Job ID = 9025590 sra ファイルのダウンロード中... Completed: 494698K bytes transferred in 99 seconds (40807K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1074 0 --:--:-- 0:00:07 --:--:-- 9761 100 46318 0 46318 0 0 5697 0 --:--:-- 0:00:08 --:--:-- 26021 100 48494 0 48494 0 0 5964 0 --:--:-- 0:00:08 --:--:-- 27228 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 18019537 spots for /home/okishinya/chipatlas/results/ce10/SRX1936235/SRR3879841.sra Written 18019537 spots total 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:47 18019537 reads; of these: 18019537 (100.00%) were unpaired; of these: 572563 (3.18%) aligned 0 times 14980095 (83.13%) aligned exactly 1 time 2466879 (13.69%) aligned >1 times 96.82% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 8 files... [bam_rmdupse_core] 2065426 / 17446974 = 0.1184 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 @ Sat, 03 Jun 2017 04:37:08: # Command line: callpeak -t SRX1936235.bam -f BAM -g ce -n SRX1936235.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936235.05 # format = BAM # ChIP-seq file = ['SRX1936235.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 INFO @ Sat, 03 Jun 2017 04:37:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:08: # Command line: callpeak -t SRX1936235.bam -f BAM -g ce -n SRX1936235.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936235.20 # format = BAM # ChIP-seq file = ['SRX1936235.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 INFO @ Sat, 03 Jun 2017 04:37:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:08: # Command line: callpeak -t SRX1936235.bam -f BAM -g ce -n SRX1936235.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936235.10 # format = BAM # ChIP-seq file = ['SRX1936235.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 INFO @ Sat, 03 Jun 2017 04:37:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:14: 1000000 INFO @ Sat, 03 Jun 2017 04:37:15: 1000000 INFO @ Sat, 03 Jun 2017 04:37:15: 1000000 INFO @ Sat, 03 Jun 2017 04:37:21: 2000000 INFO @ Sat, 03 Jun 2017 04:37:21: 2000000 INFO @ Sat, 03 Jun 2017 04:37:21: 2000000 INFO @ Sat, 03 Jun 2017 04:37:27: 3000000 INFO @ Sat, 03 Jun 2017 04:37:28: 3000000 INFO @ Sat, 03 Jun 2017 04:37:28: 3000000 INFO @ Sat, 03 Jun 2017 04:37:34: 4000000 INFO @ Sat, 03 Jun 2017 04:37:35: 4000000 INFO @ Sat, 03 Jun 2017 04:37:35: 4000000 INFO @ Sat, 03 Jun 2017 04:37:40: 5000000 INFO @ Sat, 03 Jun 2017 04:37:42: 5000000 INFO @ Sat, 03 Jun 2017 04:37:43: 5000000 INFO @ Sat, 03 Jun 2017 04:37:47: 6000000 INFO @ Sat, 03 Jun 2017 04:37:49: 6000000 INFO @ Sat, 03 Jun 2017 04:37:49: 6000000 INFO @ Sat, 03 Jun 2017 04:37:54: 7000000 INFO @ Sat, 03 Jun 2017 04:37:56: 7000000 INFO @ Sat, 03 Jun 2017 04:37:56: 7000000 INFO @ Sat, 03 Jun 2017 04:38:00: 8000000 INFO @ Sat, 03 Jun 2017 04:38:03: 8000000 INFO @ Sat, 03 Jun 2017 04:38:03: 8000000 INFO @ Sat, 03 Jun 2017 04:38:07: 9000000 INFO @ Sat, 03 Jun 2017 04:38:10: 9000000 INFO @ Sat, 03 Jun 2017 04:38:10: 9000000 INFO @ Sat, 03 Jun 2017 04:38:14: 10000000 INFO @ Sat, 03 Jun 2017 04:38:17: 10000000 INFO @ Sat, 03 Jun 2017 04:38:18: 10000000 INFO @ Sat, 03 Jun 2017 04:38:21: 11000000 INFO @ Sat, 03 Jun 2017 04:38:24: 11000000 INFO @ Sat, 03 Jun 2017 04:38:26: 11000000 INFO @ Sat, 03 Jun 2017 04:38:27: 12000000 INFO @ Sat, 03 Jun 2017 04:38:30: 12000000 INFO @ Sat, 03 Jun 2017 04:38:33: 12000000 INFO @ Sat, 03 Jun 2017 04:38:33: 13000000 INFO @ Sat, 03 Jun 2017 04:38:36: 13000000 INFO @ Sat, 03 Jun 2017 04:38:40: 14000000 INFO @ Sat, 03 Jun 2017 04:38:40: 13000000 INFO @ Sat, 03 Jun 2017 04:38:43: 14000000 INFO @ Sat, 03 Jun 2017 04:38:46: 15000000 INFO @ Sat, 03 Jun 2017 04:38:47: 14000000 INFO @ Sat, 03 Jun 2017 04:38:48: 15000000 INFO @ Sat, 03 Jun 2017 04:38:48: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:38:48: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:38:48: #1 total tags in treatment: 15381548 INFO @ Sat, 03 Jun 2017 04:38:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:38:50: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:38:50: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:38:50: #1 total tags in treatment: 15381548 INFO @ Sat, 03 Jun 2017 04:38:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:38:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:38:51: #1 tags after filtering in treatment: 15378803 INFO @ Sat, 03 Jun 2017 04:38:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:38:51: #1 finished! INFO @ Sat, 03 Jun 2017 04:38:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:38:53: 15000000 INFO @ Sat, 03 Jun 2017 04:38:53: #1 tags after filtering in treatment: 15378803 INFO @ Sat, 03 Jun 2017 04:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:38:53: #1 finished! INFO @ Sat, 03 Jun 2017 04:38:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:38:54: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 04:38:54: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 04:38:54: start model_add_line... INFO @ Sat, 03 Jun 2017 04:38:55: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:38:55: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:38:55: #1 total tags in treatment: 15381548 INFO @ Sat, 03 Jun 2017 04:38:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:38:56: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 04:38:56: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 04:38:56: start model_add_line... INFO @ Sat, 03 Jun 2017 04:38:57: start X-correlation... INFO @ Sat, 03 Jun 2017 04:38:57: end of X-cor INFO @ Sat, 03 Jun 2017 04:38:57: #2 finished! INFO @ Sat, 03 Jun 2017 04:38:57: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:38:57: #2 alternative fragment length(s) may be 3,51,503,524,559 bps INFO @ Sat, 03 Jun 2017 04:38:57: #2.2 Generate R script for model : SRX1936235.20_model.r WARNING @ Sat, 03 Jun 2017 04:38:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:38:57: #2 You may need to consider one of the other alternative d(s): 3,51,503,524,559 WARNING @ Sat, 03 Jun 2017 04:38:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:38:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:38:58: #1 tags after filtering in treatment: 15378803 INFO @ Sat, 03 Jun 2017 04:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:38:58: #1 finished! INFO @ Sat, 03 Jun 2017 04:38:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:38:59: start X-correlation... INFO @ Sat, 03 Jun 2017 04:38:59: end of X-cor INFO @ Sat, 03 Jun 2017 04:38:59: #2 finished! INFO @ Sat, 03 Jun 2017 04:38:59: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:38:59: #2 alternative fragment length(s) may be 3,51,503,524,559 bps INFO @ Sat, 03 Jun 2017 04:38:59: #2.2 Generate R script for model : SRX1936235.10_model.r WARNING @ Sat, 03 Jun 2017 04:38:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:38:59: #2 You may need to consider one of the other alternative d(s): 3,51,503,524,559 WARNING @ Sat, 03 Jun 2017 04:38:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:38:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:38:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:39:00: #2 number of paired peaks: 118 WARNING @ Sat, 03 Jun 2017 04:39:00: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sat, 03 Jun 2017 04:39:00: start model_add_line... INFO @ Sat, 03 Jun 2017 04:39:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:39:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:39:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:39:03: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:39:03: #2 alternative fragment length(s) may be 3,51,503,524,559 bps INFO @ Sat, 03 Jun 2017 04:39:03: #2.2 Generate R script for model : SRX1936235.05_model.r WARNING @ Sat, 03 Jun 2017 04:39:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:39:03: #2 You may need to consider one of the other alternative d(s): 3,51,503,524,559 WARNING @ Sat, 03 Jun 2017 04:39:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:39:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:40:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:40:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:40:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:41:04: #4 Write output xls file... SRX1936235.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:04: #4 Write peak in narrowPeak format file... SRX1936235.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:04: #4 Write summits bed file... SRX1936235.20_summits.bed INFO @ Sat, 03 Jun 2017 04:41:04: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (117 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:41:14: #4 Write output xls file... SRX1936235.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:14: #4 Write peak in narrowPeak format file... SRX1936235.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:14: #4 Write summits bed file... SRX1936235.10_summits.bed INFO @ Sat, 03 Jun 2017 04:41:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:41:19: #4 Write output xls file... SRX1936235.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:41:19: #4 Write peak in narrowPeak format file... SRX1936235.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:41:19: #4 Write summits bed file... SRX1936235.05_summits.bed INFO @ Sat, 03 Jun 2017 04:41:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (548 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。