Job ID = 9029583 sra ファイルのダウンロード中... Completed: 847209K bytes transferred in 9 seconds (694235K 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 1076 0 --:--:-- 0:00:07 --:--:-- 11138 100 24454 0 24454 0 0 3078 0 --:--:-- 0:00:07 --:--:-- 16109 100 54862 0 54862 0 0 6136 0 --:--:-- 0:00:08 --:--:-- 21831 100 63440 0 63440 0 0 7095 0 --:--:-- 0:00:08 --:--:-- 25234 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 25790809 spots for /home/okishinya/chipatlas/results/dm3/SRX1848136/SRR3671299.sra Written 25790809 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: 00:09:15 25790809 reads; of these: 25790809 (100.00%) were unpaired; of these: 1073917 (4.16%) aligned 0 times 18707510 (72.54%) aligned exactly 1 time 6009382 (23.30%) aligned >1 times 95.84% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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 12 files... [bam_rmdupse_core] 11006528 / 24716892 = 0.4453 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 14:29:25: # Command line: callpeak -t SRX1848136.bam -f BAM -g dm -n SRX1848136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1848136.05 # format = BAM # ChIP-seq file = ['SRX1848136.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 14:29:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:25: # Command line: callpeak -t SRX1848136.bam -f BAM -g dm -n SRX1848136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1848136.10 # format = BAM # ChIP-seq file = ['SRX1848136.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 14:29:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:25: # Command line: callpeak -t SRX1848136.bam -f BAM -g dm -n SRX1848136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1848136.20 # format = BAM # ChIP-seq file = ['SRX1848136.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 14:29:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:29:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:29:32: 1000000 INFO @ Sat, 03 Jun 2017 14:29:32: 1000000 INFO @ Sat, 03 Jun 2017 14:29:32: 1000000 INFO @ Sat, 03 Jun 2017 14:29:39: 2000000 INFO @ Sat, 03 Jun 2017 14:29:39: 2000000 INFO @ Sat, 03 Jun 2017 14:29:39: 2000000 INFO @ Sat, 03 Jun 2017 14:29:46: 3000000 INFO @ Sat, 03 Jun 2017 14:29:46: 3000000 INFO @ Sat, 03 Jun 2017 14:29:46: 3000000 INFO @ Sat, 03 Jun 2017 14:29:53: 4000000 INFO @ Sat, 03 Jun 2017 14:29:53: 4000000 INFO @ Sat, 03 Jun 2017 14:29:53: 4000000 INFO @ Sat, 03 Jun 2017 14:30:00: 5000000 INFO @ Sat, 03 Jun 2017 14:30:00: 5000000 INFO @ Sat, 03 Jun 2017 14:30:00: 5000000 INFO @ Sat, 03 Jun 2017 14:30:07: 6000000 INFO @ Sat, 03 Jun 2017 14:30:07: 6000000 INFO @ Sat, 03 Jun 2017 14:30:07: 6000000 INFO @ Sat, 03 Jun 2017 14:30:14: 7000000 INFO @ Sat, 03 Jun 2017 14:30:14: 7000000 INFO @ Sat, 03 Jun 2017 14:30:15: 7000000 INFO @ Sat, 03 Jun 2017 14:30:21: 8000000 INFO @ Sat, 03 Jun 2017 14:30:22: 8000000 INFO @ Sat, 03 Jun 2017 14:30:22: 8000000 INFO @ Sat, 03 Jun 2017 14:30:27: 9000000 INFO @ Sat, 03 Jun 2017 14:30:29: 9000000 INFO @ Sat, 03 Jun 2017 14:30:30: 9000000 INFO @ Sat, 03 Jun 2017 14:30:34: 10000000 INFO @ Sat, 03 Jun 2017 14:30:37: 10000000 INFO @ Sat, 03 Jun 2017 14:30:40: 10000000 INFO @ Sat, 03 Jun 2017 14:30:42: 11000000 INFO @ Sat, 03 Jun 2017 14:30:46: 11000000 INFO @ Sat, 03 Jun 2017 14:30:49: 11000000 INFO @ Sat, 03 Jun 2017 14:30:49: 12000000 INFO @ Sat, 03 Jun 2017 14:30:53: 12000000 INFO @ Sat, 03 Jun 2017 14:30:56: 13000000 INFO @ Sat, 03 Jun 2017 14:30:58: 12000000 INFO @ Sat, 03 Jun 2017 14:31:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:31:01: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:31:01: #1 total tags in treatment: 13710364 INFO @ Sat, 03 Jun 2017 14:31:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:01: #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 14:31:01: 13000000 INFO @ Sat, 03 Jun 2017 14:31:03: #1 tags after filtering in treatment: 13703445 INFO @ Sat, 03 Jun 2017 14:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:03: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:06: #2 number of paired peaks: 1002 INFO @ Sat, 03 Jun 2017 14:31:06: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:06: 13000000 INFO @ Sat, 03 Jun 2017 14:31:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:31:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:31:06: #1 total tags in treatment: 13710364 INFO @ Sat, 