Job ID = 11170842 sra ファイルのダウンロード中... Completed: 938814K bytes transferred in 57 seconds (133502K 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 32930092 spots for /home/okishinya/chipatlas/results/ce10/SRX3583342/SRR6493998.sra Written 32930092 spots for /home/okishinya/chipatlas/results/ce10/SRX3583342/SRR6493998.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 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: 00:11:52 32930092 reads; of these: 32930092 (100.00%) were unpaired; of these: 714219 (2.17%) aligned 0 times 28338938 (86.06%) aligned exactly 1 time 3876935 (11.77%) aligned >1 times 97.83% overall alignment rate Time searching: 00:11:52 Overall time: 00:11:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6227426 / 32215873 = 0.1933 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 11:48:07: # Command line: callpeak -t SRX3583342.bam -f BAM -g ce -n SRX3583342.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583342.10 # format = BAM # ChIP-seq file = ['SRX3583342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:48:07: # Command line: callpeak -t SRX3583342.bam -f BAM -g ce -n SRX3583342.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583342.05 # format = BAM # ChIP-seq file = ['SRX3583342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:48:07: # Command line: callpeak -t SRX3583342.bam -f BAM -g ce -n SRX3583342.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583342.20 # format = BAM # ChIP-seq file = ['SRX3583342.bam'] # control file = None # effective genome size = 9.00e+07 # 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 11:48:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:48:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:48:14: 1000000 INFO @ Sat, 08 Sep 2018 11:48:14: 1000000 INFO @ Sat, 08 Sep 2018 11:48:14: 1000000 INFO @ Sat, 08 Sep 2018 11:48:20: 2000000 INFO @ Sat, 08 Sep 2018 11:48:21: 2000000 INFO @ Sat, 08 Sep 2018 11:48:21: 2000000 INFO @ Sat, 08 Sep 2018 11:48:27: 3000000 INFO @ Sat, 08 Sep 2018 11:48:27: 3000000 INFO @ Sat, 08 Sep 2018 11:48:27: 3000000 INFO @ Sat, 08 Sep 2018 11:48:34: 4000000 INFO @ Sat, 08 Sep 2018 11:48:34: 4000000 INFO @ Sat, 08 Sep 2018 11:48:34: 4000000 INFO @ Sat, 08 Sep 2018 11:48:40: 5000000 INFO @ Sat, 08 Sep 2018 11:48:40: 5000000 INFO @ Sat, 08 Sep 2018 11:48:41: 5000000 INFO @ Sat, 08 Sep 2018 11:48:47: 6000000 INFO @ Sat, 08 Sep 2018 11:48:47: 6000000 INFO @ Sat, 08 Sep 2018 11:48:47: 6000000 INFO @ Sat, 08 Sep 2018 11:48:53: 7000000 INFO @ Sat, 08 Sep 2018 11:48:53: 7000000 INFO @ Sat, 08 Sep 2018 11:48:54: 7000000 INFO @ Sat, 08 Sep 2018 11:49:00: 8000000 INFO @ Sat, 08 Sep 2018 11:49:00: 8000000 INFO @ Sat, 08 Sep 2018 11:49:01: 8000000 INFO @ Sat, 08 Sep 2018 11:49:06: 9000000 INFO @ Sat, 08 Sep 2018 11:49:07: 9000000 INFO @ Sat, 08 Sep 2018 11:49:07: 9000000 INFO @ Sat, 08 Sep 2018 11:49:13: 10000000 INFO @ Sat, 08 Sep 2018 11:49:13: 10000000 INFO @ Sat, 08 Sep 2018 11:49:14: 10000000 INFO @ Sat, 08 Sep 2018 11:49:19: 11000000 INFO @ Sat, 08 Sep 2018 11:49:20: 11000000 INFO @ Sat, 08 Sep 2018 11:49:21: 11000000 INFO @ Sat, 08 Sep 2018 11:49:26: 12000000 INFO @ Sat, 08 Sep 2018 11:49:26: 12000000 INFO @ Sat, 08 Sep 2018 11:49:28: 12000000 INFO @ Sat, 08 Sep 2018 11:49:32: 13000000 INFO @ Sat, 08 Sep 2018 11:49:33: 13000000 INFO @ Sat, 08 Sep 2018 11:49:35: 13000000 INFO @ Sat, 08 Sep 2018 11:49:39: 14000000 INFO @ Sat, 08 Sep 2018 11:49:39: 14000000 INFO @ Sat, 08 Sep 2018 11:49:42: 14000000 INFO @ Sat, 08 Sep 2018 11:49:46: 15000000 INFO @ Sat, 08 Sep 2018 11:49:46: 15000000 INFO @ Sat, 08 Sep 2018 11:49:49: 15000000 INFO @ Sat, 08 Sep 2018 11:49:52: 16000000 INFO @ Sat, 08 Sep 2018 11:49:52: 16000000 INFO @ Sat, 08 Sep 2018 11:49:55: 16000000 INFO @ Sat, 08 Sep 2018 11:49:59: 17000000 INFO @ Sat, 08 Sep 2018 11:49:59: 17000000 INFO @ Sat, 08 Sep 2018 11:50:02: 17000000 INFO @ Sat, 08 Sep 2018 11:50:05: 18000000 INFO @ Sat, 08 Sep 2018 11:50:06: 18000000 INFO @ Sat, 08 Sep 2018 11:50:09: 18000000 INFO @ Sat, 08 Sep 2018 11:50:11: 19000000 INFO @ Sat, 08 Sep 2018 11:50:13: 19000000 INFO @ Sat, 08 Sep 2018 11:50:16: 19000000 INFO @ Sat, 08 Sep 2018 11:50:18: 20000000 INFO @ Sat, 08 Sep 2018 11:50:19: 20000000 INFO @ Sat, 08 Sep 2018 11:50:23: 20000000 INFO @ Sat, 08 Sep 2018 11:50:24: 21000000 INFO @ Sat, 08 Sep 2018 11:50:26: 21000000 INFO @ Sat, 08 Sep 2018 11:50:30: 21000000 INFO @ Sat, 08 Sep 2018 11:50:30: 22000000 INFO @ Sat, 08 Sep 2018 11:50:33: 22000000 INFO @ Sat, 08 Sep 2018 11:50:36: 22000000 INFO @ Sat, 08 Sep 2018 11:50:37: 23000000 INFO @ Sat, 08 Sep 2018 11:50:39: 23000000 INFO @ Sat, 08 Sep 2018 11:50:43: 24000000 INFO @ Sat, 08 Sep 2018 11:50:43: 23000000 INFO @ Sat, 08 Sep 2018 11:50:46: 24000000 INFO @ Sat, 08 Sep 2018 11:50:50: 25000000 INFO @ Sat, 08 Sep 2018 11:50:50: 24000000 INFO @ Sat, 08 Sep 2018 11:50:53: 25000000 INFO @ Sat, 08 Sep 2018 