Job ID = 10451014 sra ファイルのダウンロード中... Completed: 512216K bytes transferred in 40 seconds (104210K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 26991232 spots for /home/okishinya/chipatlas/results/dm3/SRX3404052/SRR6303529.sra Written 26991232 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:42 26991232 reads; of these: 26991232 (100.00%) were unpaired; of these: 746767 (2.77%) aligned 0 times 19056986 (70.60%) aligned exactly 1 time 7187479 (26.63%) aligned >1 times 97.23% overall alignment rate Time searching: 00:19:43 Overall time: 00:19:43 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 12 files... [bam_rmdupse_core] 2213590 / 26244465 = 0.0843 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 @ Wed, 07 Feb 2018 15:29:51: # Command line: callpeak -t SRX3404052.bam -f BAM -g dm -n SRX3404052.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404052.20 # format = BAM # ChIP-seq file = ['SRX3404052.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 @ Wed, 07 Feb 2018 15:29:51: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:29:51: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:29:51: # Command line: callpeak -t SRX3404052.bam -f BAM -g dm -n SRX3404052.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404052.05 # format = BAM # ChIP-seq file = ['SRX3404052.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 @ Wed, 07 Feb 2018 15:29:51: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:29:51: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:29:51: # Command line: callpeak -t SRX3404052.bam -f BAM -g dm -n SRX3404052.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404052.10 # format = BAM # ChIP-seq file = ['SRX3404052.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 @ Wed, 07 Feb 2018 15:29:51: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:29:51: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:30:00: 1000000 INFO @ Wed, 07 Feb 2018 15:30:08: 2000000 INFO @ Wed, 07 Feb 2018 15:30:09: 1000000 INFO @ Wed, 07 Feb 2018 15:30:09: 1000000 INFO @ Wed, 07 Feb 2018 15:30:17: 3000000 INFO @ Wed, 07 Feb 2018 15:30:25: 4000000 INFO @ Wed, 07 Feb 2018 15:30:27: 2000000 INFO @ Wed, 07 Feb 2018 15:30:28: 2000000 INFO @ Wed, 07 Feb 2018 15:30:34: 5000000 INFO @ Wed, 07 Feb 2018 15:30:42: 6000000 INFO @ Wed, 07 Feb 2018 15:30:45: 3000000 INFO @ Wed, 07 Feb 2018 15:30:47: 3000000 INFO @ Wed, 07 Feb 2018 15:30:51: 7000000 INFO @ Wed, 07 Feb 2018 15:31:01: 8000000 INFO @ Wed, 07 Feb 2018 15:31:05: 4000000 INFO @ Wed, 07 Feb 2018 15:31:08: 4000000 INFO @ Wed, 07 Feb 2018 15:31:10: 9000000 INFO @ Wed, 07 Feb 2018 15:31:20: 10000000 INFO @ Wed, 07 Feb 2018 15:31:26: 5000000 INFO @ Wed, 07 Feb 2018 15:31:26: 5000000 INFO @ Wed, 07 Feb 2018 15:31:29: 11000000 INFO @ Wed, 07 Feb 2018 15:31:37: 12000000 INFO @ Wed, 07 Feb 2018 15:31:42: 6000000 INFO @ Wed, 07 Feb 2018 15:31:45: 6000000 INFO @ Wed, 07 Feb 2018 15:31:46: 13000000 INFO @ Wed, 07 Feb 2018 15:31:55: 14000000 INFO @ Wed, 07 Feb 2018 15:32:00: 7000000 INFO @ Wed, 07 Feb 2018 15:32:04: 15000000 INFO @ Wed, 07 Feb 2018 15:32:05: 7000000 INFO @ Wed, 07 Feb 2018 15:32:13: 16000000 INFO @ Wed, 07 Feb 2018 15:32:19: 8000000 INFO @ Wed, 07 Feb 2018 15:32:21: 17000000 INFO @ Wed, 07 Feb 2018 15:32:25: 8000000 INFO @ Wed, 07 Feb 2018 15:32:31: 18000000 INFO @ Wed, 07 Feb 2018 15:32:38: 9000000 INFO @ Wed, 07 Feb 2018 15:32:40: 19000000 INFO @ Wed, 07 Feb 2018 15:32:45: 9000000 INFO @ Wed, 07 Feb 2018 15:32:48: 20000000 INFO @ Wed, 07 Feb 2018 15:32:56: 10000000 INFO @ Wed, 07 Feb 2018 15:32:57: 21000000 INFO @ Wed, 07 Feb 2018 15:33:04: 10000000 INFO @ Wed, 07 Feb 2018 15:33:05: 22000000 INFO @ Wed, 07 Feb 2018 15:33:14: 23000000 INFO @ Wed, 07 Feb 2018 15:33:14: 11000000 INFO @ Wed, 07 Feb 2018 15:33:34: 24000000 INFO @ Wed, 07 Feb 2018 15:33:35: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:33:35: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:33:35: #1 total tags in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:33:35: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:33:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:33:36: #1 tags after filtering in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:33:36: #1 finished! INFO @ Wed, 07 Feb 2018 15:33:36: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:33:37: 11000000 INFO @ Wed, 07 Feb 2018 15:33:38: #2 number of paired peaks: 180 WARNING @ Wed, 07 Feb 2018 15:33:38: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 07 Feb 2018 15:33:38: start model_add_line... INFO @ Wed, 07 Feb 2018 15:33:38: start X-correlation... INFO @ Wed, 07 Feb 2018 15:33:38: end of X-cor INFO @ Wed, 07 Feb 2018 15:33:38: #2 finished! INFO @ Wed, 07 Feb 2018 15:33:38: #2 predicted fragment length is 41 bps INFO @ Wed, 07 Feb 2018 15:33:38: #2 alternative fragment length(s) may be 2,41,559 bps INFO @ Wed, 07 Feb 2018 15:33:38: #2.2 Generate R script for model : SRX3404052.20_model.r WARNING @ Wed, 07 Feb 2018 15:33:38: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:33:38: #2 You may need to consider one of the other alternative d(s): 2,41,559 WARNING @ Wed, 07 Feb 2018 15:33:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:33:38: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:33:47: 12000000 INFO @ Wed, 07 Feb 2018 15:33:56: 12000000 INFO @ Wed, 07 Feb 2018 15:34:07: 13000000 INFO @ Wed, 07 Feb 2018 15:34:16: 13000000 INFO @ Wed, 07 Feb 2018 15:34:30: 14000000 INFO @ Wed, 07 Feb 2018 15:34:36: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:34:42: 14000000 INFO @ Wed, 07 Feb 2018 15:34:56: 15000000 INFO @ Wed, 07 Feb 2018 15:35:08: 15000000 INFO @ Wed, 07 Feb 2018 15:35:13: #4 Write output xls file... SRX3404052.