Job ID = 2590613 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 76,168,129 reads read : 152,336,258 reads written : 76,168,129 reads 0-length : 76,168,129 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: 00:41:32 76168129 reads; of these: 76168129 (100.00%) were unpaired; of these: 1378398 (1.81%) aligned 0 times 25310330 (33.23%) aligned exactly 1 time 49479401 (64.96%) aligned >1 times 98.19% overall alignment rate Time searching: 00:41:32 Overall time: 00:41:32 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 32 files... [bam_rmdupse_core] 31470290 / 74789731 = 0.4208 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 23:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.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 23:52:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:52:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.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 23:52:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:52:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.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 23:52:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:52:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:52:52: 1000000 INFO @ Mon, 12 Aug 2019 23:52:54: 1000000 INFO @ Mon, 12 Aug 2019 23:52:54: 1000000 INFO @ Mon, 12 Aug 2019 23:53:01: 2000000 INFO @ Mon, 12 Aug 2019 23:53:02: 2000000 INFO @ Mon, 12 Aug 2019 23:53:02: 2000000 INFO @ Mon, 12 Aug 2019 23:53:11: 3000000 INFO @ Mon, 12 Aug 2019 23:53:12: 3000000 INFO @ Mon, 12 Aug 2019 23:53:12: 3000000 INFO @ Mon, 12 Aug 2019 23:53:20: 4000000 INFO @ Mon, 12 Aug 2019 23:53:20: 4000000 INFO @ Mon, 12 Aug 2019 23:53:21: 4000000 INFO @ Mon, 12 Aug 2019 23:53:28: 5000000 INFO @ Mon, 12 Aug 2019 23:53:28: 5000000 INFO @ Mon, 12 Aug 2019 23:53:30: 5000000 INFO @ Mon, 12 Aug 2019 23:53:36: 6000000 INFO @ Mon, 12 Aug 2019 23:53:37: 6000000 INFO @ Mon, 12 Aug 2019 23:53:38: 6000000 INFO @ Mon, 12 Aug 2019 23:53:44: 7000000 INFO @ Mon, 12 Aug 2019 23:53:45: 7000000 INFO @ Mon, 12 Aug 2019 23:53:46: 7000000 INFO @ Mon, 12 Aug 2019 23:53:51: 8000000 INFO @ Mon, 12 Aug 2019 23:53:53: 8000000 INFO @ Mon, 12 Aug 2019 23:53:55: 8000000 INFO @ Mon, 12 Aug 2019 23:53:58: 9000000 INFO @ Mon, 12 Aug 2019 23:54:00: 9000000 INFO @ Mon, 12 Aug 2019 23:54:02: 9000000 INFO @ Mon, 12 Aug 2019 23:54:04: 10000000 INFO @ Mon, 12 Aug 2019 23:54:07: 10000000 INFO @ Mon, 12 Aug 2019 23:54:10: 10000000 INFO @ Mon, 12 Aug 2019 23:54:12: 11000000 INFO @ Mon, 12 Aug 2019 23:54:14: 11000000 INFO @ Mon, 12 Aug 2019 23:54:18: 11000000 INFO @ Mon, 12 Aug 2019 23:54:20: 12000000 INFO @ Mon, 12 Aug 2019 23:54:22: 12000000 INFO @ Mon, 12 Aug 2019 23:54:25: 12000000 INFO @ Mon, 12 Aug 2019 23:54:28: 13000000 INFO @ Mon, 12 Aug 2019 23:54:30: 13000000 INFO @ Mon, 12 Aug 2019 23:54:32: 13000000 INFO @ Mon, 12 Aug 2019 23:54:36: 14000000 INFO @ Mon, 12 Aug 2019 23:54:38: 14000000 INFO @ Mon, 12 Aug 2019 23:54:39: 14000000 INFO @ Mon, 12 Aug 2019 23:54:43: 15000000 INFO @ Mon, 12 Aug 2019 23:54:45: 15000000 INFO @ Mon, 12 Aug 2019 23:54:46: 15000000 INFO @ Mon, 12 Aug 2019 23:54:52: 16000000 INFO @ Mon, 12 Aug 2019 23:54:53: 16000000 INFO @ Mon, 12 Aug 2019 23:54:53: 16000000 INFO @ Mon, 12 Aug 2019 23:54:59: 17000000 INFO @ Mon, 12 Aug 2019 23:55:01: 17000000 INFO @ Mon, 12 Aug 2019 23:55:02: 17000000 INFO @ Mon, 12 Aug 2019 23:55:06: 18000000 INFO @ Mon, 12 Aug 2019 23:55:07: 18000000 INFO @ Mon, 12 Aug 2019 23:55:10: 18000000 INFO @ Mon, 12 Aug 2019 23:55:13: 19000000 INFO @ Mon, 12 Aug 2019 23:55:14: 19000000 INFO @ Mon, 12 Aug 2019 23:55:19: 19000000 INFO @ Mon, 12 Aug 2019 23:55:19: 20000000 INFO @ Mon, 12 Aug 2019 23:55:21: 20000000 INFO @ Mon, 12 Aug 2019 23:55:26: 21000000 INFO @ Mon, 12 Aug 2019 23:55:26: 