Job ID = 9029563 sra ファイルのダウンロード中... Completed: 818757K bytes transferred in 15 seconds (440822K 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 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2858 0 --:--:-- 0:00:07 --:--:-- 16114 100 46318 0 46318 0 0 5361 0 --:--:-- 0:00:08 --:--:-- 20920 100 76422 0 76422 0 0 8518 0 --:--:-- 0:00:08 --:--:-- 29992 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 12722065 spots for /home/okishinya/chipatlas/results/dm3/SRX1840076/SRR3661302.sra Written 12722065 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: 00:10:45 12722065 reads; of these: 12722065 (100.00%) were unpaired; of these: 307362 (2.42%) aligned 0 times 8589601 (67.52%) aligned exactly 1 time 3825102 (30.07%) aligned >1 times 97.58% overall alignment rate Time searching: 00:10:45 Overall time: 00:10:45 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] 3974906 / 12414703 = 0.3202 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 14:25:17: # Command line: callpeak -t SRX1840076.bam -f BAM -g dm -n SRX1840076.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1840076.10 # format = BAM # ChIP-seq file = ['SRX1840076.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 14:25:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:25:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:25:17: # Command line: callpeak -t SRX1840076.bam -f BAM -g dm -n SRX1840076.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1840076.05 # format = BAM # ChIP-seq file = ['SRX1840076.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 14:25:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:25:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:25:17: # Command line: callpeak -t SRX1840076.bam -f BAM -g dm -n SRX1840076.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1840076.20 # format = BAM # ChIP-seq file = ['SRX1840076.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 14:25:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:25:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:25:27: 1000000 INFO @ Sat, 03 Jun 2017 14:25:28: 1000000 INFO @ Sat, 03 Jun 2017 14:25:28: 1000000 INFO @ Sat, 03 Jun 2017 14:25:38: 2000000 INFO @ Sat, 03 Jun 2017 14:25:40: 2000000 INFO @ Sat, 03 Jun 2017 14:25:40: 2000000 INFO @ Sat, 03 Jun 2017 14:25:49: 3000000 INFO @ Sat, 03 Jun 2017 14:25:52: 3000000 INFO @ Sat, 03 Jun 2017 14:25:52: 3000000 INFO @ Sat, 03 Jun 2017 14:26:00: 4000000 INFO @ Sat, 03 Jun 2017 14:26:04: 4000000 INFO @ Sat, 03 Jun 2017 14:26:04: 4000000 INFO @ Sat, 03 Jun 2017 14:26:11: 5000000 INFO @ Sat, 03 Jun 2017 14:26:15: 5000000 INFO @ Sat, 03 Jun 2017 14:26:16: 5000000 INFO @ Sat, 03 Jun 2017 14:26:22: 6000000 INFO @ Sat, 03 Jun 2017 14:26:27: 6000000 INFO @ Sat, 03 Jun 2017 14:26:27: 6000000 INFO @ Sat, 03 Jun 2017 14:26:33: 7000000 INFO @ Sat, 03 Jun 2017 14:26:39: 7000000 INFO @ Sat, 03 Jun 2017 14:26:39: 7000000 INFO @ Sat, 03 Jun 2017 14:26:44: 8000000 INFO @ Sat, 03 Jun 2017 14:26:48: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:26:48: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:26:48: #1 total tags in treatment: 8439797 INFO @ Sat, 03 Jun 2017 14:26:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:26:48: #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 14:26:49: 8000000 INFO @ Sat, 03 Jun 2017 14:26:50: #1 tags after filtering in treatment: 8432976 INFO @ Sat, 03 Jun 2017 14:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:26:50: #1 finished! INFO @ Sat, 03 Jun 2017 14:26:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:26:50: 8000000 INFO @ Sat, 03 Jun 2017 14:26:51: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 14:26:51: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 14:26:51: start model_add_line... INFO @ Sat, 03 Jun 2017 14:26:53: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:26:53: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:26:53: #1 total tags in treatment: 8439797 INFO @ Sat, 03 Jun 2017 14:26:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:26:53: #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 14:26:53: start X-correlation... INFO @ Sat, 03 Jun 2017 14:26:53: end of X-cor INFO @ Sat, 03 Jun 2017 14:26:53: #2 finished! INFO @ Sat, 03 Jun 2017 14:26:53: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Jun 2017 14:26:53: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Jun 2017 14:26:53: #2.2 Generate R script for model : SRX1840076.10_model.r WARNING @ Sat, 03 Jun 2017 14:26:53: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:26:53: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Jun 2017 14:26:53: #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 14:26:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:26:53: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:26:53: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:26:53: #1 total tags in treatment: 8439797 INFO @ Sat, 03 Jun 2017 14:26:53: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:26:53: #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 14:26:55: #1 tags after filtering in treatment: 8432976 INFO @ Sat, 03 Jun 2017 14:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:26:55: #1 finished! INFO @ Sat, 03 Jun 2017 14:26:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:26:55: #1 tags after filtering in treatment: 8432976 INFO @ Sat, 03 Jun 2017 14:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:26:55: #1 finished! INFO @ Sat, 03 Jun 2017 14:26:55: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:26:56: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 14:26:56: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 14:26:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:26:56: #2 number of paired peaks: 213 WARNING @ Sat, 03 Jun 2017 14:26:56: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Sat, 03 Jun 2017 14:26:56: start model_add_line... INFO @ Sat, 03 Jun 2017 14:26:57: start X-correlation... INFO @ Sat, 03 Jun 2017 14:26:57: end of X-cor INFO @ Sat, 03 Jun 2017 14:26:57: #2 finished! INFO @ Sat, 03 Jun 2017 14:26:57: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Jun 2017 14:26:57: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Jun 2017 14:26:57: #2.2 Generate R script for model : SRX1840076.20_model.r WARNING @ Sat, 03 Jun 2017 14:26:58: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:26:58: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Jun 2017 14:26:58: #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 14:26:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:26:58: start X-correlation... INFO @ Sat, 03 Jun 2017 14:26:58: end of X-cor INFO @ Sat, 03 Jun 2017 14:26:58: #2 finished! INFO @ Sat, 03 Jun 2017 14:26:58: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Jun 2017 14:26:58: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Jun 2017 14:26:58: #2.2 Generate R script for model : SRX1840076.05_model.r WARNING @ Sat, 03 Jun 2017 14:26:58: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:26:58: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Jun 2017 14:26:58: #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 14:26:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:27:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:27:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:28:16: #4 Write output xls file... SRX1840076.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:28:16: #4 Write peak in narrowPeak format file... SRX1840076.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:28:16: #4 Write summits bed file... SRX1840076.10_summits.bed INFO @ Sat, 03 Jun 2017 14:28:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (957 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:28:18: #4 Write output xls file... SRX1840076.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:28:18: #4 Write peak in narrowPeak format file... SRX1840076.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:28:18: #4 Write summits bed file... SRX1840076.20_summits.bed INFO @ Sat, 03 Jun 2017 14:28:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:28:23: #4 Write output xls file... SRX1840076.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:28:23: #4 Write peak in narrowPeak format file... SRX1840076.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:28:23: #4 Write summits bed file... SRX1840076.05_summits.bed INFO @ Sat, 03 Jun 2017 14:28:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1527 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。