Job ID = 10714374 sra ファイルのダウンロード中... Completed: 300082K bytes transferred in 23 seconds (103335K 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 14123310 spots for /home/okishinya/chipatlas/results/ce10/SRX4082334/SRR7164152.sra Written 14123310 spots for /home/okishinya/chipatlas/results/ce10/SRX4082334/SRR7164152.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:40 14123310 reads; of these: 14123310 (100.00%) were unpaired; of these: 271936 (1.93%) aligned 0 times 12622942 (89.38%) aligned exactly 1 time 1228432 (8.70%) aligned >1 times 98.07% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 3935073 / 13851374 = 0.2841 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 12:35:31: # Command line: callpeak -t SRX4082334.bam -f BAM -g ce -n SRX4082334.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082334.10 # format = BAM # ChIP-seq file = ['SRX4082334.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 12:35:31: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:31: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:31: # Command line: callpeak -t SRX4082334.bam -f BAM -g ce -n SRX4082334.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082334.05 # format = BAM # ChIP-seq file = ['SRX4082334.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 12:35:31: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:31: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:31: # Command line: callpeak -t SRX4082334.bam -f BAM -g ce -n SRX4082334.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082334.20 # format = BAM # ChIP-seq file = ['SRX4082334.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 12:35:31: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:31: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:38: 1000000 INFO @ Sun, 03 Jun 2018 12:35:38: 1000000 INFO @ Sun, 03 Jun 2018 12:35:39: 1000000 INFO @ Sun, 03 Jun 2018 12:35:44: 2000000 INFO @ Sun, 03 Jun 2018 12:35:45: 2000000 INFO @ Sun, 03 Jun 2018 12:35:46: 2000000 INFO @ Sun, 03 Jun 2018 12:35:51: 3000000 INFO @ Sun, 03 Jun 2018 12:35:52: 3000000 INFO @ Sun, 03 Jun 2018 12:35:53: 3000000 INFO @ Sun, 03 Jun 2018 12:35:58: 4000000 INFO @ Sun, 03 Jun 2018 12:35:59: 4000000 INFO @ Sun, 03 Jun 2018 12:36:01: 4000000 INFO @ Sun, 03 Jun 2018 12:36:05: 5000000 INFO @ Sun, 03 Jun 2018 12:36:06: 5000000 INFO @ Sun, 03 Jun 2018 12:36:08: 5000000 INFO @ Sun, 03 Jun 2018 12:36:11: 6000000 INFO @ Sun, 03 Jun 2018 12:36:13: 6000000 INFO @ Sun, 03 Jun 2018 12:36:14: 6000000 INFO @ Sun, 03 Jun 2018 12:36:17: 7000000 INFO @ Sun, 03 Jun 2018 12:36:19: 7000000 INFO @ Sun, 03 Jun 2018 12:36:20: 7000000 INFO @ Sun, 03 Jun 2018 12:36:23: 8000000 INFO @ Sun, 03 Jun 2018 12:36:25: 8000000 INFO @ Sun, 03 Jun 2018 12:36:26: 8000000 INFO @ Sun, 03 Jun 2018 12:36:30: 9000000 INFO @ Sun, 03 Jun 2018 12:36:32: 9000000 INFO @ Sun, 03 Jun 2018 12:36:32: 9000000 INFO @ Sun, 03 Jun 2018 12:36:35: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:35: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:35: #1 total tags in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:35: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:35: #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 12:36:35: #1 tags after filtering in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:35: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:35: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:37: #2 number of paired peaks: 5927 INFO @ Sun, 03 Jun 2018 12:36:37: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:37: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:37: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:37: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:37: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 12:36:37: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 03 Jun 2018 12:36:37: #2.2 Generate R script for model : SRX4082334.10_model.r INFO @ Sun, 03 Jun 2018 12:36:37: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:37: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:37: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:37: #1 total tags in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:37: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:37: #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 12:36:38: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:36:38: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:36:38: #1 total tags in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:38: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:36:38: #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 12:36:38: #1 tags after filtering in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:38: #1 tags after filtering in treatment: 9916301 INFO @ Sun, 03 Jun 2018 12:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:36:38: #1 finished! INFO @ Sun, 03 Jun 2018 12:36:38: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:36:39: #2 number of paired peaks: 5927 INFO @ Sun, 03 Jun 2018 12:36:39: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:39: #2 number of paired peaks: 5927 INFO @ Sun, 03 Jun 2018 12:36:39: start model_add_line... INFO @ Sun, 03 Jun 2018 12:36:39: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:39: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:39: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:39: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 12:36:39: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 03 Jun 2018 12:36:39: #2.2 Generate R script for model : SRX4082334.20_model.r INFO @ Sun, 03 Jun 2018 12:36:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:36:39: start X-correlation... INFO @ Sun, 03 Jun 2018 12:36:39: end of X-cor INFO @ Sun, 03 Jun 2018 12:36:39: #2 finished! INFO @ Sun, 03 Jun 2018 12:36:39: #2 predicted fragment length is 147 bps INFO @ Sun, 03 Jun 2018 12:36:39: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 03 Jun 2018 12:36:39: #2.2 Generate R script for model : SRX4082334.05_model.r INFO @ Sun, 03 Jun 2018 12:36:39: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:05: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:18: #4 Write output xls file... SRX4082334.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:18: #4 Write peak in narrowPeak format file... SRX4082334.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:18: #4 Write summits bed file... SRX4082334.10_summits.bed INFO @ Sun, 03 Jun 2018 12:37:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5980 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:21: #4 Write output xls file... SRX4082334.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:21: #4 Write peak in narrowPeak format file... SRX4082334.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:21: #4 Write summits bed file... SRX4082334.20_summits.bed INFO @ Sun, 03 Jun 2018 12:37:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4793 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write output xls file... SRX4082334.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write peak in narrowPeak format file... SRX4082334.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:23: #4 Write summits bed file... SRX4082334.05_summits.bed INFO @ Sun, 03 Jun 2018 12:37:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7520 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。