Job ID = 10480740 sra ファイルのダウンロード中... Completed: 365905K bytes transferred in 8 seconds (346617K 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 11836864 spots for /home/okishinya/chipatlas/results/dm3/SRX3380799/SRR6278162.sra Written 11836864 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: 00:00:00 Multiseed full-index search: 00:03:50 11836864 reads; of these: 11836864 (100.00%) were unpaired; of these: 335019 (2.83%) aligned 0 times 9320723 (78.74%) aligned exactly 1 time 2181122 (18.43%) aligned >1 times 97.17% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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 8 files... [bam_rmdupse_core] 3375102 / 11501845 = 0.2934 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 @ Fri, 16 Mar 2018 07:52:58: # Command line: callpeak -t SRX3380799.bam -f BAM -g dm -n SRX3380799.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380799.05 # format = BAM # ChIP-seq file = ['SRX3380799.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 @ Fri, 16 Mar 2018 07:52:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:58: # Command line: callpeak -t SRX3380799.bam -f BAM -g dm -n SRX3380799.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380799.20 # format = BAM # ChIP-seq file = ['SRX3380799.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 @ Fri, 16 Mar 2018 07:52:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:58: # Command line: callpeak -t SRX3380799.bam -f BAM -g dm -n SRX3380799.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380799.10 # format = BAM # ChIP-seq file = ['SRX3380799.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 @ Fri, 16 Mar 2018 07:52:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:04: 1000000 INFO @ Fri, 16 Mar 2018 07:53:05: 1000000 INFO @ Fri, 16 Mar 2018 07:53:05: 1000000 INFO @ Fri, 16 Mar 2018 07:53:11: 2000000 INFO @ Fri, 16 Mar 2018 07:53:12: 2000000 INFO @ Fri, 16 Mar 2018 07:53:12: 2000000 INFO @ Fri, 16 Mar 2018 07:53:18: 3000000 INFO @ Fri, 16 Mar 2018 07:53:19: 3000000 INFO @ Fri, 16 Mar 2018 07:53:20: 3000000 INFO @ Fri, 16 Mar 2018 07:53:24: 4000000 INFO @ Fri, 16 Mar 2018 07:53:26: 4000000 INFO @ Fri, 16 Mar 2018 07:53:27: 4000000 INFO @ Fri, 16 Mar 2018 07:53:31: 5000000 INFO @ Fri, 16 Mar 2018 07:53:33: 5000000 INFO @ Fri, 16 Mar 2018 07:53:35: 5000000 INFO @ Fri, 16 Mar 2018 07:53:38: 6000000 INFO @ Fri, 16 Mar 2018 07:53:41: 6000000 INFO @ Fri, 16 Mar 2018 07:53:42: 6000000 INFO @ Fri, 16 Mar 2018 07:53:45: 7000000 INFO @ Fri, 16 Mar 2018 07:53:48: 7000000 INFO @ Fri, 16 Mar 2018 07:53:50: 7000000 INFO @ Fri, 16 Mar 2018 07:53:51: 8000000 INFO @ Fri, 16 Mar 2018 07:53:52: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:52: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:52: #1 total tags in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:52: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:52: #1 tags after filtering in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:52: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:52: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:54: #2 number of paired peaks: 11067 INFO @ Fri, 16 Mar 2018 07:53:54: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:54: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:54: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:54: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:54: #2 predicted fragment length is 219 bps INFO @ Fri, 16 Mar 2018 07:53:54: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 16 Mar 2018 07:53:54: #2.2 Generate R script for model : SRX3380799.20_model.r INFO @ Fri, 16 Mar 2018 07:53:54: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:56: 8000000 INFO @ Fri, 16 Mar 2018 07:53:57: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:57: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:57: #1 total tags in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:57: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:57: #1 tags after filtering in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:57: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:57: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:58: 8000000 INFO @ Fri, 16 Mar 2018 07:53:58: #2 number of paired peaks: 11067 INFO @ Fri, 16 Mar 2018 07:53:58: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:59: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:59: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:59: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:59: #2 predicted fragment length is 219 bps INFO @ Fri, 16 Mar 2018 07:53:59: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 16 Mar 2018 07:53:59: #2.2 Generate R script for model : SRX3380799.05_model.r INFO @ Fri, 16 Mar 2018 07:53:59: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:59: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:59: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:59: #1 total tags in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:59: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:59: #1 tags after filtering in treatment: 8126743 INFO @ Fri, 16 Mar 2018 07:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:59: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:59: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:00: #2 number of paired peaks: 11067 INFO @ Fri, 16 Mar 2018 07:54:00: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:01: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:01: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:01: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:01: #2 predicted fragment length is 219 bps INFO @ Fri, 16 Mar 2018 07:54:01: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 16 Mar 2018 07:54:01: #2.2 Generate R script for model : SRX3380799.10_model.r INFO @ Fri, 16 Mar 2018 07:54:01: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:31: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:43: #4 Write output xls file... SRX3380799.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:43: #4 Write peak in narrowPeak format file... SRX3380799.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:43: #4 Write summits bed file... SRX3380799.20_summits.bed INFO @ Fri, 16 Mar 2018 07:54:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6359 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:54:47: #4 Write output xls file... SRX3380799.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:48: #4 Write peak in narrowPeak format file... SRX3380799.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:48: #4 Write summits bed file... SRX3380799.05_summits.bed INFO @ Fri, 16 Mar 2018 07:54:48: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10259 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:54:50: #4 Write output xls file... SRX3380799.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:50: #4 Write peak in narrowPeak format file... SRX3380799.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:50: #4 Write summits bed file... SRX3380799.10_summits.bed INFO @ Fri, 16 Mar 2018 07:54:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8584 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。