Job ID = 1295178 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,553,061 reads read : 15,553,061 reads written : 15,553,061 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: 00:04:02 15553061 reads; of these: 15553061 (100.00%) were unpaired; of these: 764995 (4.92%) aligned 0 times 13318641 (85.63%) aligned exactly 1 time 1469425 (9.45%) aligned >1 times 95.08% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 1229262 / 14788066 = 0.0831 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 12:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.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 12:36:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.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 12:36:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.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 12:36:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:36:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:37:02: 1000000 INFO @ Mon, 03 Jun 2019 12:37:02: 1000000 INFO @ Mon, 03 Jun 2019 12:37:04: 1000000 INFO @ Mon, 03 Jun 2019 12:37:09: 2000000 INFO @ Mon, 03 Jun 2019 12:37:09: 2000000 INFO @ Mon, 03 Jun 2019 12:37:15: 2000000 INFO @ Mon, 03 Jun 2019 12:37:16: 3000000 INFO @ Mon, 03 Jun 2019 12:37:17: 3000000 INFO @ Mon, 03 Jun 2019 12:37:24: 4000000 INFO @ Mon, 03 Jun 2019 12:37:24: 4000000 INFO @ Mon, 03 Jun 2019 12:37:24: 3000000 INFO @ Mon, 03 Jun 2019 12:37:32: 5000000 INFO @ Mon, 03 Jun 2019 12:37:32: 5000000 INFO @ Mon, 03 Jun 2019 12:37:34: 4000000 INFO @ Mon, 03 Jun 2019 12:37:40: 6000000 INFO @ Mon, 03 Jun 2019 12:37:40: 6000000 INFO @ Mon, 03 Jun 2019 12:37:44: 5000000 INFO @ Mon, 03 Jun 2019 12:37:48: 7000000 INFO @ Mon, 03 Jun 2019 12:37:48: 7000000 INFO @ Mon, 03 Jun 2019 12:37:53: 6000000 INFO @ Mon, 03 Jun 2019 12:37:55: 8000000 INFO @ Mon, 03 Jun 2019 12:37:55: 8000000 INFO @ Mon, 03 Jun 2019 12:38:03: 9000000 INFO @ Mon, 03 Jun 2019 12:38:03: 7000000 INFO @ Mon, 03 Jun 2019 12:38:03: 9000000 INFO @ Mon, 03 Jun 2019 12:38:10: 10000000 INFO @ Mon, 03 Jun 2019 12:38:10: 10000000 INFO @ Mon, 03 Jun 2019 12:38:12: 8000000 INFO @ Mon, 03 Jun 2019 12:38:18: 11000000 INFO @ Mon, 03 Jun 2019 12:38:18: 11000000 INFO @ Mon, 03 Jun 2019 12:38:22: 9000000 INFO @ Mon, 03 Jun 2019 12:38:25: 12000000 INFO @ Mon, 03 Jun 2019 12:38:25: 12000000 INFO @ Mon, 03 Jun 2019 12:38:32: 10000000 INFO @ Mon, 03 Jun 2019 12:38:32: 13000000 INFO @ Mon, 03 Jun 2019 12:38:32: 13000000 INFO @ Mon, 03 Jun 2019 12:38:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:38:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:38:36: #1 total tags in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:38:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:38:36: #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 12:38:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:38:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:38:36: #1 total tags in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:38:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:38:36: #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 12:38:36: #1 tags after filtering in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:38:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:38:36: #1 finished! INFO @ Mon, 03 Jun 2019 12:38:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:38:36: #1 tags after filtering in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:38:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:38:36: #1 finished! INFO @ Mon, 03 Jun 2019 12:38:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:38:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:38:37: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 12:38:37: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 12:38:37: start model_add_line... INFO @ Mon, 03 Jun 2019 12:38:37: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 12:38:37: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 12:38:37: start model_add_line... INFO @ Mon, 03 Jun 2019 12:38:37: start X-correlation... INFO @ Mon, 03 Jun 2019 12:38:37: start X-correlation... INFO @ Mon, 03 Jun 2019 12:38:37: end of X-cor INFO @ Mon, 03 Jun 2019 12:38:37: #2 finished! INFO @ Mon, 03 Jun 2019 12:38:37: #2 predicted fragment length is 248 bps INFO @ Mon, 03 Jun 2019 12:38:37: #2 alternative fragment length(s) may be 2,248,269 bps INFO @ Mon, 03 Jun 2019 12:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20_model.r INFO @ Mon, 03 Jun 2019 12:38:37: end of X-cor INFO @ Mon, 03 Jun 2019 12:38:37: #2 finished! INFO @ Mon, 03 Jun 2019 12:38:37: #2 predicted fragment length is 248 bps INFO @ Mon, 03 Jun 2019 12:38:37: #2 alternative fragment length(s) may be 2,248,269 bps INFO @ Mon, 03 Jun 2019 12:38:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10_model.r INFO @ Mon, 03 Jun 2019 12:38:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:38:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:38:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:38:41: 11000000 INFO @ Mon, 03 Jun 2019 12:38:52: 12000000 INFO @ Mon, 03 Jun 2019 12:39:01: 13000000 INFO @ Mon, 03 Jun 2019 12:39:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:39:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:39:06: #1 total tags in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:39:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:39:06: #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 12:39:07: #1 tags after filtering in treatment: 13558804 INFO @ Mon, 03 Jun 2019 12:39:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:39:07: #1 finished! INFO @ Mon, 03 Jun 2019 12:39:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:39:08: #2 number of paired peaks: 832 WARNING @ Mon, 03 Jun 2019 12:39:08: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Mon, 03 Jun 2019 12:39:08: start model_add_line... INFO @ Mon, 03 Jun 2019 12:39:08: start X-correlation... INFO @ Mon, 03 Jun 2019 12:39:08: end of X-cor INFO @ Mon, 03 Jun 2019 12:39:08: #2 finished! INFO @ Mon, 03 Jun 2019 12:39:08: #2 predicted fragment length is 248 bps INFO @ Mon, 03 Jun 2019 12:39:08: #2 alternative fragment length(s) may be 2,248,269 bps INFO @ Mon, 03 Jun 2019 12:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05_model.r INFO @ Mon, 03 Jun 2019 12:39:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:39:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:39:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.10_summits.bed INFO @ Mon, 03 Jun 2019 12:39:38: Done! INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.20_summits.bed INFO @ Mon, 03 Jun 2019 12:39:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:39:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:40:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:40:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:40:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331368/SRX331368.05_summits.bed INFO @ Mon, 03 Jun 2019 12:40:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3746 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。