Job ID = 9025470 sra ファイルのダウンロード中... Completed: 472978K bytes transferred in 6 seconds (569114K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 100 22318 0 22318 0 0 1962 0 --:--:-- 0:00:11 --:--:-- 4614 100 48592 0 48592 0 0 3929 0 --:--:-- 0:00:12 --:--:-- 10058 100 48592 0 48592 0 0 3929 0 --:--:-- 0:00:12 --:--:-- 12690 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 14191303 spots for /home/okishinya/chipatlas/results/ce10/SRX1132912/SRR2144361.sra Written 14191303 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: 00:05:29 14191303 reads; of these: 14191303 (100.00%) were unpaired; of these: 959184 (6.76%) aligned 0 times 11322347 (79.78%) aligned exactly 1 time 1909772 (13.46%) aligned >1 times 93.24% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 3315389 / 13232119 = 0.2506 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 04:08:26: # Command line: callpeak -t SRX1132912.bam -f BAM -g ce -n SRX1132912.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1132912.05 # format = BAM # ChIP-seq file = ['SRX1132912.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 04:08:26: # Command line: callpeak -t SRX1132912.bam -f BAM -g ce -n SRX1132912.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1132912.10 # format = BAM # ChIP-seq file = ['SRX1132912.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 04:08:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:26: # Command line: callpeak -t SRX1132912.bam -f BAM -g ce -n SRX1132912.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1132912.20 # format = BAM # ChIP-seq file = ['SRX1132912.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 04:08:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:08:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:08:33: 1000000 INFO @ Sat, 03 Jun 2017 04:08:33: 1000000 INFO @ Sat, 03 Jun 2017 04:08:33: 1000000 INFO @ Sat, 03 Jun 2017 04:08:40: 2000000 INFO @ Sat, 03 Jun 2017 04:08:40: 2000000 INFO @ Sat, 03 Jun 2017 04:08:40: 2000000 INFO @ Sat, 03 Jun 2017 04:08:46: 3000000 INFO @ Sat, 03 Jun 2017 04:08:46: 3000000 INFO @ Sat, 03 Jun 2017 04:08:47: 3000000 INFO @ Sat, 03 Jun 2017 04:08:53: 4000000 INFO @ Sat, 03 Jun 2017 04:08:53: 4000000 INFO @ Sat, 03 Jun 2017 04:08:54: 4000000 INFO @ Sat, 03 Jun 2017 04:09:00: 5000000 INFO @ Sat, 03 Jun 2017 04:09:00: 5000000 INFO @ Sat, 03 Jun 2017 04:09:01: 5000000 INFO @ Sat, 03 Jun 2017 04:09:07: 6000000 INFO @ Sat, 03 Jun 2017 04:09:08: 6000000 INFO @ Sat, 03 Jun 2017 04:09:08: 6000000 INFO @ Sat, 03 Jun 2017 04:09:14: 7000000 INFO @ Sat, 03 Jun 2017 04:09:14: 7000000 INFO @ Sat, 03 Jun 2017 04:09:15: 7000000 INFO @ Sat, 03 Jun 2017 04:09:21: 8000000 INFO @ Sat, 03 Jun 2017 04:09:21: 8000000 INFO @ Sat, 03 Jun 2017 04:09:22: 8000000 INFO @ Sat, 03 Jun 2017 04:09:28: 9000000 INFO @ Sat, 03 Jun 2017 04:09:29: 9000000 INFO @ Sat, 03 Jun 2017 04:09:30: 9000000 INFO @ Sat, 03 Jun 2017 04:09:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:09:34: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:09:34: #1 total tags in treatment: 9916730 INFO @ Sat, 03 Jun 2017 04:09:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:34: #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 04:09:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:09:35: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:09:35: #1 total tags in treatment: 9916730 INFO @ Sat, 03 Jun 2017 04:09:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:35: #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 04:09:36: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:09:36: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:09:36: #1 total tags in treatment: 9916730 INFO @ Sat, 03 Jun 2017 04:09:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:36: #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 04:09:36: #1 tags after filtering in treatment: 9712725 INFO @ Sat, 03 Jun 2017 04:09:36: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:09:36: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:37: #1 tags after filtering in treatment: 9712725 INFO @ Sat, 03 Jun 2017 04:09:37: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:09:37: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:38: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 04:09:38: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:38: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:38: #1 tags after filtering in treatment: 9712725 INFO @ Sat, 03 Jun 2017 04:09:38: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:09:38: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:38: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 04:09:38: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:38: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:40: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:40: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:40: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:40: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:09:40: #2 alternative fragment length(s) may be 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 bps INFO @ Sat, 03 Jun 2017 04:09:40: #2.2 Generate R script for model : SRX1132912.10_model.r WARNING @ Sat, 03 Jun 2017 04:09:40: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:40: #2 You may need to consider one of the other alternative d(s): 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 WARNING @ Sat, 03 Jun 2017 04:09:40: #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 04:09:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:09:40: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 04:09:40: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:40: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:40: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:40: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:40: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:40: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:09:40: #2 alternative fragment length(s) may be 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 bps INFO @ Sat, 03 Jun 2017 04:09:40: #2.2 Generate R script for model : SRX1132912.20_model.r WARNING @ Sat, 03 Jun 2017 04:09:40: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:40: #2 You may need to consider one of the other alternative d(s): 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 WARNING @ Sat, 03 Jun 2017 04:09:40: #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 04:09:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:09:41: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:41: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:41: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:41: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 04:09:41: #2 alternative fragment length(s) may be 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 bps INFO @ Sat, 03 Jun 2017 04:09:41: #2.2 Generate R script for model : SRX1132912.05_model.r WARNING @ Sat, 03 Jun 2017 04:09:41: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:41: #2 You may need to consider one of the other alternative d(s): 2,59,85,111,128,134,162,185,217,288,313,367,478,524,554,576 WARNING @ Sat, 03 Jun 2017 04:09:41: #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 04:09:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:11:05: #4 Write output xls file... SRX1132912.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:11:05: #4 Write peak in narrowPeak format file... SRX1132912.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:11:05: #4 Write summits bed file... SRX1132912.05_summits.bed INFO @ Sat, 03 Jun 2017 04:11:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:11:07: #4 Write output xls file... SRX1132912.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:11:07: #4 Write peak in narrowPeak format file... SRX1132912.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:11:07: #4 Write summits bed file... SRX1132912.10_summits.bed INFO @ Sat, 03 Jun 2017 04:11:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:11:14: #4 Write output xls file... SRX1132912.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:11:14: #4 Write peak in narrowPeak format file... SRX1132912.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:11:14: #4 Write summits bed file... SRX1132912.20_summits.bed INFO @ Sat, 03 Jun 2017 04:11:14: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。