Job ID = 10196136 sra ファイルのダウンロード中... Completed: 902479K bytes transferred in 26 seconds (276759K 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: PAIRED fastq に変換中... Written 6829144 spots for /home/okishinya/chipatlas/results/ce10/SRX2035134/SRR4044258.sra Written 6829144 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:31 6829144 reads; of these: 6829144 (100.00%) were paired; of these: 1034879 (15.15%) aligned concordantly 0 times 5272529 (77.21%) aligned concordantly exactly 1 time 521736 (7.64%) aligned concordantly >1 times ---- 1034879 pairs aligned concordantly 0 times; of these: 487308 (47.09%) aligned discordantly 1 time ---- 547571 pairs aligned 0 times concordantly or discordantly; of these: 1095142 mates make up the pairs; of these: 927401 (84.68%) aligned 0 times 76616 (7.00%) aligned exactly 1 time 91125 (8.32%) aligned >1 times 93.21% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 193397 / 6268859 = 0.0309 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, 11 Nov 2017 14:13:08: # Command line: callpeak -t SRX2035134.bam -f BAM -g ce -n SRX2035134.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2035134.20 # format = BAM # ChIP-seq file = ['SRX2035134.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, 11 Nov 2017 14:13:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:13:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 14:13:08: # Command line: callpeak -t SRX2035134.bam -f BAM -g ce -n SRX2035134.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2035134.10 # format = BAM # ChIP-seq file = ['SRX2035134.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, 11 Nov 2017 14:13:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:13:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 14:13:08: # Command line: callpeak -t SRX2035134.bam -f BAM -g ce -n SRX2035134.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2035134.05 # format = BAM # ChIP-seq file = ['SRX2035134.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, 11 Nov 2017 14:13:08: #1 read tag files... INFO @ Sat, 11 Nov 2017 14:13:08: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 14:13:26: 1000000 INFO @ Sat, 11 Nov 2017 14:13:26: 1000000 INFO @ Sat, 11 Nov 2017 14:13:28: 1000000 INFO @ Sat, 11 Nov 2017 14:13:41: 2000000 INFO @ Sat, 11 Nov 2017 14:13:44: 2000000 INFO @ Sat, 11 Nov 2017 14:13:51: 2000000 INFO @ Sat, 11 Nov 2017 14:13:55: 3000000 INFO @ Sat, 11 Nov 2017 14:14:01: 3000000 INFO @ Sat, 11 Nov 2017 14:14:10: 4000000 INFO @ Sat, 11 Nov 2017 14:14:13: 3000000 INFO @ Sat, 11 Nov 2017 14:14:18: 4000000 INFO @ Sat, 11 Nov 2017 14:14:25: 5000000 INFO @ Sat, 11 Nov 2017 14:14:34: 4000000 INFO @ Sat, 11 Nov 2017 14:14:36: 5000000 INFO @ Sat, 11 Nov 2017 14:14:40: 6000000 INFO @ Sat, 11 Nov 2017 14:14:50: 6000000 INFO @ Sat, 11 Nov 2017 14:14:54: 5000000 INFO @ Sat, 11 Nov 2017 14:14:55: 7000000 INFO @ Sat, 11 Nov 2017 14:15:06: 7000000 INFO @ Sat, 11 Nov 2017 14:15:12: 8000000 INFO @ Sat, 11 Nov 2017 14:15:15: 6000000 INFO @ Sat, 11 Nov 2017 14:15:23: 8000000 INFO @ Sat, 11 Nov 2017 14:15:26: 9000000 INFO @ Sat, 11 Nov 2017 14:15:37: 7000000 INFO @ Sat, 11 Nov 2017 14:15:40: 9000000 INFO @ Sat, 11 Nov 2017 14:15:42: 10000000 INFO @ Sat, 11 Nov 2017 14:15:55: 10000000 INFO @ Sat, 11 Nov 2017 14:15:55: 8000000 INFO @ Sat, 11 Nov 2017 14:15:56: 11000000 INFO @ Sat, 11 Nov 2017 14:16:10: 9000000 INFO @ Sat, 11 Nov 2017 14:16:12: 12000000 INFO @ Sat, 11 Nov 2017 14:16:14: 11000000 INFO @ Sat, 11 Nov 2017 14:16:18: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 14:16:18: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 14:16:18: #1 total tags in treatment: 5605796 INFO @ Sat, 11 Nov 2017 14:16:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:16:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 14:16:18: #1 tags after filtering in treatment: 5025683 INFO @ Sat, 11 Nov 2017 14:16:18: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Nov 2017 14:16:18: #1 finished! INFO @ Sat, 11 Nov 2017 14:16:18: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 14:16:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 14:16:19: #2 number of paired peaks: 4810 INFO @ Sat, 11 Nov 2017 14:16:19: start model_add_line... INFO @ Sat, 11 Nov 2017 14:16:19: start X-correlation... INFO @ Sat, 11 Nov 2017 14:16:19: end of X-cor INFO @ Sat, 11 Nov 2017 14:16:19: #2 finished! INFO @ Sat, 11 Nov 2017 14:16:19: #2 predicted fragment length is 272 