Job ID = 2590582 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,733,286 reads read : 67,466,572 reads written : 33,733,286 reads 0-length : 33,733,286 rm: cannot remove ‘[DSE]RR*’: 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: 00:10:38 33733286 reads; of these: 33733286 (100.00%) were unpaired; of these: 2157224 (6.39%) aligned 0 times 25676765 (76.12%) aligned exactly 1 time 5899297 (17.49%) aligned >1 times 93.61% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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 16 files... [bam_rmdupse_core] 7965168 / 31576062 = 0.2523 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, 12 Aug 2019 22:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.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, 12 Aug 2019 22:54:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:54:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.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, 12 Aug 2019 22:54:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:54:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.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, 12 Aug 2019 22:54:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:54:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:54:39: 1000000 INFO @ Mon, 12 Aug 2019 22:54:41: 1000000 INFO @ Mon, 12 Aug 2019 22:54:41: 1000000 INFO @ Mon, 12 Aug 2019 22:54:46: 2000000 INFO @ Mon, 12 Aug 2019 22:54:48: 2000000 INFO @ Mon, 12 Aug 2019 22:54:50: 2000000 INFO @ Mon, 12 Aug 2019 22:54:53: 3000000 INFO @ Mon, 12 Aug 2019 22:54:56: 3000000 INFO @ Mon, 12 Aug 2019 22:54:59: 3000000 INFO @ Mon, 12 Aug 2019 22:55:01: 4000000 INFO @ Mon, 12 Aug 2019 22:55:03: 4000000 INFO @ Mon, 12 Aug 2019 22:55:08: 4000000 INFO @ Mon, 12 Aug 2019 22:55:08: 5000000 INFO @ Mon, 12 Aug 2019 22:55:10: 5000000 INFO @ Mon, 12 Aug 2019 22:55:16: 6000000 INFO @ Mon, 12 Aug 2019 22:55:16: 5000000 INFO @ Mon, 12 Aug 2019 22:55:18: 6000000 INFO @ Mon, 12 Aug 2019 22:55:23: 7000000 INFO @ Mon, 12 Aug 2019 22:55:25: 7000000 INFO @ Mon, 12 Aug 2019 22:55:25: 6000000 INFO @ Mon, 12 Aug 2019 22:55:30: 8000000 INFO @ Mon, 12 Aug 2019 22:55:32: 8000000 INFO @ Mon, 12 Aug 2019 22:55:34: 7000000 INFO @ Mon, 12 Aug 2019 22:55:37: 9000000 INFO @ Mon, 12 Aug 2019 22:55:39: 9000000 INFO @ Mon, 12 Aug 2019 22:55:42: 8000000 INFO @ Mon, 12 Aug 2019 22:55:45: 10000000 INFO @ Mon, 12 Aug 2019 22:55:47: 10000000 INFO @ Mon, 12 Aug 2019 22:55:51: 9000000 INFO @ Mon, 12 Aug 2019 22:55:52: 11000000 INFO @ Mon, 12 Aug 2019 22:55:54: 11000000 INFO @ Mon, 12 Aug 2019 22:55:59: 12000000 INFO @ Mon, 12 Aug 2019 22:56:00: 10000000 INFO @ Mon, 12 Aug 2019 22:56:01: 12000000 INFO @ Mon, 12 Aug 2019 22:56:07: 13000000 INFO @ Mon, 12 Aug 2019 22:56:08: 11000000 INFO @ Mon, 12 Aug 2019 22:56:09: 13000000 INFO @ Mon, 12 Aug 2019 22:56:14: 14000000 INFO @ Mon, 12 Aug 2019 22:56:16: 14000000 INFO @ Mon, 12 Aug 2019 22:56:17: 12000000 INFO @ Mon, 12 Aug 2019 22:56:21: 15000000 INFO @ Mon, 12 Aug 2019 22:56:23: 15000000 INFO @ Mon, 12 Aug 2019 22:56:25: 13000000 INFO @ Mon, 12 Aug 2019 22:56:28: 16000000 INFO @ Mon, 12 Aug 2019 22:56:30: 16000000 INFO @ Mon, 12 Aug 2019 22:56:34: 14000000 INFO @ Mon, 12 Aug 2019 22:56:36: 17000000 INFO @ Mon, 12 Aug 2019 22:56:37: 17000000 INFO @ Mon, 12 Aug 2019 22:56:42: 15000000 INFO @ Mon, 12 Aug 2019 22:56:43: 18000000 INFO @ Mon, 12 Aug 2019 22:56:45: 18000000 INFO @ Mon, 12 Aug 2019 22:56:50: 19000000 INFO @ Mon, 12 Aug 2019 22:56:51: 16000000 INFO @ Mon, 12 Aug 2019 22:56:52: 19000000 INFO @ Mon, 12 Aug 2019 22:56:57: 20000000 INFO @ Mon, 12 Aug 2019 22:56:59: 20000000 INFO @ Mon, 12 Aug 2019 22:56:59: 17000000 INFO @ Mon, 12 Aug 2019 22:57:05: 21000000 INFO @ Mon, 12 Aug 2019 22:57:06: 21000000 INFO @ Mon, 12 Aug 2019 22:57:08: 18000000 INFO @ Mon, 12 Aug 2019 22:57:12: 22000000 INFO @ Mon, 12 Aug 2019 22:57:13: 22000000 INFO @ Mon, 12 Aug 2019 22:57:16: 19000000 INFO @ Mon, 12 Aug 2019 22:57:19: 23000000 INFO @ Mon, 12 Aug 2019 22:57:21: 23000000 INFO @ Mon, 12 Aug 2019 22:57:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:57:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:57:24: #1 total tags in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:57:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:57:24: #1 tags after filtering in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:57:24: #1 finished! INFO @ Mon, 12 Aug 2019 22:57:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:57:25: 