Job ID = 1294941 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,725,225 reads read : 13,725,225 reads written : 13,725,225 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: 00:04:36 13725225 reads; of these: 13725225 (100.00%) were unpaired; of these: 1060663 (7.73%) aligned 0 times 10485726 (76.40%) aligned exactly 1 time 2178836 (15.87%) aligned >1 times 92.27% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 2073434 / 12664562 = 0.1637 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 11:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.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 11:04:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.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 11:04:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.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 11:04:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:04:19: 1000000 INFO @ Mon, 03 Jun 2019 11:04:20: 1000000 INFO @ Mon, 03 Jun 2019 11:04:20: 1000000 INFO @ Mon, 03 Jun 2019 11:04:27: 2000000 INFO @ Mon, 03 Jun 2019 11:04:28: 2000000 INFO @ Mon, 03 Jun 2019 11:04:29: 2000000 INFO @ Mon, 03 Jun 2019 11:04:35: 3000000 INFO @ Mon, 03 Jun 2019 11:04:36: 3000000 INFO @ Mon, 03 Jun 2019 11:04:37: 3000000 INFO @ Mon, 03 Jun 2019 11:04:43: 4000000 INFO @ Mon, 03 Jun 2019 11:04:45: 4000000 INFO @ Mon, 03 Jun 2019 11:04:46: 4000000 INFO @ Mon, 03 Jun 2019 11:04:51: 5000000 INFO @ Mon, 03 Jun 2019 11:04:52: 5000000 INFO @ Mon, 03 Jun 2019 11:04:54: 5000000 INFO @ Mon, 03 Jun 2019 11:04:59: 6000000 INFO @ Mon, 03 Jun 2019 11:05:00: 6000000 INFO @ Mon, 03 Jun 2019 11:05:02: 6000000 INFO @ Mon, 03 Jun 2019 11:05:06: 7000000 INFO @ Mon, 03 Jun 2019 11:05:08: 7000000 INFO @ Mon, 03 Jun 2019 11:05:10: 7000000 INFO @ Mon, 03 Jun 2019 11:05:12: 8000000 INFO @ Mon, 03 Jun 2019 11:05:16: 8000000 INFO @ Mon, 03 Jun 2019 11:05:19: 8000000 INFO @ Mon, 03 Jun 2019 11:05:19: 9000000 INFO @ Mon, 03 Jun 2019 11:05:24: 9000000 INFO @ Mon, 03 Jun 2019 11:05:26: 10000000 INFO @ Mon, 03 Jun 2019 11:05:27: 9000000 INFO @ Mon, 03 Jun 2019 11:05:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:30: #1 total tags in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:30: #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 11:05:30: #1 tags after filtering in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:30: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:32: #2 number of paired peaks: 4462 INFO @ Mon, 03 Jun 2019 11:05:32: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:32: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:32: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:32: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:32: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:05:32: #2 alternative fragment length(s) may be 251 bps INFO @ Mon, 03 Jun 2019 11:05:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05_model.r INFO @ Mon, 03 Jun 2019 11:05:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:32: 10000000 INFO @ Mon, 03 Jun 2019 11:05:35: 10000000 INFO @ Mon, 03 Jun 2019 11:05:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:37: #1 total tags in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:37: #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 11:05:37: #1 tags after filtering in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:37: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:38: #2 number of paired peaks: 4462 INFO @ Mon, 03 Jun 2019 11:05:38: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:39: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:05:39: #2 alternative fragment length(s) may be 251 bps INFO @ Mon, 03 Jun 2019 11:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20_model.r INFO @ Mon, 03 Jun 2019 11:05:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:40: #1 total tags in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:40: #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 11:05:40: #1 tags after filtering in treatment: 10591128 INFO @ Mon, 03 Jun 2019 11:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:42: #2 number of paired peaks: 4462 INFO @ Mon, 03 Jun 2019 11:05:42: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:42: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:42: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:42: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:42: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:05:42: #2 alternative fragment length(s) may be 251 bps INFO @ Mon, 03 Jun 2019 11:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10_model.r INFO @ Mon, 03 Jun 2019 11:05:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:06:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.05_summits.bed INFO @ Mon, 03 Jun 2019 11:06:26: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8807 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.20_summits.bed INFO @ Mon, 03 Jun 2019 11:06:33: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5250 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288005/SRX288005.10_summits.bed INFO @ Mon, 03 Jun 2019 11:06:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7028 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。