Job ID = 11170887 sra ファイルのダウンロード中... Completed: 145840K bytes transferred in 9 seconds (123044K bits/sec), in 1 file. Completed: 143481K bytes transferred in 11 seconds (105895K bits/sec), in 1 file. Completed: 141850K bytes transferred in 8 seconds (140669K bits/sec), in 1 file. Completed: 139302K bytes transferred in 5 seconds (208688K 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 6166756 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084567.sra Written 6166756 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084567.sra Read 6294781 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084566.sra Written 6294781 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084566.sra Read 6327624 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084565.sra Written 6327624 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084565.sra Read 6403967 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084564.sra Written 6403967 spots for /home/okishinya/chipatlas/results/dm3/SRX1078885/SRR2084564.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 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: 00:08:45 25193128 reads; of these: 25193128 (100.00%) were unpaired; of these: 3715988 (14.75%) aligned 0 times 15778077 (62.63%) aligned exactly 1 time 5699063 (22.62%) aligned >1 times 85.25% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5232000 / 21477140 = 0.2436 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, 08 Sep 2018 11:40:31: # Command line: callpeak -t SRX1078885.bam -f BAM -g dm -n SRX1078885.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1078885.05 # format = BAM # ChIP-seq file = ['SRX1078885.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 11:40:31: # Command line: callpeak -t SRX1078885.bam -f BAM -g dm -n SRX1078885.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1078885.10 # format = BAM # ChIP-seq file = ['SRX1078885.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 11:40:31: # Command line: callpeak -t SRX1078885.bam -f BAM -g dm -n SRX1078885.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1078885.20 # format = BAM # ChIP-seq file = ['SRX1078885.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 11:40:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:40:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:40:37: 1000000 INFO @ Sat, 08 Sep 2018 11:40:37: 1000000 INFO @ Sat, 08 Sep 2018 11:40:38: 1000000 INFO @ Sat, 08 Sep 2018 11:40:44: 2000000 INFO @ Sat, 08 Sep 2018 11:40:44: 2000000 INFO @ Sat, 08 Sep 2018 11:40:44: 2000000 INFO @ Sat, 08 Sep 2018 11:40:51: 3000000 INFO @ Sat, 08 Sep 2018 11:40:51: 3000000 INFO @ Sat, 08 Sep 2018 11:40:52: 3000000 INFO @ Sat, 08 Sep 2018 11:40:58: 4000000 INFO @ Sat, 08 Sep 2018 11:40:58: 4000000 INFO @ Sat, 08 Sep 2018 11:41:01: 4000000 INFO @ Sat, 08 Sep 2018 11:41:04: 5000000 INFO @ Sat, 08 Sep 2018 11:41:04: 5000000 INFO @ Sat, 08 Sep 2018 11:41:10: 5000000 INFO @ Sat, 08 Sep 2018 11:41:11: 6000000 INFO @ Sat, 08 Sep 2018 11:41:11: 6000000 INFO @ Sat, 08 Sep 2018 11:41:18: 7000000 INFO @ Sat, 08 Sep 2018 11:41:18: 7000000 INFO @ Sat, 08 Sep 2018 11:41:19: 6000000 INFO @ Sat, 08 Sep 2018 11:41:24: 8000000 INFO @ Sat, 08 Sep 2018 11:41:24: 8000000 INFO @ Sat, 08 Sep 2018 11:41:28: 7000000 INFO @ Sat, 08 Sep 2018 11:41:31: 9000000 INFO @ Sat, 08 Sep 2018 11:41:31: 9000000 INFO @ Sat, 08 Sep 2018 11:41:37: 8000000 INFO @ Sat, 08 Sep 2018 11:41:37: 10000000 INFO @ Sat, 08 Sep 2018 11:41:37: 10000000 INFO @ Sat, 08 Sep 2018 11:41:44: 11000000 INFO @ Sat, 08 Sep 2018 11:41:44: 11000000 INFO @ Sat, 08 Sep 2018 11:41:46: 9000000 INFO @ Sat, 08 Sep 2018 11:41:51: 12000000 INFO @ Sat, 08 Sep 2018 11:41:51: 12000000 INFO @ Sat, 08 Sep 2018 11:41:54: 10000000 INFO @ Sat, 08 Sep 2018 11:41:57: 13000000 INFO @ Sat, 08 Sep 2018 11:41:57: 13000000 INFO @ Sat, 08 Sep 2018 11:42:03: 11000000 INFO @ Sat, 08 Sep 2018 11:42:04: 14000000 INFO @ Sat, 08 Sep 2018 11:42:04: 14000000 INFO @ Sat, 08 Sep 2018 11:42:11: 15000000 INFO @ Sat, 08 Sep 2018 11:42:11: 15000000 INFO @ Sat, 08 Sep 2018 11:42:13: 12000000 INFO @ Sat, 08 Sep 2018 11:42:18: 16000000 INFO @ Sat, 08 Sep 2018 11:42:18: 16000000 INFO @ Sat, 08 Sep 2018 11:42:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:20: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:20: #1 total tags