Job ID = 9730418 sra ファイルのダウンロード中... Completed: 506525K bytes transferred in 8 seconds (507435K bits/sec), in 2 files, 3 directories. 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 12318783 spots for /home/okishinya/chipatlas/results/ce10/SRX2582952/SRR5279127.sra Written 12318783 spots total Written 12676985 spots for /home/okishinya/chipatlas/results/ce10/SRX2582952/SRR5279128.sra Written 12676985 spots total 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: 00:06:05 24995768 reads; of these: 24995768 (100.00%) were unpaired; of these: 2944989 (11.78%) aligned 0 times 18532404 (74.14%) aligned exactly 1 time 3518375 (14.08%) aligned >1 times 88.22% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2104098 / 22050779 = 0.0954 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 @ Sun, 03 Sep 2017 01:05:04: # Command line: callpeak -t SRX2582952.bam -f BAM -g ce -n SRX2582952.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2582952.20 # format = BAM # ChIP-seq file = ['SRX2582952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Sep 2017 01:05:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:05:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:05:04: # Command line: callpeak -t SRX2582952.bam -f BAM -g ce -n SRX2582952.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2582952.10 # format = BAM # ChIP-seq file = ['SRX2582952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Sep 2017 01:05:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:05:04: # Command line: callpeak -t SRX2582952.bam -f BAM -g ce -n SRX2582952.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2582952.05 # format = BAM # ChIP-seq file = ['SRX2582952.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Sep 2017 01:05:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:05:04: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:05:04: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:05:11: 1000000 INFO @ Sun, 03 Sep 2017 01:05:14: 1000000 INFO @ Sun, 03 Sep 2017 01:05:14: 1000000 INFO @ Sun, 03 Sep 2017 01:05:18: 2000000 INFO @ Sun, 03 Sep 2017 01:05:23: 2000000 INFO @ Sun, 03 Sep 2017 01:05:23: 2000000 INFO @ Sun, 03 Sep 2017 01:05:26: 3000000 INFO @ Sun, 03 Sep 2017 01:05:33: 3000000 INFO @ Sun, 03 Sep 2017 01:05:33: 3000000 INFO @ Sun, 03 Sep 2017 01:05:34: 4000000 INFO @ Sun, 03 Sep 2017 01:05:42: 4000000 INFO @ Sun, 03 Sep 2017 01:05:42: 4000000 INFO @ Sun, 03 Sep 2017 01:05:42: 5000000 INFO @ Sun, 03 Sep 2017 01:05:50: 6000000 INFO @ Sun, 03 Sep 2017 01:05:51: 5000000 INFO @ Sun, 03 Sep 2017 01:05:51: 5000000 INFO @ Sun, 03 Sep 2017 01:05:58: 7000000 INFO @ Sun, 03 Sep 2017 01:06:01: 6000000 INFO @ Sun, 03 Sep 2017 01:06:01: 6000000 INFO @ Sun, 03 Sep 2017 01:06:06: 8000000 INFO @ Sun, 03 Sep 2017 01:06:10: 7000000 INFO @ Sun, 03 Sep 2017 01:06:10: 7000000 INFO @ Sun, 03 Sep 2017 01:06:13: 9000000 INFO @ Sun, 03 Sep 2017 01:06:19: 8000000 INFO @ Sun, 03 Sep 2017 01:06:19: 8000000 INFO @ Sun, 03 Sep 2017 01:06:21: 10000000 INFO @ Sun, 03 Sep 2017 01:06:29: 9000000 INFO @ Sun, 03 Sep 2017 01:06:29: 9000000 INFO @ Sun, 03 Sep 2017 01:06:29: 11000000 INFO @ Sun, 03 Sep 2017 01:06:37: 12000000 INFO @ Sun, 03 Sep 2017 01:06:37: 10000000 INFO @ Sun, 03 Sep 2017 01:06:38: 10000000 INFO @ Sun, 03 Sep 2017 01:06:46: 13000000 INFO @ Sun, 03 Sep 2017 01:06:46: 11000000 INFO @ Sun, 03 Sep 2017 01:06:47: 11000000 INFO @ Sun, 03 Sep 2017 01:06:54: 14000000 INFO @ Sun, 03 Sep 2017 01:06:55: 12000000 INFO @ Sun, 03 Sep 2017 01:06:56: 12000000 INFO @ Sun, 03 Sep 2017 01:07:02: 15000000 INFO @ Sun, 03 Sep 2017 01:07:04: 13000000 INFO @ Sun, 03 Sep 2017 01:07:05: 13000000 INFO @ Sun, 03 Sep 2017 01:07:11: 16000000 INFO @ Sun, 03 Sep 2017 01:07:13: 14000000 INFO @ Sun, 03 Sep 2017 01:07:14: 14000000 INFO @ Sun, 03 Sep 2017 01:07:19: 17000000 INFO @ Sun, 03 Sep 2017 01:07:22: 15000000 INFO @ Sun, 03 Sep 2017 01:07:23: 15000000 INFO @ Sun, 03 Sep 2017 01:07:27: 18000000 INFO @ Sun, 03 Sep 2017 01:07:30: 16000000 INFO @ Sun, 03 Sep 2017 01:07:32: 16000000 INFO @ Sun, 03 Sep 2017 01:07:35: 19000000 INFO @ Sun, 03 Sep 2017 01:07:37: 17000000 INFO @ Sun, 03 Sep 2017 01:07:41: 17000000 INFO @ Sun, 03 Sep 2017 01:07:43: #1 tag size is determined as 49 bps INFO @ Sun, 03 Sep 2017 01:07:43: #1 tag size = 49 INFO @ Sun, 03 Sep 2017 01:07:43: #1 total tags in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:07:43: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:43: #1 tags after filtering in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:43: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:43: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:44: 18000000 INFO @ Sun, 03 Sep 2017 01:07:44: #2 number of paired peaks: 140 WARNING @ Sun, 03 Sep 2017 