Job ID = 9029231 sra ファイルのダウンロード中... Completed: 565926K bytes transferred in 12 seconds (374804K 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 14324 0 14324 0 0 1898 0 --:--:-- 0:00:07 --:--:-- 13337 100 54317 0 54317 0 0 6359 0 --:--:-- 0:00:08 --:--:-- 26240 100 105k 0 105k 0 0 11743 0 --:--:-- 0:00:09 --:--:-- 39525 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 22849299 spots for /home/okishinya/chipatlas/results/dm3/SRX1433371/SRR2919836.sra Written 22849299 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: 00:07:53 22849299 reads; of these: 22849299 (100.00%) were unpaired; of these: 8786842 (38.46%) aligned 0 times 10356527 (45.33%) aligned exactly 1 time 3705930 (16.22%) aligned >1 times 61.54% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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 8 files... [bam_rmdupse_core] 4113789 / 14062457 = 0.2925 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 13:05:14: # Command line: callpeak -t SRX1433371.bam -f BAM -g dm -n SRX1433371.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433371.05 # format = BAM # ChIP-seq file = ['SRX1433371.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 INFO @ Sat, 03 Jun 2017 13:05:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:14: # Command line: callpeak -t SRX1433371.bam -f BAM -g dm -n SRX1433371.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433371.20 # format = BAM # ChIP-seq file = ['SRX1433371.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 INFO @ Sat, 03 Jun 2017 13:05:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:14: # Command line: callpeak -t SRX1433371.bam -f BAM -g dm -n SRX1433371.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433371.10 # format = BAM # ChIP-seq file = ['SRX1433371.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 INFO @ Sat, 03 Jun 2017 13:05:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:05:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:05:21: 1000000 INFO @ Sat, 03 Jun 2017 13:05:21: 1000000 INFO @ Sat, 03 Jun 2017 13:05:21: 1000000 INFO @ Sat, 03 Jun 2017 13:05:28: 2000000 INFO @ Sat, 03 Jun 2017 13:05:28: 2000000 INFO @ Sat, 03 Jun 2017 13:05:29: 2000000 INFO @ Sat, 03 Jun 2017 13:05:35: 3000000 INFO @ Sat, 03 Jun 2017 13:05:36: 3000000 INFO @ Sat, 03 Jun 2017 13:05:36: 3000000 INFO @ Sat, 03 Jun 2017 13:05:43: 4000000 INFO @ Sat, 03 Jun 2017 13:05:43: 4000000 INFO @ Sat, 03 Jun 2017 13:05:43: 4000000 INFO @ Sat, 03 Jun 2017 13:05:50: 5000000 INFO @ Sat, 03 Jun 2017 13:05:50: 5000000 INFO @ Sat, 03 Jun 2017 13:05:51: 5000000 INFO @ Sat, 03 Jun 2017 13:05:57: 6000000 INFO @ Sat, 03 Jun 2017 13:05:57: 6000000 INFO @ Sat, 03 Jun 2017 13:05:58: 6000000 INFO @ Sat, 03 Jun 2017 13:06:04: 7000000 INFO @ Sat, 03 Jun 2017 13:06:04: 7000000 INFO @ Sat, 03 Jun 2017 13:06:05: 7000000 INFO @ Sat, 03 Jun 2017 13:06:11: 8000000 INFO @ Sat, 03 Jun 2017 13:06:11: 8000000 INFO @ Sat, 03 Jun 2017 13:06:12: 8000000 INFO @ Sat, 03 Jun 2017 13:06:18: 9000000 INFO @ Sat, 03 Jun 2017 13:06:19: 9000000 INFO @ Sat, 03 Jun 2017 13:06:19: 9000000 INFO @ Sat, 03 Jun 2017 13:06:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:25: #1 total tags in treatment: 9948668 INFO @ Sat, 03 Jun 2017 13:06:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:25: #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 13:06:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:25: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:25: #1 total tags in treatment: 9948668 INFO @ Sat, 03 Jun 2017 13:06:25: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:25: #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 13:06:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:06:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:06:26: #1 total tags in treatment: 9948668 INFO @ Sat, 03 Jun 2017 13:06:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:06:26: #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 13:06:27: #1 tags after filtering in treatment: 9947017 INFO @ Sat, 03 Jun 2017 13:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:27: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:27: #1 tags after filtering in treatment: 9947017 INFO @ Sat, 03 Jun 2017 13:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:27: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:27: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:28: #1 tags after filtering in treatment: 9947017 INFO @ Sat, 03 Jun 2017 13:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:06:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:06:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:06:29: #2 number of paired peaks: 563 WARNING @ Sat, 03 Jun 2017 13:06:29: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Jun 2017 13:06:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:29: #2 number of paired peaks: 563 WARNING @ Sat, 03 Jun 2017 13:06:29: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Jun 2017 13:06:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:29: #2 number of paired peaks: 563 WARNING @ Sat, 03 Jun 2017 13:06:29: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sat, 03 Jun 2017 13:06:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:06:33: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:33: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:33: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:33: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:06:33: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:06:33: #2.2 Generate R script for model : SRX1433371.20_model.r WARNING @ Sat, 03 Jun 2017 13:06:33: #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 13:06:33: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:06:33: #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 13:06:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:06:33: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:33: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:33: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:33: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:06:33: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:06:33: #2.2 Generate R script for model : SRX1433371.05_model.r WARNING @ Sat, 03 Jun 2017 13:06:33: #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 13:06:33: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:06:33: #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 13:06:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:06:34: start X-correlation... INFO @ Sat, 03 Jun 2017 13:06:34: end of X-cor INFO @ Sat, 03 Jun 2017 13:06:34: #2 finished! INFO @ Sat, 03 Jun 2017 13:06:34: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 13:06:34: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 03 Jun 2017 13:06:34: #2.2 Generate R script for model : SRX1433371.10_model.r WARNING @ Sat, 03 Jun 2017 13:06:34: #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 13:06:34: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 03 Jun 2017 13:06:34: #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 13:06:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:07:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:07:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:07:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:08:09: #4 Write output xls file... SRX1433371.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:09: #4 Write peak in narrowPeak format file... SRX1433371.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:09: #4 Write summits bed file... SRX1433371.20_summits.bed INFO @ Sat, 03 Jun 2017 13:08:09: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:08:13: #4 Write output xls file... SRX1433371.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:13: #4 Write peak in narrowPeak format file... SRX1433371.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:13: #4 Write summits bed file... SRX1433371.05_summits.bed INFO @ Sat, 03 Jun 2017 13:08:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2851 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:08:16: #4 Write output xls file... SRX1433371.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:08:16: #4 Write peak in narrowPeak format file... SRX1433371.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:08:16: #4 Write summits bed file... SRX1433371.10_summits.bed INFO @ Sat, 03 Jun 2017 13:08:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1762 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。