019 14:27:15: start model_add_line... INFO @ Mon, 03 Jun 2019 14:27:15: start X-correlation... INFO @ Mon, 03 Jun 2019 14:27:15: end of X-cor INFO @ Mon, 03 Jun 2019 14:27:15: #2 finished! INFO @ Mon, 03 Jun 2019 14:27:15: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 14:27:15: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 14:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10_model.r INFO @ Mon, 03 Jun 2019 14:27:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:27:16: 8000000 INFO @ Mon, 03 Jun 2019 14:27:17: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:27:17: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:27:17: #1 total tags in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:27:17: #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 14:27:17: #1 tags after filtering in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:27:17: #1 finished! INFO @ Mon, 03 Jun 2019 14:27:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:27:18: #2 number of paired peaks: 1224 INFO @ Mon, 03 Jun 2019 14:27:18: start model_add_line... INFO @ Mon, 03 Jun 2019 14:27:18: start X-correlation... INFO @ Mon, 03 Jun 2019 14:27:18: end of X-cor INFO @ Mon, 03 Jun 2019 14:27:18: #2 finished! INFO @ Mon, 03 Jun 2019 14:27:18: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 14:27:18: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 14:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05_model.r INFO @ Mon, 03 Jun 2019 14:27:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:27:21: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:27:21: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:27:21: #1 total tags in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:27:21: #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 14:27:21: #1 tags after filtering in treatment: 8513933 INFO @ Mon, 03 Jun 2019 14:27:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:27:21: #1 finished! INFO @ Mon, 03 Jun 2019 14:27:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:27:22: #2 number of paired peaks: 1224 INFO @ Mon, 03 Jun 2019 14:27:22: start model_add_line... INFO @ Mon, 03 Jun 2019 14:27:22: start X-correlation... INFO @ Mon, 03 Jun 2019 14:27:22: end of X-cor INFO @ Mon, 03 Jun 2019 14:27:22: #2 finished! INFO @ Mon, 03 Jun 2019 14:27:22: #2 predicted fragment length is 121 bps INFO @ Mon, 03 Jun 2019 14:27:22: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 03 Jun 2019 14:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20_model.r INFO @ Mon, 03 Jun 2019 14:27:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:27:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:27:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:27:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.10_summits.bed INFO @ Mon, 03 Jun 2019 14:27:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2802 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.05_summits.bed INFO @ Mon, 03 Jun 2019 14:27:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5743 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:28:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:28:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:28:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365699/SRX365699.20_summits.bed INFO @ Mon, 03 Jun 2019 14:28:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1472 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。