bps INFO @ Sat, 11 Nov 2017 14:16:19: #2 alternative fragment length(s) may be 272 bps INFO @ Sat, 11 Nov 2017 14:16:19: #2.2 Generate R script for model : SRX2035134.10_model.r INFO @ Sat, 11 Nov 2017 14:16:20: #3 Call peaks... INFO @ Sat, 11 Nov 2017 14:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 14:16:24: 10000000 INFO @ Sat, 11 Nov 2017 14:16:31: 12000000 INFO @ Sat, 11 Nov 2017 14:16:35: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 14:16:35: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 14:16:35: #1 total tags in treatment: 5605796 INFO @ Sat, 11 Nov 2017 14:16:35: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:16:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 14:16:35: #1 tags after filtering in treatment: 5025683 INFO @ Sat, 11 Nov 2017 14:16:35: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Nov 2017 14:16:35: #1 finished! INFO @ Sat, 11 Nov 2017 14:16:35: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 14:16:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 14:16:36: #2 number of paired peaks: 4810 INFO @ Sat, 11 Nov 2017 14:16:36: start model_add_line... INFO @ Sat, 11 Nov 2017 14:16:36: start X-correlation... INFO @ Sat, 11 Nov 2017 14:16:36: end of X-cor INFO @ Sat, 11 Nov 2017 14:16:36: #2 finished! INFO @ Sat, 11 Nov 2017 14:16:36: #2 predicted fragment length is 272 bps INFO @ Sat, 11 Nov 2017 14:16:36: #2 alternative fragment length(s) may be 272 bps INFO @ Sat, 11 Nov 2017 14:16:36: #2.2 Generate R script for model : SRX2035134.20_model.r INFO @ Sat, 11 Nov 2017 14:16:36: #3 Call peaks... INFO @ Sat, 11 Nov 2017 14:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 14:16:38: 11000000 INFO @ Sat, 11 Nov 2017 14:16:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 14:16:53: #4 Write output xls file... SRX2035134.10_peaks.xls INFO @ Sat, 11 Nov 2017 14:16:53: #4 Write peak in narrowPeak format file... SRX2035134.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 14:16:53: #4 Write summits bed file... SRX2035134.10_summits.bed INFO @ Sat, 11 Nov 2017 14:16:53: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3430 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 14:16:53: 12000000 INFO @ Sat, 11 Nov 2017 14:16:58: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 14:16:58: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 14:16:58: #1 total tags in treatment: 5605796 INFO @ Sat, 11 Nov 2017 14:16:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 14:16:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 14:16:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 14:16:58: #1 tags after filtering in treatment: 5025683 INFO @ Sat, 11 Nov 2017 14:16:58: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Nov 2017 14:16:58: #1 finished! INFO @ Sat, 11 Nov 2017 14:16:58: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 14:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 14:16:59: #2 number of paired peaks: 4810 INFO @ Sat, 11 Nov 2017 14:16:59: start model_add_line... INFO @ Sat, 11 Nov 2017 14:17:00: start X-correlation... INFO @ Sat, 11 Nov 2017 14:17:00: end of X-cor INFO @ Sat, 11 Nov 2017 14:17:00: #2 finished! INFO @ Sat, 11 Nov 2017 14:17:00: #2 predicted fragment length is 272 bps INFO @ Sat, 11 Nov 2017 14:17:00: #2 alternative fragment length(s) may be 272 bps INFO @ Sat, 11 Nov 2017 14:17:00: #2.2 Generate R script for model : SRX2035134.05_model.r INFO @ Sat, 11 Nov 2017 14:17:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 14:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 14:17:08: #4 Write output xls file... SRX2035134.20_peaks.xls INFO @ Sat, 11 Nov 2017 14:17:08: #4 Write peak in narrowPeak format file... SRX2035134.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 14:17:08: #4 Write summits bed file... SRX2035134.20_summits.bed INFO @ Sat, 11 Nov 2017 14:17:08: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2663 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 14:17:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 14:17:33: #4 Write output xls file... SRX2035134.05_peaks.xls INFO @ Sat, 11 Nov 2017 14:17:33: #4 Write peak in narrowPeak format file... SRX2035134.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 14:17:33: #4 Write summits bed file... SRX2035134.05_summits.bed INFO @ Sat, 11 Nov 2017 14:17:33: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4357 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。