01:07:44: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:44: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:45: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:45: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:45: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:45: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:07:45: #2 alternative fragment length(s) may be 1,46,568 bps INFO @ Sun, 03 Sep 2017 01:07:45: #2.2 Generate R script for model : SRX2582952.20_model.r WARNING @ Sun, 03 Sep 2017 01:07:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:45: #2 You may need to consider one of the other alternative d(s): 1,46,568 WARNING @ Sun, 03 Sep 2017 01:07:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:07:45: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:48: 18000000 INFO @ Sun, 03 Sep 2017 01:07:51: 19000000 INFO @ Sun, 03 Sep 2017 01:07:54: 19000000 INFO @ Sun, 03 Sep 2017 01:07:58: #1 tag size is determined as 49 bps INFO @ Sun, 03 Sep 2017 01:07:58: #1 tag size = 49 INFO @ Sun, 03 Sep 2017 01:07:58: #1 total tags in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:07:58: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:07:58: #1 tags after filtering in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:58: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:58: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:59: #2 number of paired peaks: 140 WARNING @ Sun, 03 Sep 2017 01:07:59: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:59: start model_add_line... INFO @ Sun, 03 Sep 2017 01:08:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:08:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:08:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:08:00: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:08:00: #2 alternative fragment length(s) may be 1,46,568 bps INFO @ Sun, 03 Sep 2017 01:08:00: #2.2 Generate R script for model : SRX2582952.10_model.r WARNING @ Sun, 03 Sep 2017 01:08:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:08:00: #2 You may need to consider one of the other alternative d(s): 1,46,568 WARNING @ Sun, 03 Sep 2017 01:08:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:08:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:08:01: #1 tag size is determined as 49 bps INFO @ Sun, 03 Sep 2017 01:08:01: #1 tag size = 49 INFO @ Sun, 03 Sep 2017 01:08:01: #1 total tags in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:08:01: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:08:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:08:01: #1 tags after filtering in treatment: 19946681 INFO @ Sun, 03 Sep 2017 01:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:08:01: #1 finished! INFO @ Sun, 03 Sep 2017 01:08:01: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:08:03: #2 number of paired peaks: 140 WARNING @ Sun, 03 Sep 2017 01:08:03: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 03 Sep 2017 01:08:03: start model_add_line... INFO @ Sun, 03 Sep 2017 01:08:03: start X-correlation... INFO @ Sun, 03 Sep 2017 01:08:03: end of X-cor INFO @ Sun, 03 Sep 2017 01:08:03: #2 finished! INFO @ Sun, 03 Sep 2017 01:08:03: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:08:03: #2 alternative fragment length(s) may be 1,46,568 bps INFO @ Sun, 03 Sep 2017 01:08:03: #2.2 Generate R script for model : SRX2582952.05_model.r WARNING @ Sun, 03 Sep 2017 01:08:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:08:03: #2 You may need to consider one of the other alternative d(s): 1,46,568 WARNING @ Sun, 03 Sep 2017 01:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:08:03: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:08:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:32: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:35: #4 Write output xls file... SRX2582952.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:35: #4 Write peak in narrowPeak format file... SRX2582952.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:35: #4 Write summits bed file... SRX2582952.20_summits.bed INFO @ Sun, 03 Sep 2017 01:08:35: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:08:50: #4 Write output xls file... SRX2582952.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:50: #4 Write peak in narrowPeak format file... SRX2582952.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:50: #4 Write summits bed file... SRX2582952.10_summits.bed INFO @ Sun, 03 Sep 2017 01:08:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:08:56: #4 Write output xls file... SRX2582952.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:56: #4 Write peak in narrowPeak format file... SRX2582952.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:56: #4 Write summits bed file... SRX2582952.05_summits.bed INFO @ Sun, 03 Sep 2017 01:08:56: 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。