Job ID = 1293810 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,371,298 reads read : 22,371,298 reads written : 22,371,298 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: 00:05:39 22371298 reads; of these: 22371298 (100.00%) were unpaired; of these: 1731198 (7.74%) aligned 0 times 18269548 (81.67%) aligned exactly 1 time 2370552 (10.60%) aligned >1 times 92.26% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 11433642 / 20640100 = 0.5540 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 02:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.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 02:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.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 02:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.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 02:50:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:50:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:50:17: 1000000 INFO @ Mon, 03 Jun 2019 02:50:18: 1000000 INFO @ Mon, 03 Jun 2019 02:50:19: 1000000 INFO @ Mon, 03 Jun 2019 02:50:24: 2000000 INFO @ Mon, 03 Jun 2019 02:50:25: 2000000 INFO @ Mon, 03 Jun 2019 02:50:26: 2000000 INFO @ Mon, 03 Jun 2019 02:50:30: 3000000 INFO @ Mon, 03 Jun 2019 02:50:32: 3000000 INFO @ Mon, 03 Jun 2019 02:50:34: 3000000 INFO @ Mon, 03 Jun 2019 02:50:36: 4000000 INFO @ Mon, 03 Jun 2019 02:50:39: 4000000 INFO @ Mon, 03 Jun 2019 02:50:42: 4000000 INFO @ Mon, 03 Jun 2019 02:50:43: 5000000 INFO @ Mon, 03 Jun 2019 02:50:46: 5000000 INFO @ Mon, 03 Jun 2019 02:50:49: 6000000 INFO @ Mon, 03 Jun 2019 02:50:49: 5000000 INFO @ Mon, 03 Jun 2019 02:50:53: 6000000 INFO @ Mon, 03 Jun 2019 02:50:56: 7000000 INFO @ Mon, 03 Jun 2019 02:50:57: 6000000 INFO @ Mon, 03 Jun 2019 02:51:00: 7000000 INFO @ Mon, 03 Jun 2019 02:51:02: 8000000 INFO @ Mon, 03 Jun 2019 02:51:05: 7000000 INFO @ Mon, 03 Jun 2019 02:51:08: 8000000 INFO @ Mon, 03 Jun 2019 02:51:09: 9000000 INFO @ Mon, 03 Jun 2019 02:51:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:11: #1 total tags in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:11: #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 02:51:11: #1 tags after filtering in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:11: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:12: #2 number of paired peaks: 3254 INFO @ Mon, 03 Jun 2019 02:51:12: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:12: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:12: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:12: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:12: #2 predicted fragment length is 209 bps INFO @ Mon, 03 Jun 2019 02:51:12: #2 alternative fragment length(s) may be 209 bps INFO @ Mon, 03 Jun 2019 02:51:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05_model.r INFO @ Mon, 03 Jun 2019 02:51:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:13: 8000000 INFO @ Mon, 03 Jun 2019 02:51:15: 9000000 INFO @ Mon, 03 Jun 2019 02:51:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:16: #1 total tags in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:16: #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 02:51:17: #1 tags after filtering in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:17: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:18: #2 number of paired peaks: 3254 INFO @ Mon, 03 Jun 2019 02:51:18: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:18: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:18: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:18: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:18: #2 predicted fragment length is 209 bps INFO @ Mon, 03 Jun 2019 02:51:18: #2 alternative fragment length(s) may be 209 bps INFO @ Mon, 03 Jun 2019 02:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20_model.r INFO @ Mon, 03 Jun 2019 02:51:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:20: 9000000 INFO @ Mon, 03 Jun 2019 02:51:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 02:51:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 02:51:22: #1 total tags in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:51:22: #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 02:51:22: #1 tags after filtering in treatment: 9206458 INFO @ Mon, 03 Jun 2019 02:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:51:22: #1 finished! INFO @ Mon, 03 Jun 2019 02:51:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:51:24: #2 number of paired peaks: 3254 INFO @ Mon, 03 Jun 2019 02:51:24: start model_add_line... INFO @ Mon, 03 Jun 2019 02:51:24: start X-correlation... INFO @ Mon, 03 Jun 2019 02:51:24: end of X-cor INFO @ Mon, 03 Jun 2019 02:51:24: #2 finished! INFO @ Mon, 03 Jun 2019 02:51:24: #2 predicted fragment length is 209 bps INFO @ Mon, 03 Jun 2019 02:51:24: #2 alternative fragment length(s) may be 209 bps INFO @ Mon, 03 Jun 2019 02:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10_model.r INFO @ Mon, 03 Jun 2019 02:51:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:51:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.05_summits.bed INFO @ Mon, 03 Jun 2019 02:52:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6443 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.20_summits.bed INFO @ Mon, 03 Jun 2019 02:52:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3350 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1134710/SRX1134710.10_summits.bed INFO @ Mon, 03 Jun 2019 02:52:11: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4750 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。