Job ID = 9371922 sra ファイルのダウンロード中... Completed: 371232K bytes transferred in 18 seconds (162136K bits/sec), in 1 file, 2 directories. 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 14188970 spots for /home/okishinya/chipatlas/results/dm3/SRX2520646/SRR5206765.sra Written 14188970 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 14188970 reads; of these: 14188970 (100.00%) were unpaired; of these: 256534 (1.81%) aligned 0 times 9600942 (67.66%) aligned exactly 1 time 4331494 (30.53%) aligned >1 times 98.19% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 2788464 / 13932436 = 0.2001 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 @ Fri, 04 Aug 2017 15:00:04: # Command line: callpeak -t SRX2520646.bam -f BAM -g dm -n SRX2520646.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2520646.20 # format = BAM # ChIP-seq file = ['SRX2520646.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 @ Fri, 04 Aug 2017 15:00:04: # Command line: callpeak -t SRX2520646.bam -f BAM -g dm -n SRX2520646.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2520646.05 # format = BAM # ChIP-seq file = ['SRX2520646.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 @ Fri, 04 Aug 2017 15:00:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:00:04: # Command line: callpeak -t SRX2520646.bam -f BAM -g dm -n SRX2520646.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2520646.10 # format = BAM # ChIP-seq file = ['SRX2520646.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 @ Fri, 04 Aug 2017 15:00:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:00:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:00:04: #1 read tag files... INFO @ Fri, 04 Aug 2017 15:00:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:00:04: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 15:00:11: 1000000 INFO @ Fri, 04 Aug 2017 15:00:11: 1000000 INFO @ Fri, 04 Aug 2017 15:00:12: 1000000 INFO @ Fri, 04 Aug 2017 15:00:18: 2000000 INFO @ Fri, 04 Aug 2017 15:00:19: 2000000 INFO @ Fri, 04 Aug 2017 15:00:21: 2000000 INFO @ Fri, 04 Aug 2017 15:00:25: 3000000 INFO @ Fri, 04 Aug 2017 15:00:27: 3000000 INFO @ Fri, 04 Aug 2017 15:00:29: 3000000 INFO @ Fri, 04 Aug 2017 15:00:32: 4000000 INFO @ Fri, 04 Aug 2017 15:00:34: 4000000 INFO @ Fri, 04 Aug 2017 15:00:37: 4000000 INFO @ Fri, 04 Aug 2017 15:00:39: 5000000 INFO @ Fri, 04 Aug 2017 15:00:42: 5000000 INFO @ Fri, 04 Aug 2017 15:00:46: 5000000 INFO @ Fri, 04 Aug 2017 15:00:46: 6000000 INFO @ Fri, 04 Aug 2017 15:00:50: 6000000 INFO @ Fri, 04 Aug 2017 15:00:53: 7000000 INFO @ Fri, 04 Aug 2017 15:00:54: 6000000 INFO @ Fri, 04 Aug 2017 15:00:57: 7000000 INFO @ Fri, 04 Aug 2017 15:01:00: 8000000 INFO @ Fri, 04 Aug 2017 15:01:02: 7000000 INFO @ Fri, 04 Aug 2017 15:01:05: 8000000 INFO @ Fri, 04 Aug 2017 15:01:07: 9000000 INFO @ Fri, 04 Aug 2017 15:01:11: 8000000 INFO @ Fri, 04 Aug 2017 15:01:13: 9000000 INFO @ Fri, 04 Aug 2017 15:01:13: 10000000 INFO @ Fri, 04 Aug 2017 15:01:19: 9000000 INFO @ Fri, 04 Aug 2017 15:01:20: 10000000 INFO @ Fri, 04 Aug 2017 15:01:20: 11000000 INFO @ Fri, 04 Aug 2017 15:01:21: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:01:21: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:01:21: #1 total tags in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:21: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:01:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:01:21: #1 tags after filtering in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:01:21: #1 finished! INFO @ Fri, 04 Aug 2017 15:01:21: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:01:22: #2 number of paired peaks: 211 WARNING @ Fri, 04 Aug 2017 15:01:22: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 04 Aug 2017 15:01:22: start model_add_line... INFO @ Fri, 04 Aug 2017 15:01:22: start X-correlation... INFO @ Fri, 04 Aug 2017 15:01:22: end of X-cor INFO @ Fri, 04 Aug 2017 15:01:22: #2 finished! INFO @ Fri, 04 Aug 2017 15:01:22: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:01:22: #2 alternative fragment length(s) may be 4,49,533 bps INFO @ Fri, 04 Aug 2017 15:01:22: #2.2 Generate R script for model : SRX2520646.10_model.r WARNING @ Fri, 04 Aug 2017 15:01:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:01:22: #2 You may need to consider one of the other alternative d(s): 4,49,533 WARNING @ Fri, 04 Aug 2017 15:01:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:01:22: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:01:27: 10000000 