11:50:56: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:50:56: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:50:56: #1 total tags in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:50:56: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:50:56: #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 11:50:57: #1 tags after filtering in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:50:57: #1 finished! INFO @ Sat, 08 Sep 2018 11:50:57: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:50:57: 25000000 INFO @ Sat, 08 Sep 2018 11:50:58: #2 number of paired peaks: 501 WARNING @ Sat, 08 Sep 2018 11:50:58: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Sat, 08 Sep 2018 11:50:58: start model_add_line... INFO @ Sat, 08 Sep 2018 11:50:59: start X-correlation... INFO @ Sat, 08 Sep 2018 11:50:59: end of X-cor INFO @ Sat, 08 Sep 2018 11:50:59: #2 finished! INFO @ Sat, 08 Sep 2018 11:50:59: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 11:50:59: #2 alternative fragment length(s) may be 3,161,186 bps INFO @ Sat, 08 Sep 2018 11:50:59: #2.2 Generate R script for model : SRX3583342.05_model.r INFO @ Sat, 08 Sep 2018 11:50:59: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:50:59: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:50:59: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:50:59: #1 total tags in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:50:59: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:50:59: #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 11:51:00: #1 tags after filtering in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:00: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:00: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:02: #2 number of paired peaks: 501 WARNING @ Sat, 08 Sep 2018 11:51:02: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:02: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:02: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:02: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:02: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:02: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 11:51:02: #2 alternative fragment length(s) may be 3,161,186 bps INFO @ Sat, 08 Sep 2018 11:51:02: #2.2 Generate R script for model : SRX3583342.20_model.r INFO @ Sat, 08 Sep 2018 11:51:02: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:04: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:51:04: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:51:04: #1 total tags in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:51:04: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:51:04: #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 11:51:04: #1 tags after filtering in treatment: 25988447 INFO @ Sat, 08 Sep 2018 11:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:51:04: #1 finished! INFO @ Sat, 08 Sep 2018 11:51:04: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:51:06: #2 number of paired peaks: 501 WARNING @ Sat, 08 Sep 2018 11:51:06: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Sat, 08 Sep 2018 11:51:06: start model_add_line... INFO @ Sat, 08 Sep 2018 11:51:06: start X-correlation... INFO @ Sat, 08 Sep 2018 11:51:06: end of X-cor INFO @ Sat, 08 Sep 2018 11:51:06: #2 finished! INFO @ Sat, 08 Sep 2018 11:51:06: #2 predicted fragment length is 161 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2 alternative fragment length(s) may be 3,161,186 bps INFO @ Sat, 08 Sep 2018 11:51:06: #2.2 Generate R script for model : SRX3583342.10_model.r INFO @ Sat, 08 Sep 2018 11:51:06: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:51:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:51:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:52:18: #4 Write output xls file... SRX3583342.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:18: #4 Write peak in narrowPeak format file... SRX3583342.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:18: #4 Write summits bed file... SRX3583342.05_summits.bed INFO @ Sat, 08 Sep 2018 11:52:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5824 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:52:23: #4 Write output xls file... SRX3583342.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:24: #4 Write peak in narrowPeak format file... SRX3583342.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:24: #4 Write summits bed file... SRX3583342.20_summits.bed INFO @ Sat, 08 Sep 2018 11:52:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3187 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:52:26: #4 Write output xls file... SRX3583342.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:52:26: #4 Write peak in narrowPeak format file... SRX3583342.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:52:26: #4 Write summits bed file... SRX3583342.10_summits.bed INFO @ Sat, 08 Sep 2018 11:52:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4371 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。