Job ID = 10480666 sra ファイルのダウンロード中... Completed: 503427K bytes transferred in 11 seconds (354995K 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... Written 15706097 spots for /home/okishinya/chipatlas/results/dm3/SRX2832102/SRR5573766.sra Written 15706097 spots total 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 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: 00:06:59 15706097 reads; of these: 15706097 (100.00%) were unpaired; of these: 647924 (4.13%) aligned 0 times 8086588 (51.49%) aligned exactly 1 time 6971585 (44.39%) aligned >1 times 95.87% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 2927482 / 15058173 = 0.1944 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, 16 Mar 2018 07:37:14: # Command line: callpeak -t SRX2832102.bam -f BAM -g dm -n SRX2832102.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832102.05 # format = BAM # ChIP-seq file = ['SRX2832102.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, 16 Mar 2018 07:37:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:37:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:37:14: # Command line: callpeak -t SRX2832102.bam -f BAM -g dm -n SRX2832102.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832102.20 # format = BAM # ChIP-seq file = ['SRX2832102.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, 16 Mar 2018 07:37:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:37:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:37:14: # Command line: callpeak -t SRX2832102.bam -f BAM -g dm -n SRX2832102.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832102.10 # format = BAM # ChIP-seq file = ['SRX2832102.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, 16 Mar 2018 07:37:14: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:37:14: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:37:21: 1000000 INFO @ Fri, 16 Mar 2018 07:37:21: 1000000 INFO @ Fri, 16 Mar 2018 07:37:21: 1000000 INFO @ Fri, 16 Mar 2018 07:37:27: 2000000 INFO @ Fri, 16 Mar 2018 07:37:27: 2000000 INFO @ Fri, 16 Mar 2018 07:37:27: 2000000 INFO @ Fri, 16 Mar 2018 07:37:34: 3000000 INFO @ Fri, 16 Mar 2018 07:37:34: 3000000 INFO @ Fri, 16 Mar 2018 07:37:34: 3000000 INFO @ Fri, 16 Mar 2018 07:37:41: 4000000 INFO @ Fri, 16 Mar 2018 07:37:41: 4000000 INFO @ Fri, 16 Mar 2018 07:37:41: 4000000 INFO @ Fri, 16 Mar 2018 07:37:48: 5000000 INFO @ Fri, 16 Mar 2018 07:37:48: 5000000 INFO @ Fri, 16 Mar 2018 07:37:49: 5000000 INFO @ Fri, 16 Mar 2018 07:37:55: 6000000 INFO @ Fri, 16 Mar 2018 07:37:55: 6000000 INFO @ Fri, 16 Mar 2018 07:37:56: 6000000 INFO @ Fri, 16 Mar 2018 07:38:02: 7000000 INFO @ Fri, 16 Mar 2018 07:38:02: 7000000 INFO @ Fri, 16 Mar 2018 07:38:03: 7000000 INFO @ Fri, 16 Mar 2018 07:38:09: 8000000 INFO @ Fri, 16 Mar 2018 07:38:10: 8000000 INFO @ Fri, 16 Mar 2018 07:38:10: 8000000 INFO @ Fri, 16 Mar 2018 07:38:16: 9000000 INFO @ Fri, 16 Mar 2018 07:38:17: 9000000 INFO @ Fri, 16 Mar 2018 07:38:18: 9000000 INFO @ Fri, 16 Mar 2018 07:38:23: 10000000 INFO @ Fri, 16 Mar 2018 07:38:24: 10000000 INFO @ Fri, 16 Mar 2018 07:38:25: 10000000 INFO @ Fri, 16 Mar 2018 07:38:30: 11000000 INFO @ Fri, 16 Mar 2018 07:38:31: 11000000 INFO @ Fri, 16 Mar 2018 07:38:32: 11000000 INFO @ Fri, 16 Mar 2018 07:38:37: 12000000 INFO @ Fri, 16 Mar 2018 07:38:38: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:38:38: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:38:38: #1 total tags in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:38: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:38:38: #1 tags after filtering in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:38: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:38: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:38: 12000000 INFO @ Fri, 16 Mar 2018 07:38:39: #2 number of paired peaks: 674 WARNING @ Fri, 16 Mar 2018 07:38:39: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:39: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:39: 12000000 INFO @ Fri, 16 Mar 2018 07:38:39: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:38:39: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:38:39: #1 total tags in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:39: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:38:39: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:39: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:39: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:39: #2 predicted fragment length is 75 bps INFO @ Fri, 16 Mar 2018 07:38:39: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 16 Mar 2018 07:38:39: #2.2 Generate R script for model : SRX2832102.10_model.r WARNING @ Fri, 16 Mar 2018 07:38:39: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:39: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Fri, 16 Mar 2018 07:38:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:38:39: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:38:40: #1 tags after filtering in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:40: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:40: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:40: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:38:40: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:38:40: #1 total tags in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:40: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:38:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:38:41: #1 tags after filtering in treatment: 12130691 INFO @ Fri, 16 Mar 2018 07:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:38:41: #1 finished! INFO @ Fri, 16 Mar 2018 07:38:41: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:38:41: #2 number of paired peaks: 674 WARNING @ Fri, 16 Mar 2018 07:38:41: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:41: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:41: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:41: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:41: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:41: #2 predicted fragment length is 75 bps INFO @ Fri, 16 Mar 2018 07:38:41: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 16 Mar 2018 07:38:41: #2.2 Generate R script for model : SRX2832102.20_model.r WARNING @ Fri, 16 Mar 2018 07:38:41: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:41: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Fri, 16 Mar 2018 07:38:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:38:41: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:38:42: #2 number of paired peaks: 674 WARNING @ Fri, 16 Mar 2018 07:38:42: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Fri, 16 Mar 2018 07:38:42: start model_add_line... INFO @ Fri, 16 Mar 2018 07:38:42: start X-correlation... INFO @ Fri, 16 Mar 2018 07:38:42: end of X-cor INFO @ Fri, 16 Mar 2018 07:38:42: #2 finished! INFO @ Fri, 16 Mar 2018 07:38:42: #2 predicted fragment length is 75 bps INFO @ Fri, 16 Mar 2018 07:38:42: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 16 Mar 2018 07:38:42: #2.2 Generate R script for model : SRX2832102.05_model.r WARNING @ Fri, 16 Mar 2018 07:38:42: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:38:42: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Fri, 16 Mar 2018 07:38:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:38:42: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:39:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:39:07: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:39:08: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:39:22: #4 Write output xls file... SRX2832102.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:39:22: #4 Write peak in narrowPeak format file... SRX2832102.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:39:22: #4 Write summits bed file... SRX2832102.05_summits.bed INFO @ Fri, 16 Mar 2018 07:39:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6141 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:39:23: #4 Write output xls file... SRX2832102.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:39:23: #4 Write peak in narrowPeak format file... SRX2832102.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:39:23: #4 Write summits bed file... SRX2832102.20_summits.bed INFO @ Fri, 16 Mar 2018 07:39:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1196 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:39:25: #4 Write output xls file... SRX2832102.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:39:25: #4 Write peak in narrowPeak format file... SRX2832102.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:39:25: #4 Write summits bed file... SRX2832102.10_summits.bed INFO @ Fri, 16 Mar 2018 07:39:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2835 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。