20000000 INFO @ Mon, 12 Aug 2019 22:57:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:57:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:57:25: #1 total tags in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:57:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:57:26: #1 tags after filtering in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:57:26: #1 finished! INFO @ Mon, 12 Aug 2019 22:57:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:57:26: #2 number of paired peaks: 127 WARNING @ Mon, 12 Aug 2019 22:57:26: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 12 Aug 2019 22:57:26: start model_add_line... INFO @ Mon, 12 Aug 2019 22:57:26: start X-correlation... INFO @ Mon, 12 Aug 2019 22:57:26: end of X-cor INFO @ Mon, 12 Aug 2019 22:57:26: #2 finished! INFO @ Mon, 12 Aug 2019 22:57:26: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:57:26: #2 alternative fragment length(s) may be 1,33,51,115,159,216,258,346,401,438,492,499,570 bps INFO @ Mon, 12 Aug 2019 22:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05_model.r WARNING @ Mon, 12 Aug 2019 22:57:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:57:26: #2 You may need to consider one of the other alternative d(s): 1,33,51,115,159,216,258,346,401,438,492,499,570 WARNING @ Mon, 12 Aug 2019 22:57:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:57:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:57:28: #2 number of paired peaks: 127 WARNING @ Mon, 12 Aug 2019 22:57:28: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 12 Aug 2019 22:57:28: start model_add_line... INFO @ Mon, 12 Aug 2019 22:57:28: start X-correlation... INFO @ Mon, 12 Aug 2019 22:57:28: end of X-cor INFO @ Mon, 12 Aug 2019 22:57:28: #2 finished! INFO @ Mon, 12 Aug 2019 22:57:28: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:57:28: #2 alternative fragment length(s) may be 1,33,51,115,159,216,258,346,401,438,492,499,570 bps INFO @ Mon, 12 Aug 2019 22:57:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20_model.r WARNING @ Mon, 12 Aug 2019 22:57:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:57:28: #2 You may need to consider one of the other alternative d(s): 1,33,51,115,159,216,258,346,401,438,492,499,570 WARNING @ Mon, 12 Aug 2019 22:57:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:57:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:57:33: 21000000 INFO @ Mon, 12 Aug 2019 22:57:41: 22000000 INFO @ Mon, 12 Aug 2019 22:57:49: 23000000 INFO @ Mon, 12 Aug 2019 22:57:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:57:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:57:55: #1 total tags in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:57:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:57:55: #1 tags after filtering in treatment: 23610894 INFO @ Mon, 12 Aug 2019 22:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:57:55: #1 finished! INFO @ Mon, 12 Aug 2019 22:57:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:57:57: #2 number of paired peaks: 127 WARNING @ Mon, 12 Aug 2019 22:57:57: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Mon, 12 Aug 2019 22:57:57: start model_add_line... INFO @ Mon, 12 Aug 2019 22:57:57: start X-correlation... INFO @ Mon, 12 Aug 2019 22:57:57: end of X-cor INFO @ Mon, 12 Aug 2019 22:57:57: #2 finished! INFO @ Mon, 12 Aug 2019 22:57:57: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 22:57:57: #2 alternative fragment length(s) may be 1,33,51,115,159,216,258,346,401,438,492,499,570 bps INFO @ Mon, 12 Aug 2019 22:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10_model.r WARNING @ Mon, 12 Aug 2019 22:57:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:57:57: #2 You may need to consider one of the other alternative d(s): 1,33,51,115,159,216,258,346,401,438,492,499,570 WARNING @ Mon, 12 Aug 2019 22:57:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:57:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:58:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:58:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.05_summits.bed INFO @ Mon, 12 Aug 2019 22:58:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.20_summits.bed INFO @ Mon, 12 Aug 2019 22:58:47: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:58:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923175/SRX4923175.10_summits.bed INFO @ Mon, 12 Aug 2019 22:59:17: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。