Job ID = 10714401 sra ファイルのダウンロード中... Completed: 409464K bytes transferred in 11 seconds (292795K 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 18785774 spots for /home/okishinya/chipatlas/results/ce10/SRX4082361/SRR7164179.sra Written 18785774 spots for /home/okishinya/chipatlas/results/ce10/SRX4082361/SRR7164179.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: 00:04:43 18785774 reads; of these: 18785774 (100.00%) were unpaired; of these: 233397 (1.24%) aligned 0 times 16552710 (88.11%) aligned exactly 1 time 1999667 (10.64%) aligned >1 times 98.76% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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 8 files... [bam_rmdupse_core] 3529421 / 18552377 = 0.1902 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 @ Sun, 03 Jun 2018 12:39:11: # Command line: callpeak -t SRX4082361.bam -f BAM -g ce -n SRX4082361.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082361.05 # format = BAM # ChIP-seq file = ['SRX4082361.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 @ Sun, 03 Jun 2018 12:39:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:11: # Command line: callpeak -t SRX4082361.bam -f BAM -g ce -n SRX4082361.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082361.20 # format = BAM # ChIP-seq file = ['SRX4082361.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 @ Sun, 03 Jun 2018 12:39:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:11: # Command line: callpeak -t SRX4082361.bam -f BAM -g ce -n SRX4082361.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082361.10 # format = BAM # ChIP-seq file = ['SRX4082361.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 @ Sun, 03 Jun 2018 12:39:11: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:39:11: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:39:18: 1000000 INFO @ Sun, 03 Jun 2018 12:39:18: 1000000 INFO @ Sun, 03 Jun 2018 12:39:18: 1000000 INFO @ Sun, 03 Jun 2018 12:39:24: 2000000 INFO @ Sun, 03 Jun 2018 12:39:25: 2000000 INFO @ Sun, 03 Jun 2018 12:39:25: 2000000 INFO @ Sun, 03 Jun 2018 12:39:31: 3000000 INFO @ Sun, 03 Jun 2018 12:39:32: 3000000 INFO @ Sun, 03 Jun 2018 12:39:32: 3000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:38: 4000000 INFO @ Sun, 03 Jun 2018 12:39:44: 5000000 INFO @ Sun, 03 Jun 2018 12:39:45: 5000000 INFO @ Sun, 03 Jun 2018 12:39:45: 5000000 INFO @ Sun, 03 Jun 2018 12:39:51: 6000000 INFO @ Sun, 03 Jun 2018 12:39:52: 6000000 INFO @ Sun, 03 Jun 2018 12:39:52: 6000000 INFO @ Sun, 03 Jun 2018 12:39:57: 7000000 INFO @ Sun, 03 Jun 2018 12:39:59: 7000000 INFO @ Sun, 03 Jun 2018 12:39:59: 7000000 INFO @ Sun, 03 Jun 2018 12:40:04: 8000000 INFO @ Sun, 03 Jun 2018 12:40:06: 8000000 INFO @ Sun, 03 Jun 2018 12:40:06: 8000000 INFO @ Sun, 03 Jun 2018 12:40:10: 9000000 INFO @ Sun, 03 Jun 2018 12:40:12: 9000000 INFO @ Sun, 03 Jun 2018 12:40:12: 9000000 INFO @ Sun, 03 Jun 2018 12:40:17: 10000000 INFO @ Sun, 03 Jun 2018 12:40:19: 10000000 INFO @ Sun, 03 Jun 2018 12:40:19: 10000000 INFO @ Sun, 03 Jun 2018 12:40:24: 11000000 INFO @ Sun, 03 Jun 2018 12:40:26: 11000000 INFO @ Sun, 03 Jun 2018 12:40:26: 11000000 INFO @ Sun, 03 Jun 2018 12:40:30: 12000000 INFO @ Sun, 03 Jun 2018 12:40:33: 12000000 INFO @ Sun, 03 Jun 2018 12:40:33: 12000000 INFO @ Sun, 03 Jun 2018 12:40:37: 13000000 INFO @ Sun, 03 Jun 2018 12:40:40: 13000000 INFO @ Sun, 03 Jun 2018 12:40:40: 13000000 INFO @ Sun, 03 Jun 2018 12:40:43: 14000000 INFO @ Sun, 03 Jun 2018 12:40:47: 14000000 INFO @ Sun, 03 Jun 2018 12:40:47: 14000000 INFO @ Sun, 03 Jun 2018 12:40:50: 15000000 INFO @ Sun, 03 Jun 2018 12:40:50: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:50: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:50: #1 total tags in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:51: #1 tags after filtering in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:51: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:52: #2 number of paired peaks: 2471 INFO @ Sun, 03 Jun 2018 12:40:52: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:52: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:52: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:52: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:52: #2 predicted fragment length is 119 bps INFO @ Sun, 03 Jun 2018 12:40:52: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Sun, 03 Jun 2018 12:40:52: #2.2 Generate R script for model : SRX4082361.10_model.r INFO @ Sun, 03 Jun 2018 12:40:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:54: 15000000 INFO @ Sun, 03 Jun 2018 12:40:54: 15000000 INFO @ Sun, 03 Jun 2018 12:40:54: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:54: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:54: #1 total tags in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:54: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:40:54: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:40:54: #1 total tags in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:40:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:40:55: #1 tags after filtering in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:55: #1 tags after filtering in treatment: 15022956 INFO @ Sun, 03 Jun 2018 12:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:40:55: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:55: #1 finished! INFO @ Sun, 03 Jun 2018 12:40:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:55: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:40:56: #2 number of paired peaks: 2471 INFO @ Sun, 03 Jun 2018 12:40:56: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:56: #2 number of paired peaks: 2471 INFO @ Sun, 03 Jun 2018 12:40:56: start model_add_line... INFO @ Sun, 03 Jun 2018 12:40:56: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:56: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:56: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:56: #2 predicted fragment length is 119 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2.2 Generate R script for model : SRX4082361.05_model.r INFO @ Sun, 03 Jun 2018 12:40:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:40:56: start X-correlation... INFO @ Sun, 03 Jun 2018 12:40:56: end of X-cor INFO @ Sun, 03 Jun 2018 12:40:56: #2 finished! INFO @ Sun, 03 Jun 2018 12:40:56: #2 predicted fragment length is 119 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2 alternative fragment length(s) may be 3,119,123,139 bps INFO @ Sun, 03 Jun 2018 12:40:56: #2.2 Generate R script for model : SRX4082361.20_model.r INFO @ Sun, 03 Jun 2018 12:40:56: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:41:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:32: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:41:46: #4 Write output xls file... SRX4082361.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:46: #4 Write peak in narrowPeak format file... SRX4082361.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:46: #4 Write summits bed file... SRX4082361.10_summits.bed INFO @ Sun, 03 Jun 2018 12:41:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6410 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:50: #4 Write output xls file... SRX4082361.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:50: #4 Write peak in narrowPeak format file... SRX4082361.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:50: #4 Write summits bed file... SRX4082361.20_summits.bed INFO @ Sun, 03 Jun 2018 12:41:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:41:52: #4 Write output xls file... SRX4082361.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:41:53: #4 Write peak in narrowPeak format file... SRX4082361.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:41:53: #4 Write summits bed file... SRX4082361.05_summits.bed INFO @ Sun, 03 Jun 2018 12:41:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11025 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。