Job ID = 1309283 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,833,594 reads read : 11,667,188 reads written : 5,833,594 reads 0-length : 5,833,594 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: 00:05:23 5833594 reads; of these: 5833594 (100.00%) were unpaired; of these: 105562 (1.81%) aligned 0 times 4668876 (80.03%) aligned exactly 1 time 1059156 (18.16%) aligned >1 times 98.19% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 155447 / 5728032 = 0.0271 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 23:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.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 23:27:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:27:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.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 23:27:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:27:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.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 23:27:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:27:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:27:19: 1000000 INFO @ Mon, 03 Jun 2019 23:27:20: 1000000 INFO @ Mon, 03 Jun 2019 23:27:21: 1000000 INFO @ Mon, 03 Jun 2019 23:27:29: 2000000 INFO @ Mon, 03 Jun 2019 23:27:30: 2000000 INFO @ Mon, 03 Jun 2019 23:27:34: 2000000 INFO @ Mon, 03 Jun 2019 23:27:40: 3000000 INFO @ Mon, 03 Jun 2019 23:27:40: 3000000 INFO @ Mon, 03 Jun 2019 23:27:45: 3000000 INFO @ Mon, 03 Jun 2019 23:27:50: 4000000 INFO @ Mon, 03 Jun 2019 23:27:51: 4000000 INFO @ Mon, 03 Jun 2019 23:27:56: 4000000 INFO @ Mon, 03 Jun 2019 23:28:00: 5000000 INFO @ Mon, 03 Jun 2019 23:28:01: 5000000 INFO @ Mon, 03 Jun 2019 23:28:06: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:28:06: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:28:06: #1 total tags in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:28:06: #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 23:28:06: #1 tags after filtering in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:28:06: #1 finished! INFO @ Mon, 03 Jun 2019 23:28:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:28:07: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 23:28:07: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 23:28:07: start model_add_line... INFO @ Mon, 03 Jun 2019 23:28:07: start X-correlation... INFO @ Mon, 03 Jun 2019 23:28:07: end of X-cor INFO @ Mon, 03 Jun 2019 23:28:07: #2 finished! INFO @ Mon, 03 Jun 2019 23:28:07: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 23:28:07: #2 alternative fragment length(s) may be 157,534,536,567,595 bps INFO @ Mon, 03 Jun 2019 23:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20_model.r WARNING @ Mon, 03 Jun 2019 23:28:07: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:28:07: #2 You may need to consider one of the other alternative d(s): 157,534,536,567,595 WARNING @ Mon, 03 Jun 2019 23:28:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 23:28:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:28:07: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:28:07: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:28:07: #1 total tags in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:28:07: #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 23:28:07: #1 tags after filtering in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:28:07: #1 finished! INFO @ Mon, 03 Jun 2019 23:28:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:28:08: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 23:28:08: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 23:28:08: start model_add_line... INFO @ Mon, 03 Jun 2019 23:28:08: start X-correlation... INFO @ Mon, 03 Jun 2019 23:28:08: end of X-cor INFO @ Mon, 03 Jun 2019 23:28:08: #2 finished! INFO @ Mon, 03 Jun 2019 23:28:08: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 23:28:08: #2 alternative fragment length(s) may be 157,534,536,567,595 bps INFO @ Mon, 03 Jun 2019 23:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10_model.r WARNING @ Mon, 03 Jun 2019 23:28:08: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:28:08: #2 You may need to consider one of the other alternative d(s): 157,534,536,567,595 WARNING @ Mon, 03 Jun 2019 23:28:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 23:28:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:28:08: 5000000 INFO @ Mon, 03 Jun 2019 23:28:14: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 23:28:14: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 23:28:14: #1 total tags in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:28:14: #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 23:28:15: #1 tags after filtering in treatment: 5572585 INFO @ Mon, 03 Jun 2019 23:28:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:28:15: #1 finished! INFO @ Mon, 03 Jun 2019 23:28:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:28:15: #2 number of paired peaks: 110 WARNING @ Mon, 03 Jun 2019 23:28:15: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Mon, 03 Jun 2019 23:28:15: start model_add_line... INFO @ Mon, 03 Jun 2019 23:28:15: start X-correlation... INFO @ Mon, 03 Jun 2019 23:28:15: end of X-cor INFO @ Mon, 03 Jun 2019 23:28:15: #2 finished! INFO @ Mon, 03 Jun 2019 23:28:15: #2 predicted fragment length is 157 bps INFO @ Mon, 03 Jun 2019 23:28:15: #2 alternative fragment length(s) may be 157,534,536,567,595 bps INFO @ Mon, 03 Jun 2019 23:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05_model.r WARNING @ Mon, 03 Jun 2019 23:28:15: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:28:15: #2 You may need to consider one of the other alternative d(s): 157,534,536,567,595 WARNING @ Mon, 03 Jun 2019 23:28:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 23:28:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:28:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:28:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:28:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.20_summits.bed INFO @ Mon, 03 Jun 2019 23:28:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.10_summits.bed INFO @ Mon, 03 Jun 2019 23:28:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864530/SRX864530.05_summits.bed INFO @ Mon, 03 Jun 2019 23:28:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。