in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:20: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:20: #1 total tags in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:21: #1 tags after filtering in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:21: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:21: #1 tags after filtering in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:21: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:21: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:22: #2 number of paired peaks: 5172 INFO @ Sat, 08 Sep 2018 11:42:22: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:22: #2 number of paired peaks: 5172 INFO @ Sat, 08 Sep 2018 11:42:22: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:23: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:23: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:23: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:23: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:23: #2 predicted fragment length is 164 bps INFO @ Sat, 08 Sep 2018 11:42:23: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:23: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 08 Sep 2018 11:42:23: #2.2 Generate R script for model : SRX1078885.05_model.r INFO @ Sat, 08 Sep 2018 11:42:23: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:23: #2 predicted fragment length is 164 bps INFO @ Sat, 08 Sep 2018 11:42:23: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 08 Sep 2018 11:42:23: #2.2 Generate R script for model : SRX1078885.20_model.r INFO @ Sat, 08 Sep 2018 11:42:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:23: 13000000 INFO @ Sat, 08 Sep 2018 11:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:42:33: 14000000 INFO @ Sat, 08 Sep 2018 11:42:43: 15000000 INFO @ Sat, 08 Sep 2018 11:42:54: 16000000 INFO @ Sat, 08 Sep 2018 11:42:56: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:42:56: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:42:56: #1 total tags in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:56: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:42:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:42:56: #1 tags after filtering in treatment: 16245140 INFO @ Sat, 08 Sep 2018 11:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:42:56: #1 finished! INFO @ Sat, 08 Sep 2018 11:42:56: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:42:58: #2 number of paired peaks: 5172 INFO @ Sat, 08 Sep 2018 11:42:58: start model_add_line... INFO @ Sat, 08 Sep 2018 11:42:58: start X-correlation... INFO @ Sat, 08 Sep 2018 11:42:58: end of X-cor INFO @ Sat, 08 Sep 2018 11:42:58: #2 finished! INFO @ Sat, 08 Sep 2018 11:42:58: #2 predicted fragment length is 164 bps INFO @ Sat, 08 Sep 2018 11:42:58: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 08 Sep 2018 11:42:58: #2.2 Generate R script for model : SRX1078885.10_model.r INFO @ Sat, 08 Sep 2018 11:42:58: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:43:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:43:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:43:35: #4 Write output xls file... SRX1078885.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:43:35: #4 Write peak in narrowPeak format file... SRX1078885.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:43:35: #4 Write summits bed file... SRX1078885.20_summits.bed INFO @ Sat, 08 Sep 2018 11:43:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6279 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:43:36: #4 Write output xls file... SRX1078885.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:43:36: #4 Write peak in narrowPeak format file... SRX1078885.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:43:36: #4 Write summits bed file... SRX1078885.05_summits.bed INFO @ Sat, 08 Sep 2018 11:43:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10511 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:43:51: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:44:13: #4 Write output xls file... SRX1078885.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:44:13: #4 Write peak in narrowPeak format file... SRX1078885.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:44:13: #4 Write summits bed file... SRX1078885.10_summits.bed INFO @ Sat, 08 Sep 2018 11:44:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8548 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。