INFO @ Fri, 04 Aug 2017 15:01:27: 11000000 INFO @ Fri, 04 Aug 2017 15:01:29: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:01:29: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:01:29: #1 total tags in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:29: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:01:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:01:29: #1 tags after filtering in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:01:29: #1 finished! INFO @ Fri, 04 Aug 2017 15:01:29: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:01:30: #2 number of paired peaks: 211 WARNING @ Fri, 04 Aug 2017 15:01:30: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 04 Aug 2017 15:01:30: start model_add_line... INFO @ Fri, 04 Aug 2017 15:01:30: start X-correlation... INFO @ Fri, 04 Aug 2017 15:01:30: end of X-cor INFO @ Fri, 04 Aug 2017 15:01:30: #2 finished! INFO @ Fri, 04 Aug 2017 15:01:30: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:01:30: #2 alternative fragment length(s) may be 4,49,533 bps INFO @ Fri, 04 Aug 2017 15:01:30: #2.2 Generate R script for model : SRX2520646.20_model.r WARNING @ Fri, 04 Aug 2017 15:01:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:01:30: #2 You may need to consider one of the other alternative d(s): 4,49,533 WARNING @ Fri, 04 Aug 2017 15:01:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:01:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:01:34: 11000000 INFO @ Fri, 04 Aug 2017 15:01:35: #1 tag size is determined as 50 bps INFO @ Fri, 04 Aug 2017 15:01:35: #1 tag size = 50 INFO @ Fri, 04 Aug 2017 15:01:35: #1 total tags in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:35: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 15:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 15:01:35: #1 tags after filtering in treatment: 11143972 INFO @ Fri, 04 Aug 2017 15:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 Aug 2017 15:01:35: #1 finished! INFO @ Fri, 04 Aug 2017 15:01:35: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 15:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 15:01:36: #2 number of paired peaks: 211 WARNING @ Fri, 04 Aug 2017 15:01:36: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Fri, 04 Aug 2017 15:01:36: start model_add_line... INFO @ Fri, 04 Aug 2017 15:01:36: start X-correlation... INFO @ Fri, 04 Aug 2017 15:01:36: end of X-cor INFO @ Fri, 04 Aug 2017 15:01:36: #2 finished! INFO @ Fri, 04 Aug 2017 15:01:36: #2 predicted fragment length is 49 bps INFO @ Fri, 04 Aug 2017 15:01:36: #2 alternative fragment length(s) may be 4,49,533 bps INFO @ Fri, 04 Aug 2017 15:01:36: #2.2 Generate R script for model : SRX2520646.05_model.r WARNING @ Fri, 04 Aug 2017 15:01:36: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 15:01:36: #2 You may need to consider one of the other alternative d(s): 4,49,533 WARNING @ Fri, 04 Aug 2017 15:01:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 15:01:36: #3 Call peaks... INFO @ Fri, 04 Aug 2017 15:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 15:01:47: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:01:54: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:01:59: #4 Write output xls file... SRX2520646.10_peaks.xls INFO @ Fri, 04 Aug 2017 15:01:59: #4 Write peak in narrowPeak format file... SRX2520646.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:01:59: #4 Write summits bed file... SRX2520646.10_summits.bed INFO @ Fri, 04 Aug 2017 15:01:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1118 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:02:01: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 15:02:06: #4 Write output xls file... SRX2520646.20_peaks.xls INFO @ Fri, 04 Aug 2017 15:02:06: #4 Write peak in narrowPeak format file... SRX2520646.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:02:06: #4 Write summits bed file... SRX2520646.20_summits.bed INFO @ Fri, 04 Aug 2017 15:02:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (374 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 15:02:16: #4 Write output xls file... SRX2520646.05_peaks.xls INFO @ Fri, 04 Aug 2017 15:02:16: #4 Write peak in narrowPeak format file... SRX2520646.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 15:02:16: #4 Write summits bed file... SRX2520646.05_summits.bed INFO @ Fri, 04 Aug 2017 15:02:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2383 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。