Job ID = 10714408 sra ファイルのダウンロード中... Completed: 325291K bytes transferred in 9 seconds (269947K 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 14888088 spots for /home/okishinya/chipatlas/results/ce10/SRX4082368/SRR7164186.sra Written 14888088 spots for /home/okishinya/chipatlas/results/ce10/SRX4082368/SRR7164186.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: 00:03:44 14888088 reads; of these: 14888088 (100.00%) were unpaired; of these: 525832 (3.53%) aligned 0 times 13121879 (88.14%) aligned exactly 1 time 1240377 (8.33%) aligned >1 times 96.47% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 3131588 / 14362256 = 0.2180 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 12:36:44: # Command line: callpeak -t SRX4082368.bam -f BAM -g ce -n SRX4082368.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082368.10 # format = BAM # ChIP-seq file = ['SRX4082368.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 12:36:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:44: # Command line: callpeak -t SRX4082368.bam -f BAM -g ce -n SRX4082368.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082368.20 # format = BAM # ChIP-seq file = ['SRX4082368.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 12:36:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:44: # Command line: callpeak -t SRX4082368.bam -f BAM -g ce -n SRX4082368.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082368.05 # format = BAM # ChIP-seq file = ['SRX4082368.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 12:36:44: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:36:44: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:36:51: 1000000 INFO @ Sun, 03 Jun 2018 12:36:51: 1000000 INFO @ Sun, 03 Jun 2018 12:36:52: 1000000 INFO @ Sun, 03 Jun 2018 12:36:57: 2000000 INFO @ Sun, 03 Jun 2018 12:36:57: 2000000 INFO @ Sun, 03 Jun 2018 12:37:00: 2000000 INFO @ Sun, 03 Jun 2018 12:37:04: 3000000 INFO @ Sun, 03 Jun 2018 12:37:04: 3000000 INFO @ Sun, 03 Jun 2018 12:37:06: 3000000 INFO @ Sun, 03 Jun 2018 12:37:10: 4000000 INFO @ Sun, 03 Jun 2018 12:37:10: 4000000 INFO @ Sun, 03 Jun 2018 12:37:12: 4000000 INFO @ Sun, 03 Jun 2018 12:37:16: 5000000 INFO @ Sun, 03 Jun 2018 12:37:16: 5000000 INFO @ Sun, 03 Jun 2018 12:37:19: 5000000 INFO @ Sun, 03 Jun 2018 12:37:23: 6000000 INFO @ Sun, 03 Jun 2018 12:37:23: 6000000 INFO @ Sun, 03 Jun 2018 12:37:25: 6000000 INFO @ Sun, 03 Jun 2018 12:37:29: 7000000 INFO @ Sun, 03 Jun 2018 12:37:29: 7000000 INFO @ Sun, 03 Jun 2018 12:37:31: 7000000 INFO @ Sun, 03 Jun 2018 12:37:36: 8000000 INFO @ Sun, 03 Jun 2018 12:37:36: 8000000 INFO @ Sun, 03 Jun 2018 12:37:38: 8000000 INFO @ Sun, 03 Jun 2018 12:37:43: 9000000 INFO @ Sun, 03 Jun 2018 12:37:43: 9000000 INFO @ Sun, 03 Jun 2018 12:37:44: 9000000 INFO @ Sun, 03 Jun 2018 12:37:50: 10000000 INFO @ Sun, 03 Jun 2018 12:37:50: 10000000 INFO @ Sun, 03 Jun 2018 12:37:51: 10000000 INFO @ Sun, 03 Jun 2018 12:37:56: 11000000 INFO @ Sun, 03 Jun 2018 12:37:57: 11000000 INFO @ Sun, 03 Jun 2018 12:37:57: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:57: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:57: #1 total tags in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:57: #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 12:37:57: #1 tags after filtering in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:57: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:58: 11000000 INFO @ Sun, 03 Jun 2018 12:37:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:59: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:59: #1 total tags in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:59: #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 12:37:59: #2 number of paired peaks: 5425 INFO @ Sun, 03 Jun 2018 12:37:59: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:59: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:59: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:59: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:59: #2 predicted fragment length is 169 bps INFO @ Sun, 03 Jun 2018 12:37:59: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 03 Jun 2018 12:37:59: #2.2 Generate R script for model : SRX4082368.05_model.r INFO @ Sun, 03 Jun 2018 12:37:59: #1 tags after filtering in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:59: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:59: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:59: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:59: #1 total tags in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:59: #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 12:37:59: #1 tags after filtering in treatment: 11230668 INFO @ Sun, 03 Jun 2018 12:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:59: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:00: #2 number of paired peaks: 5425 INFO @ Sun, 03 Jun 2018 12:38:00: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:01: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:01: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:01: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:01: #2 predicted fragment length is 169 bps INFO @ Sun, 03 Jun 2018 12:38:01: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 03 Jun 2018 12:38:01: #2.2 Generate R script for model : SRX4082368.20_model.r INFO @ Sun, 03 Jun 2018 12:38:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:01: #2 number of paired peaks: 5425 INFO @ Sun, 03 Jun 2018 12:38:01: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:01: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:01: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:01: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:01: #2 predicted fragment length is 169 bps INFO @ Sun, 03 Jun 2018 12:38:01: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 03 Jun 2018 12:38:01: #2.2 Generate R script for model : SRX4082368.10_model.r INFO @ Sun, 03 Jun 2018 12:38:01: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:31: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:32: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:46: #4 Write output xls file... SRX4082368.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:46: #4 Write peak in narrowPeak format file... SRX4082368.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:46: #4 Write summits bed file... SRX4082368.05_summits.bed INFO @ Sun, 03 Jun 2018 12:38:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10593 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:47: #4 Write output xls file... SRX4082368.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:47: #4 Write peak in narrowPeak format file... SRX4082368.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:47: #4 Write summits bed file... SRX4082368.10_summits.bed INFO @ Sun, 03 Jun 2018 12:38:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6505 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:48: #4 Write output xls file... SRX4082368.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:48: #4 Write peak in narrowPeak format file... SRX4082368.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:48: #4 Write summits bed file... SRX4082368.20_summits.bed INFO @ Sun, 03 Jun 2018 12:38:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2288 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。