03 Jun 2017 14:31:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:06: #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 14:31:09: #1 tags after filtering in treatment: 13703445 INFO @ Sat, 03 Jun 2017 14:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:09: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:09: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:31:11: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:31:11: #1 total tags in treatment: 13710364 INFO @ Sat, 03 Jun 2017 14:31:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:31:11: #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 14:31:11: #2 number of paired peaks: 1002 INFO @ Sat, 03 Jun 2017 14:31:11: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:13: #1 tags after filtering in treatment: 13703445 INFO @ Sat, 03 Jun 2017 14:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:31:13: #1 finished! INFO @ Sat, 03 Jun 2017 14:31:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:31:16: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:16: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:16: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:16: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 14:31:16: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 03 Jun 2017 14:31:16: #2.2 Generate R script for model : SRX1848136.05_model.r WARNING @ Sat, 03 Jun 2017 14:31:16: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:16: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sat, 03 Jun 2017 14:31:16: #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 14:31:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:16: #2 number of paired peaks: 1002 INFO @ Sat, 03 Jun 2017 14:31:16: start model_add_line... INFO @ Sat, 03 Jun 2017 14:31:22: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:22: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:22: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:22: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 14:31:22: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 03 Jun 2017 14:31:22: #2.2 Generate R script for model : SRX1848136.10_model.r WARNING @ Sat, 03 Jun 2017 14:31:22: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:22: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sat, 03 Jun 2017 14:31:22: #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 14:31:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:31:26: start X-correlation... INFO @ Sat, 03 Jun 2017 14:31:26: end of X-cor INFO @ Sat, 03 Jun 2017 14:31:26: #2 finished! INFO @ Sat, 03 Jun 2017 14:31:26: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 14:31:26: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 03 Jun 2017 14:31:26: #2.2 Generate R script for model : SRX1848136.20_model.r WARNING @ Sat, 03 Jun 2017 14:31:26: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:31:26: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sat, 03 Jun 2017 14:31:26: #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 14:31:26: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:32:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:32:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:33:29: #4 Write output xls file... SRX1848136.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:29: #4 Write peak in narrowPeak format file... SRX1848136.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:29: #4 Write summits bed file... SRX1848136.20_summits.bed INFO @ Sat, 03 Jun 2017 14:33:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:33: #4 Write output xls file... SRX1848136.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:33: #4 Write peak in narrowPeak format file... SRX1848136.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:33: #4 Write summits bed file... SRX1848136.05_summits.bed INFO @ Sat, 03 Jun 2017 14:33:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8671 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:33:34: #4 Write output xls file... SRX1848136.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:33:35: #4 Write peak in narrowPeak format file... SRX1848136.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:33:35: #4 Write summits bed file... SRX1848136.10_summits.bed INFO @ Sat, 03 Jun 2017 14:33:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4388 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。