Job ID = 11171264 sra ファイルのダウンロード中... Completed: 108049K bytes transferred in 8 seconds (105672K bits/sec), in 1 file. Completed: 106893K bytes transferred in 15 seconds (58187K bits/sec), in 1 file. Completed: 109194K bytes transferred in 7 seconds (121241K bits/sec), in 1 file. Completed: 108010K bytes transferred in 6 seconds (144983K bits/sec), in 1 file. 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... Read 5062025 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850387.sra Written 5062025 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850387.sra Read 5080066 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850386.sra Written 5080066 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850386.sra Read 5134730 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850385.sra Written 5134730 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850385.sra Read 5153948 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850384.sra Written 5153948 spots for /home/okishinya/chipatlas/results/dm3/SRX3020531/SRR5850384.sra rm: cannot remove `[DSE]RX*': 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:10 20430769 reads; of these: 20430769 (100.00%) were unpaired; of these: 722463 (3.54%) aligned 0 times 13969641 (68.38%) aligned exactly 1 time 5738665 (28.09%) aligned >1 times 96.46% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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] 2519682 / 19708306 = 0.1278 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, 08 Sep 2018 13:34:07: # Command line: callpeak -t SRX3020531.bam -f BAM -g dm -n SRX3020531.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020531.10 # format = BAM # ChIP-seq file = ['SRX3020531.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:34:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:07: # Command line: callpeak -t SRX3020531.bam -f BAM -g dm -n SRX3020531.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020531.20 # format = BAM # ChIP-seq file = ['SRX3020531.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:34:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:07: # Command line: callpeak -t SRX3020531.bam -f BAM -g dm -n SRX3020531.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020531.05 # format = BAM # ChIP-seq file = ['SRX3020531.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:34:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:34:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:34:14: 1000000 INFO @ Sat, 08 Sep 2018 13:34:14: 1000000 INFO @ Sat, 08 Sep 2018 13:34:14: 1000000 INFO @ Sat, 08 Sep 2018 13:34:22: 2000000 INFO @ Sat, 08 Sep 2018 13:34:22: 2000000 INFO @ Sat, 08 Sep 2018 13:34:22: 2000000 INFO @ Sat, 08 Sep 2018 13:34:29: 3000000 INFO @ Sat, 08 Sep 2018 13:34:29: 3000000 INFO @ Sat, 08 Sep 2018 13:34:29: 3000000 INFO @ Sat, 08 Sep 2018 13:34:36: 4000000 INFO @ Sat, 08 Sep 2018 13:34:36: 4000000 INFO @ Sat, 08 Sep 2018 13:34:36: 4000000 INFO @ Sat, 08 Sep 2018 13:34:43: 5000000 INFO @ Sat, 08 Sep 2018 13:34:43: 5000000 INFO @ Sat, 08 Sep 2018 13:34:43: 5000000 INFO @ Sat, 08 Sep 2018 13:34:50: 6000000 INFO @ Sat, 08 Sep 2018 13:34:51: 6000000 INFO @ Sat, 08 Sep 2018 13:34:51: 6000000 INFO @ Sat, 08 Sep 2018 13:34:57: 7000000 INFO @ Sat, 08 Sep 2018 13:34:58: 7000000 INFO @ Sat, 08 Sep 2018 13:34:58: 7000000 INFO @ Sat, 08 Sep 2018 13:35:04: 8000000 INFO @ Sat, 08 Sep 2018 13:35:05: 8000000 INFO @ Sat, 08 Sep 2018 13:35:05: 8000000 INFO @ Sat, 08 Sep 2018 13:35:12: 9000000 INFO @ Sat, 08 Sep 2018 13:35:12: 9000000 INFO @ Sat, 08 Sep 2018 13:35:12: 9000000 INFO @ Sat, 08 Sep 2018 13:35:19: 10000000 INFO @ Sat, 08 Sep 2018 13:35:19: 10000000 INFO @ Sat, 08 Sep 2018 13:35:20: 10000000 INFO @ Sat, 08 Sep 2018 13:35:26: 11000000 INFO @ Sat, 08 Sep 2018 13:35:27: 11000000 INFO @ Sat, 08 Sep 2018 13:35:27: 11000000 INFO @ Sat, 08 Sep 2018 13:35:33: 12000000 INFO @ Sat, 08 Sep 2018 13:35:35: 12000000 INFO @ Sat, 08 Sep 2018 13:35:35: 12000000 INFO @ Sat, 08 Sep 2018 13:35:40: 13000000 INFO @ Sat, 08 Sep 2018 13:35:42: 13000000 INFO @ Sat, 08 Sep 2018 13:35:42: 13000000 INFO @ Sat, 08 Sep 2018 13:35:47: 14000000 INFO @ Sat, 08 Sep 2018 13:35:50: 14000000 INFO @ Sat, 08 Sep 2018 13:35:50: 14000000 INFO @ Sat, 08 Sep 2018 13:35:54: 15000000 INFO @ Sat, 08 Sep 2018 13:35:57: 15000000 INFO @ Sat, 08 Sep 2018 13:35:57: 15000000 INFO @ Sat, 08 Sep 2018 13:36:02: 16000000 INFO @ Sat, 08 Sep 2018 13:36:05: 16000000 INFO @ Sat, 08 Sep 2018 13:36:05: 16000000 INFO @ Sat, 08 Sep 2018 13:36:09: 17000000 INFO @ Sat, 08 Sep 2018 13:36:10: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:36:10: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:36:10: #1 total tags in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:10: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:10: #1 tags after filtering in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:10: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:10: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:12: #2 number of paired peaks: 530 WARNING @ Sat, 08 Sep 2018 13:36:12: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 08 Sep 2018 13:36:12: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:12: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:12: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:12: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:12: #2 predicted fragment length is 57 bps INFO @ Sat, 08 Sep 2018 13:36:12: #2 alternative fragment length(s) may be 3,57,597 bps INFO @ Sat, 08 Sep 2018 13:36:12: #2.2 Generate R script for model : SRX3020531.20_model.r WARNING @ Sat, 08 Sep 2018 13:36:12: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:36:12: #2 You may need to consider one of the other alternative d(s): 3,57,597 WARNING @ Sat, 08 Sep 2018 13:36:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:36:12: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:13: 17000000 INFO @ Sat, 08 Sep 2018 13:36:13: 17000000 INFO @ Sat, 08 Sep 2018 13:36:14: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:36:14: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:36:14: #1 total tags in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:14: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:14: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:36:14: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:36:14: #1 total tags in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:14: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:36:14: #1 tags after filtering in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:14: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:14: #1 tags after filtering in treatment: 17188624 INFO @ Sat, 08 Sep 2018 13:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:36:14: #1 finished! INFO @ Sat, 08 Sep 2018 13:36:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:36:16: #2 number of paired peaks: 530 WARNING @ Sat, 08 Sep 2018 13:36:16: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 08 Sep 2018 13:36:16: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:16: #2 number of paired peaks: 530 WARNING @ Sat, 08 Sep 2018 13:36:16: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 08 Sep 2018 13:36:16: start model_add_line... INFO @ Sat, 08 Sep 2018 13:36:16: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:16: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:16: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:16: #2 predicted fragment length is 57 bps INFO @ Sat, 08 Sep 2018 13:36:16: #2 alternative fragment length(s) may be 3,57,597 bps INFO @ Sat, 08 Sep 2018 13:36:16: #2.2 Generate R script for model : SRX3020531.10_model.r WARNING @ Sat, 08 Sep 2018 13:36:16: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:36:16: #2 You may need to consider one of the other alternative d(s): 3,57,597 WARNING @ Sat, 08 Sep 2018 13:36:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:36:16: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:16: start X-correlation... INFO @ Sat, 08 Sep 2018 13:36:16: end of X-cor INFO @ Sat, 08 Sep 2018 13:36:16: #2 finished! INFO @ Sat, 08 Sep 2018 13:36:16: #2 predicted fragment length is 57 bps INFO @ Sat, 08 Sep 2018 13:36:16: #2 alternative fragment length(s) may be 3,57,597 bps INFO @ Sat, 08 Sep 2018 13:36:16: #2.2 Generate R script for model : SRX3020531.05_model.r WARNING @ Sat, 08 Sep 2018 13:36:16: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:36:16: #2 You may need to consider one of the other alternative d(s): 3,57,597 WARNING @ Sat, 08 Sep 2018 13:36:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:36:16: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:36:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:36:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:36:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write output xls file... SRX3020531.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write peak in narrowPeak format file... SRX3020531.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:09: #4 Write summits bed file... SRX3020531.20_summits.bed INFO @ Sat, 08 Sep 2018 13:37:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:13: #4 Write output xls file... SRX3020531.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:13: #4 Write peak in narrowPeak format file... SRX3020531.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:13: #4 Write summits bed file... SRX3020531.05_summits.bed INFO @ Sat, 08 Sep 2018 13:37:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4154 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:37:17: #4 Write output xls file... SRX3020531.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:37:17: #4 Write peak in narrowPeak format file... SRX3020531.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:37:17: #4 Write summits bed file... SRX3020531.10_summits.bed INFO @ Sat, 08 Sep 2018 13:37:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2200 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。