20000000 INFO @ Mon, 12 Aug 2019 23:55:28: 21000000 INFO @ Mon, 12 Aug 2019 23:55:33: 22000000 INFO @ Mon, 12 Aug 2019 23:55:33: 21000000 INFO @ Mon, 12 Aug 2019 23:55:35: 22000000 INFO @ Mon, 12 Aug 2019 23:55:39: 23000000 INFO @ Mon, 12 Aug 2019 23:55:41: 22000000 INFO @ Mon, 12 Aug 2019 23:55:43: 23000000 INFO @ Mon, 12 Aug 2019 23:55:46: 24000000 INFO @ Mon, 12 Aug 2019 23:55:48: 23000000 INFO @ Mon, 12 Aug 2019 23:55:50: 24000000 INFO @ Mon, 12 Aug 2019 23:55:52: 25000000 INFO @ Mon, 12 Aug 2019 23:55:55: 24000000 INFO @ Mon, 12 Aug 2019 23:55:57: 25000000 INFO @ Mon, 12 Aug 2019 23:55:59: 26000000 INFO @ Mon, 12 Aug 2019 23:56:03: 25000000 INFO @ Mon, 12 Aug 2019 23:56:05: 26000000 INFO @ Mon, 12 Aug 2019 23:56:05: 27000000 INFO @ Mon, 12 Aug 2019 23:56:10: 26000000 INFO @ Mon, 12 Aug 2019 23:56:12: 27000000 INFO @ Mon, 12 Aug 2019 23:56:12: 28000000 INFO @ Mon, 12 Aug 2019 23:56:17: 27000000 INFO @ Mon, 12 Aug 2019 23:56:18: 28000000 INFO @ Mon, 12 Aug 2019 23:56:18: 29000000 INFO @ Mon, 12 Aug 2019 23:56:24: 28000000 INFO @ Mon, 12 Aug 2019 23:56:25: 30000000 INFO @ Mon, 12 Aug 2019 23:56:25: 29000000 INFO @ Mon, 12 Aug 2019 23:56:31: 31000000 INFO @ Mon, 12 Aug 2019 23:56:31: 29000000 INFO @ Mon, 12 Aug 2019 23:56:33: 30000000 INFO @ Mon, 12 Aug 2019 23:56:38: 32000000 INFO @ Mon, 12 Aug 2019 23:56:39: 30000000 INFO @ Mon, 12 Aug 2019 23:56:40: 31000000 INFO @ Mon, 12 Aug 2019 23:56:44: 33000000 INFO @ Mon, 12 Aug 2019 23:56:46: 31000000 INFO @ Mon, 12 Aug 2019 23:56:47: 32000000 INFO @ Mon, 12 Aug 2019 23:56:50: 34000000 INFO @ Mon, 12 Aug 2019 23:56:53: 32000000 INFO @ Mon, 12 Aug 2019 23:56:54: 33000000 INFO @ Mon, 12 Aug 2019 23:56:57: 35000000 INFO @ Mon, 12 Aug 2019 23:57:00: 33000000 INFO @ Mon, 12 Aug 2019 23:57:01: 34000000 INFO @ Mon, 12 Aug 2019 23:57:03: 36000000 INFO @ Mon, 12 Aug 2019 23:57:07: 34000000 INFO @ Mon, 12 Aug 2019 23:57:09: 35000000 INFO @ Mon, 12 Aug 2019 23:57:10: 37000000 INFO @ Mon, 12 Aug 2019 23:57:15: 35000000 INFO @ Mon, 12 Aug 2019 23:57:16: 36000000 INFO @ Mon, 12 Aug 2019 23:57:16: 38000000 INFO @ Mon, 12 Aug 2019 23:57:22: 36000000 INFO @ Mon, 12 Aug 2019 23:57:23: 39000000 INFO @ Mon, 12 Aug 2019 23:57:23: 37000000 INFO @ Mon, 12 Aug 2019 23:57:29: 40000000 INFO @ Mon, 12 Aug 2019 23:57:29: 37000000 INFO @ Mon, 12 Aug 2019 23:57:31: 38000000 INFO @ Mon, 12 Aug 2019 23:57:36: 41000000 INFO @ Mon, 12 Aug 2019 23:57:36: 38000000 INFO @ Mon, 12 Aug 2019 23:57:38: 39000000 INFO @ Mon, 12 Aug 2019 23:57:42: 42000000 INFO @ Mon, 12 Aug 2019 23:57:43: 39000000 INFO @ Mon, 12 Aug 2019 23:57:45: 40000000 INFO @ Mon, 12 Aug 2019 23:57:49: 43000000 INFO @ Mon, 12 Aug 2019 23:57:50: 40000000 INFO @ Mon, 12 Aug 2019 23:57:51: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:51: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:51: #1 total tags in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:57:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:51: #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 23:57:52: #1 tags after filtering in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:57:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:52: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:52: 41000000 INFO @ Mon, 12 Aug 2019 23:57:55: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 23:57:55: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 23:57:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:56: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:56: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:56: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:56: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 23:57:56: #2 alternative fragment length(s) may be 1,23,26,49 bps INFO @ Mon, 12 Aug 2019 23:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05_model.r