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:35:13: #4 Write peak in narrowPeak format file... SRX3404052.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:35:13: #4 Write summits bed file... SRX3404052.20_summits.bed INFO @ Wed, 07 Feb 2018 15:35:13: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (464 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:35:23: 16000000 INFO @ Wed, 07 Feb 2018 15:35:35: 16000000 INFO @ Wed, 07 Feb 2018 15:35:49: 17000000 INFO @ Wed, 07 Feb 2018 15:36:01: 17000000 INFO @ Wed, 07 Feb 2018 15:36:16: 18000000 INFO @ Wed, 07 Feb 2018 15:36:27: 18000000 INFO @ Wed, 07 Feb 2018 15:36:43: 19000000 INFO @ Wed, 07 Feb 2018 15:36:54: 19000000 INFO @ Wed, 07 Feb 2018 15:37:09: 20000000 INFO @ Wed, 07 Feb 2018 15:37:20: 20000000 INFO @ Wed, 07 Feb 2018 15:37:36: 21000000 INFO @ Wed, 07 Feb 2018 15:37:47: 21000000 INFO @ Wed, 07 Feb 2018 15:38:02: 22000000 INFO @ Wed, 07 Feb 2018 15:38:14: 22000000 INFO @ Wed, 07 Feb 2018 15:38:29: 23000000 INFO @ Wed, 07 Feb 2018 15:38:39: 23000000 INFO @ Wed, 07 Feb 2018 15:38:53: 24000000 INFO @ Wed, 07 Feb 2018 15:38:54: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:38:54: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:38:54: #1 total tags in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:38:54: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:38:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:38:55: #1 tags after filtering in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:38:55: #1 finished! INFO @ Wed, 07 Feb 2018 15:38:55: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:38:57: #2 number of paired peaks: 180 WARNING @ Wed, 07 Feb 2018 15:38:57: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 07 Feb 2018 15:38:57: start model_add_line... INFO @ Wed, 07 Feb 2018 15:38:57: start X-correlation... INFO @ Wed, 07 Feb 2018 15:38:57: end of X-cor INFO @ Wed, 07 Feb 2018 15:38:57: #2 finished! INFO @ Wed, 07 Feb 2018 15:38:57: #2 predicted fragment length is 41 bps INFO @ Wed, 07 Feb 2018 15:38:57: #2 alternative fragment length(s) may be 2,41,559 bps INFO @ Wed, 07 Feb 2018 15:38:57: #2.2 Generate R script for model : SRX3404052.05_model.r WARNING @ Wed, 07 Feb 2018 15:38:57: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:38:57: #2 You may need to consider one of the other alternative d(s): 2,41,559 WARNING @ Wed, 07 Feb 2018 15:38:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:38:57: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:39:04: 24000000 INFO @ Wed, 07 Feb 2018 15:39:05: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:39:05: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:39:05: #1 total tags in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:39:05: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:39:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:39:06: #1 tags after filtering in treatment: 24030875 INFO @ Wed, 07 Feb 2018 15:39:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:39:06: #1 finished! INFO @ Wed, 07 Feb 2018 15:39:06: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:39:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:39:08: #2 number of paired peaks: 180 WARNING @ Wed, 07 Feb 2018 15:39:08: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 07 Feb 2018 15:39:08: start model_add_line... INFO @ Wed, 07 Feb 2018 15:39:08: start X-correlation... INFO @ Wed, 07 Feb 2018 15:39:08: end of X-cor INFO @ Wed, 07 Feb 2018 15:39:08: #2 finished! INFO @ Wed, 07 Feb 2018 15:39:08: #2 predicted fragment length is 41 bps INFO @ Wed, 07 Feb 2018 15:39:08: #2 alternative fragment length(s) may be 2,41,559 bps INFO @ Wed, 07 Feb 2018 15:39:08: #2.2 Generate R script for model : SRX3404052.10_model.r WARNING @ Wed, 07 Feb 2018 15:39:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:39:08: #2 You may need to consider one of the other alternative d(s): 2,41,559 WARNING @ Wed, 07 Feb 2018 15:39:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:39:08: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:40:03: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:40:08: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:40:33: #4 Write output xls file... SRX3404052.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:40:33: #4 Write peak in narrowPeak format file... SRX3404052.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:40:33: #4 Write summits bed file... SRX3404052.05_summits.bed INFO @ Wed, 07 Feb 2018 15:40:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2599 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:40:38: #4 Write output xls file... SRX3404052.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:40:38: #4 Write peak in narrowPeak format file... SRX3404052.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:40:38: #4 Write summits bed file... SRX3404052.10_summits.bed INFO @ Wed, 07 Feb 2018 15:40:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1407 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。