Job ID = 10201955 sra ファイルのダウンロード中... Completed: 713407K bytes transferred in 17 seconds (332217K 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 21023417 spots for /home/okishinya/chipatlas/results/ce10/SRX2576624/SRR5272581.sra Written 21023417 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:21 21023417 reads; of these: 21023417 (100.00%) were unpaired; of these: 3578521 (17.02%) aligned 0 times 14314954 (68.09%) aligned exactly 1 time 3129942 (14.89%) aligned >1 times 82.98% overall alignment rate Time searching: 00:12:22 Overall time: 00:12:22 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] 10626963 / 17444896 = 0.6092 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 @ Mon, 13 Nov 2017 13:27:27: # Command line: callpeak -t SRX2576624.bam -f BAM -g ce -n SRX2576624.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576624.10 # format = BAM # ChIP-seq file = ['SRX2576624.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 @ Mon, 13 Nov 2017 13:27:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:27: # Command line: callpeak -t SRX2576624.bam -f BAM -g ce -n SRX2576624.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576624.05 # format = BAM # ChIP-seq file = ['SRX2576624.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 @ Mon, 13 Nov 2017 13:27:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:27: # Command line: callpeak -t SRX2576624.bam -f BAM -g ce -n SRX2576624.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576624.20 # format = BAM # ChIP-seq file = ['SRX2576624.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 @ Mon, 13 Nov 2017 13:27:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:27:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:27:47: 1000000 INFO @ Mon, 13 Nov 2017 13:27:48: 1000000 INFO @ Mon, 13 Nov 2017 13:27:48: 1000000 INFO @ Mon, 13 Nov 2017 13:28:05: 2000000 INFO @ Mon, 13 Nov 2017 13:28:07: 2000000 INFO @ Mon, 13 Nov 2017 13:28:10: 2000000 INFO @ Mon, 13 Nov 2017 13:28:23: 3000000 INFO @ Mon, 13 Nov 2017 13:28:28: 3000000 INFO @ Mon, 13 Nov 2017 13:28:31: 3000000 INFO @ Mon, 13 Nov 2017 13:28:40: 4000000 INFO @ Mon, 13 Nov 2017 13:28:49: 4000000 INFO @ Mon, 13 Nov 2017 13:28:52: 4000000 INFO @ Mon, 13 Nov 2017 13:28:59: 5000000 INFO @ Mon, 13 Nov 2017 13:29:11: 5000000 INFO @ Mon, 13 Nov 2017 13:29:14: 5000000 INFO @ Mon, 13 Nov 2017 13:29:18: 6000000 INFO @ Mon, 13 Nov 2017 13:29:32: 6000000 INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:32: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:32: #1 total tags in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:32: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:32: #1 tags after filtering in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:32: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:32: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:33: #2 number of paired peaks: 1213 INFO @ Mon, 13 Nov 2017 13:29:33: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:33: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:33: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:33: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:33: #2 predicted fragment length is 149 bps INFO @ Mon, 13 Nov 2017 13:29:33: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 13 Nov 2017 13:29:33: #2.2 Generate R script for model : SRX2576624.10_model.r INFO @ Mon, 13 Nov 2017 13:29:33: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:35: 6000000 INFO @ Mon, 13 Nov 2017 13:29:48: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:48: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:48: #1 total tags in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:48: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:48: #1 tags after filtering in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:48: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:48: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:49: #2 number of paired peaks: 1213 INFO @ Mon, 13 Nov 2017 13:29:49: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:49: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:49: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:49: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:49: #2 predicted fragment length is 149 bps INFO @ Mon, 13 Nov 2017 13:29:49: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 13 Nov 2017 13:29:49: #2.2 Generate R script for model : SRX2576624.05_model.r INFO @ Mon, 13 Nov 2017 13:29:49: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:51: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:29:51: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:29:51: #1 total tags in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:51: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:29:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:29:52: #1 tags after filtering in treatment: 6817933 INFO @ Mon, 13 Nov 2017 13:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:29:52: #1 finished! INFO @ Mon, 13 Nov 2017 13:29:52: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:29:53: #2 number of paired peaks: 1213 INFO @ Mon, 13 Nov 2017 13:29:53: start model_add_line... INFO @ Mon, 13 Nov 2017 13:29:53: start X-correlation... INFO @ Mon, 13 Nov 2017 13:29:53: end of X-cor INFO @ Mon, 13 Nov 2017 13:29:53: #2 finished! INFO @ Mon, 13 Nov 2017 13:29:53: #2 predicted fragment length is 149 bps INFO @ Mon, 13 Nov 2017 13:29:53: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 13 Nov 2017 13:29:53: #2.2 Generate R script for model : SRX2576624.20_model.r INFO @ Mon, 13 Nov 2017 13:29:53: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:29:58: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:11: #4 Write output xls file... SRX2576624.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:11: #4 Write peak in narrowPeak format file... SRX2576624.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:11: #4 Write summits bed file... SRX2576624.10_summits.bed INFO @ Mon, 13 Nov 2017 13:30:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1810 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:14: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:17: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:30:26: #4 Write output xls file... SRX2576624.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:26: #4 Write peak in narrowPeak format file... SRX2576624.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:27: #4 Write summits bed file... SRX2576624.05_summits.bed INFO @ Mon, 13 Nov 2017 13:30:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2522 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:30:30: #4 Write output xls file... SRX2576624.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:30:30: #4 Write peak in narrowPeak format file... SRX2576624.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:30:30: #4 Write summits bed file... SRX2576624.20_summits.bed INFO @ Mon, 13 Nov 2017 13:30:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1223 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。