Job ID = 1294594 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,600,850 reads read : 19,600,850 reads written : 19,600,850 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: 00:06:52 19600850 reads; of these: 19600850 (100.00%) were unpaired; of these: 1230452 (6.28%) aligned 0 times 14733038 (75.17%) aligned exactly 1 time 3637360 (18.56%) aligned >1 times 93.72% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 2205705 / 18370398 = 0.1201 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 09:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.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 09:31:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.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 09:31:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.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 09:31:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:31:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:31:16: 1000000 INFO @ Mon, 03 Jun 2019 09:31:17: 1000000 INFO @ Mon, 03 Jun 2019 09:31:19: 1000000 INFO @ Mon, 03 Jun 2019 09:31:25: 2000000 INFO @ Mon, 03 Jun 2019 09:31:28: 2000000 INFO @ Mon, 03 Jun 2019 09:31:30: 2000000 INFO @ Mon, 03 Jun 2019 09:31:34: 3000000 INFO @ Mon, 03 Jun 2019 09:31:38: 3000000 INFO @ Mon, 03 Jun 2019 09:31:41: 3000000 INFO @ Mon, 03 Jun 2019 09:31:43: 4000000 INFO @ Mon, 03 Jun 2019 09:31:49: 4000000 INFO @ Mon, 03 Jun 2019 09:31:52: 5000000 INFO @ Mon, 03 Jun 2019 09:31:52: 4000000 INFO @ Mon, 03 Jun 2019 09:32:00: 5000000 INFO @ Mon, 03 Jun 2019 09:32:01: 6000000 INFO @ Mon, 03 Jun 2019 09:32:03: 5000000 INFO @ Mon, 03 Jun 2019 09:32:10: 7000000 INFO @ Mon, 03 Jun 2019 09:32:10: 6000000 INFO @ Mon, 03 Jun 2019 09:32:14: 6000000 INFO @ Mon, 03 Jun 2019 09:32:19: 8000000 INFO @ Mon, 03 Jun 2019 09:32:21: 7000000 INFO @ Mon, 03 Jun 2019 09:32:25: 7000000 INFO @ Mon, 03 Jun 2019 09:32:28: 9000000 INFO @ Mon, 03 Jun 2019 09:32:31: 8000000 INFO @ Mon, 03 Jun 2019 09:32:36: 8000000 INFO @ Mon, 03 Jun 2019 09:32:37: 10000000 INFO @ Mon, 03 Jun 2019 09:32:42: 9000000 INFO @ Mon, 03 Jun 2019 09:32:46: 11000000 INFO @ Mon, 03 Jun 2019 09:32:47: 9000000 INFO @ Mon, 03 Jun 2019 09:32:53: 10000000 INFO @ Mon, 03 Jun 2019 09:32:55: 12000000 INFO @ Mon, 03 Jun 2019 09:32:58: 10000000 INFO @ Mon, 03 Jun 2019 09:33:03: 11000000 INFO @ Mon, 03 Jun 2019 09:33:05: 13000000 INFO @ Mon, 03 Jun 2019 09:33:09: 11000000 INFO @ Mon, 03 Jun 2019 09:33:13: 12000000 INFO @ Mon, 03 Jun 2019 09:33:14: 14000000 INFO @ Mon, 03 Jun 2019 09:33:20: 12000000 INFO @ Mon, 03 Jun 2019 09:33:23: 15000000 INFO @ Mon, 03 Jun 2019 09:33:24: 13000000 INFO @ Mon, 03 Jun 2019 09:33:32: 13000000 INFO @ Mon, 03 Jun 2019 09:33:32: 16000000 INFO @ Mon, 03 Jun 2019 09:33:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:33:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:33:33: #1 total tags in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:33:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:33:33: #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 09:33:34: #1 tags after filtering in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:33:34: #1 finished! INFO @ Mon, 03 Jun 2019 09:33:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:33:35: 14000000 INFO @ Mon, 03 Jun 2019 09:33:35: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 09:33:35: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 09:33:35: start model_add_line... INFO @ Mon, 03 Jun 2019 09:33:35: start X-correlation... INFO @ Mon, 03 Jun 2019 09:33:35: end of X-cor INFO @ Mon, 03 Jun 2019 09:33:35: #2 finished! INFO @ Mon, 03 Jun 2019 09:33:35: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 09:33:35: #2 alternative fragment length(s) may be 4,85,560 bps INFO @ Mon, 03 Jun 2019 09:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10_model.r WARNING @ Mon, 03 Jun 2019 09:33:35: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:33:35: #2 You may need to consider one of the other alternative d(s): 4,85,560 WARNING @ Mon, 03 Jun 2019 09:33:35: #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 09:33:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:33:43: 14000000 INFO @ Mon, 03 Jun 2019 09:33:46: 15000000 INFO @ Mon, 03 Jun 2019 09:33:55: 15000000 INFO @ Mon, 03 Jun 2019 09:33:56: 16000000 INFO @ Mon, 03 Jun 2019 09:33:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:33:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:33:57: #1 total tags in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:33:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:33:57: #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 09:33:58: #1 tags after filtering in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:33:58: #1 finished! INFO @ Mon, 03 Jun 2019 09:33:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:33:59: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 09:33:59: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 09:33:59: start model_add_line... INFO @ Mon, 03 Jun 2019 09:33:59: start X-correlation... INFO @ Mon, 03 Jun 2019 09:33:59: end of X-cor INFO @ Mon, 03 Jun 2019 09:33:59: #2 finished! INFO @ Mon, 03 Jun 2019 09:33:59: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 09:33:59: #2 alternative fragment length(s) may be 4,85,560 bps INFO @ Mon, 03 Jun 2019 09:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05_model.r WARNING @ Mon, 03 Jun 2019 09:33:59: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:33:59: #2 You may need to consider one of the other alternative d(s): 4,85,560 WARNING @ Mon, 03 Jun 2019 09:33:59: #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 09:33:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:34:06: 16000000 INFO @ Mon, 03 Jun 2019 09:34:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:34:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:34:07: #1 total tags in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:34:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:34:07: #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 09:34:08: #1 tags after filtering in treatment: 16164693 INFO @ Mon, 03 Jun 2019 09:34:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:34:08: #1 finished! INFO @ Mon, 03 Jun 2019 09:34:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:34:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:34:09: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 09:34:09: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 09:34:09: start model_add_line... INFO @ Mon, 03 Jun 2019 09:34:09: start X-correlation... INFO @ Mon, 03 Jun 2019 09:34:09: end of X-cor INFO @ Mon, 03 Jun 2019 09:34:09: #2 finished! INFO @ Mon, 03 Jun 2019 09:34:09: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 09:34:09: #2 alternative fragment length(s) may be 4,85,560 bps INFO @ Mon, 03 Jun 2019 09:34:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20_model.r WARNING @ Mon, 03 Jun 2019 09:34:09: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:34:09: #2 You may need to consider one of the other alternative d(s): 4,85,560 WARNING @ Mon, 03 Jun 2019 09:34:09: #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 09:34:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:34:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:34:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.10_summits.bed INFO @ Mon, 03 Jun 2019 09:34:41: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1277 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:34:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:34:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:35:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:35:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.05_summits.bed INFO @ Mon, 03 Jun 2019 09:35:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2198 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287766/SRX287766.20_summits.bed INFO @ Mon, 03 Jun 2019 09:35:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。