WARNING @ Mon, 12 Aug 2019 23:57:56: #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 23:57:56: #2 You may need to consider one of the other alternative d(s): 1,23,26,49 WARNING @ Mon, 12 Aug 2019 23:57:56: #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 23:57:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:57: 41000000 INFO @ Mon, 12 Aug 2019 23:57:59: 42000000 INFO @ Mon, 12 Aug 2019 23:58:05: 42000000 INFO @ Mon, 12 Aug 2019 23:58:06: 43000000 INFO @ Mon, 12 Aug 2019 23:58:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:58:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:58:09: #1 total tags in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:58:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:58:09: #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 23:58:10: #1 tags after filtering in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:58:10: #1 finished! INFO @ Mon, 12 Aug 2019 23:58:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:58:11: 43000000 INFO @ Mon, 12 Aug 2019 23:58:13: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 23:58:13: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 23:58:13: start model_add_line... INFO @ Mon, 12 Aug 2019 23:58:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:58:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:58:14: #1 total tags in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:58:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:58:14: #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 23:58:14: start X-correlation... INFO @ Mon, 12 Aug 2019 23:58:14: end of X-cor INFO @ Mon, 12 Aug 2019 23:58:14: #2 finished! INFO @ Mon, 12 Aug 2019 23:58:14: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 23:58:14: #2 alternative fragment length(s) may be 1,23,26,49 bps INFO @ Mon, 12 Aug 2019 23:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10_model.r WARNING @ Mon, 12 Aug 2019 23:58:14: #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 23:58:14: #2 You may need to consider one of the other alternative d(s): 1,23,26,49 WARNING @ Mon, 12 Aug 2019 23:58:14: #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 23:58:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:58:14: #1 tags after filtering in treatment: 43319441 INFO @ Mon, 12 Aug 2019 23:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:58:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:58:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:58:18: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 23:58:18: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 23:58:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:58:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:58:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:58:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:58:18: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 23:58:18: #2 alternative fragment length(s) may be 1,23,26,49 bps INFO @ Mon, 12 Aug 2019 23:58:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20_model.r WARNING @ Mon, 12 Aug 2019 23:58:18: #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 23:58:18: #2 You may need to consider one of the other alternative d(s): 1,23,26,49 WARNING @ Mon, 12 Aug 2019 23:58:18: #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 23:58:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.05_summits.bed INFO @ Mon, 12 Aug 2019 23:59:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.10_summits.bed INFO @ Mon, 12 Aug 2019 23:59:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923197/SRX4923197.20_summits.bed INFO @ Tue, 13 Aug 2019 00:00:04: Done! pass1 - making usageList (0 chroms): 1 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。