Job ID = 10609511 sra ファイルのダウンロード中... Completed: 561587K bytes transferred in 40 seconds (112847K 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 17790016 spots for /home/okishinya/chipatlas/results/dm3/SRX3011237/SRR5834714.sra Written 17790016 spots for /home/okishinya/chipatlas/results/dm3/SRX3011237/SRR5834714.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:57 17790016 reads; of these: 17790016 (100.00%) were unpaired; of these: 506349 (2.85%) aligned 0 times 14749796 (82.91%) aligned exactly 1 time 2533871 (14.24%) aligned >1 times 97.15% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 8810408 / 17283667 = 0.5098 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, 07 May 2018 11:05:51: # Command line: callpeak -t SRX3011237.bam -f BAM -g dm -n SRX3011237.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011237.05 # format = BAM # ChIP-seq file = ['SRX3011237.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 @ Mon, 07 May 2018 11:05:51: #1 read tag files... INFO @ Mon, 07 May 2018 11:05:51: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:05:51: # Command line: callpeak -t SRX3011237.bam -f BAM -g dm -n SRX3011237.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011237.10 # format = BAM # ChIP-seq file = ['SRX3011237.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 @ Mon, 07 May 2018 11:05:51: #1 read tag files... INFO @ Mon, 07 May 2018 11:05:51: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:05:51: # Command line: callpeak -t SRX3011237.bam -f BAM -g dm -n SRX3011237.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011237.20 # format = BAM # ChIP-seq file = ['SRX3011237.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 @ Mon, 07 May 2018 11:05:51: #1 read tag files... INFO @ Mon, 07 May 2018 11:05:51: #1 read treatment tags... INFO @ Mon, 07 May 2018 11:05:59: 1000000 INFO @ Mon, 07 May 2018 11:05:59: 1000000 INFO @ Mon, 07 May 2018 11:05:59: 1000000 INFO @ Mon, 07 May 2018 11:06:06: 2000000 INFO @ Mon, 07 May 2018 11:06:07: 2000000 INFO @ Mon, 07 May 2018 11:06:07: 2000000 INFO @ Mon, 07 May 2018 11:06:14: 3000000 INFO @ Mon, 07 May 2018 11:06:14: 3000000 INFO @ Mon, 07 May 2018 11:06:15: 3000000 INFO @ Mon, 07 May 2018 11:06:21: 4000000 INFO @ Mon, 07 May 2018 11:06:22: 4000000 INFO @ Mon, 07 May 2018 11:06:22: 4000000 INFO @ Mon, 07 May 2018 11:06:28: 5000000 INFO @ Mon, 07 May 2018 11:06:30: 5000000 INFO @ Mon, 07 May 2018 11:06:30: 5000000 INFO @ Mon, 07 May 2018 11:06:36: 6000000 INFO @ Mon, 07 May 2018 11:06:38: 6000000 INFO @ Mon, 07 May 2018 11:06:38: 6000000 INFO @ Mon, 07 May 2018 11:06:43: 7000000 INFO @ Mon, 07 May 2018 11:06:46: 7000000 INFO @ Mon, 07 May 2018 11:06:47: 7000000 INFO @ Mon, 07 May 2018 11:06:51: 8000000 INFO @ Mon, 07 May 2018 11:06:54: 8000000 INFO @ Mon, 07 May 2018 11:06:54: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:06:54: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:06:54: #1 total tags in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:54: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:06:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:06:54: #1 tags after filtering in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:06:54: #1 finished! INFO @ Mon, 07 May 2018 11:06:54: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:06:55: 8000000 INFO @ Mon, 07 May 2018 11:06:56: #2 number of paired peaks: 5228 INFO @ Mon, 07 May 2018 11:06:56: start model_add_line... INFO @ Mon, 07 May 2018 11:06:56: start X-correlation... INFO @ Mon, 07 May 2018 11:06:56: end of X-cor INFO @ Mon, 07 May 2018 11:06:56: #2 finished! INFO @ Mon, 07 May 2018 11:06:56: #2 predicted fragment length is 194 bps INFO @ Mon, 07 May 2018 11:06:56: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 07 May 2018 11:06:56: #2.2 Generate R script for model : SRX3011237.20_model.r INFO @ Mon, 07 May 2018 11:06:56: #3 Call peaks... INFO @ Mon, 07 May 2018 11:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:06:58: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:06:58: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:06:58: #1 total tags in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:58: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:06:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:06:58: #1 tags after filtering in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:06:58: #1 finished! INFO @ Mon, 07 May 2018 11:06:58: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:06:59: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 11:06:59: #1 tag size = 80 INFO @ Mon, 07 May 2018 11:06:59: #1 total tags in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:59: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 11:06:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 11:06:59: #1 tags after filtering in treatment: 8473259 INFO @ Mon, 07 May 2018 11:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 11:06:59: #1 finished! INFO @ Mon, 07 May 2018 11:06:59: #2 Build Peak Model... INFO @ Mon, 07 May 2018 11:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 11:06:59: #2 number of paired peaks: 5228 INFO @ Mon, 07 May 2018 11:06:59: start model_add_line... INFO @ Mon, 07 May 2018 11:06:59: start X-correlation... INFO @ Mon, 07 May 2018 11:06:59: end of X-cor INFO @ Mon, 07 May 2018 11:06:59: #2 finished! INFO @ Mon, 07 May 2018 11:06:59: #2 predicted fragment length is 194 bps INFO @ Mon, 07 May 2018 11:06:59: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 07 May 2018 11:06:59: #2.2 Generate R script for model : SRX3011237.10_model.r INFO @ Mon, 07 May 2018 11:06:59: #3 Call peaks... INFO @ Mon, 07 May 2018 11:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:07:00: #2 number of paired peaks: 5228 INFO @ Mon, 07 May 2018 11:07:00: start model_add_line... INFO @ Mon, 07 May 2018 11:07:00: start X-correlation... INFO @ Mon, 07 May 2018 11:07:00: end of X-cor INFO @ Mon, 07 May 2018 11:07:00: #2 finished! INFO @ Mon, 07 May 2018 11:07:00: #2 predicted fragment length is 194 bps INFO @ Mon, 07 May 2018 11:07:00: #2 alternative fragment length(s) may be 194 bps INFO @ Mon, 07 May 2018 11:07:00: #2.2 Generate R script for model : SRX3011237.05_model.r INFO @ Mon, 07 May 2018 11:07:00: #3 Call peaks... INFO @ Mon, 07 May 2018 11:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 11:07:23: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:07:26: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:07:27: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 11:07:37: #4 Write output xls file... SRX3011237.20_peaks.xls INFO @ Mon, 07 May 2018 11:07:37: #4 Write peak in narrowPeak format file... SRX3011237.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:07:37: #4 Write summits bed file... SRX3011237.20_summits.bed INFO @ Mon, 07 May 2018 11:07:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5293 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 11:07:40: #4 Write output xls file... SRX3011237.10_peaks.xls INFO @ Mon, 07 May 2018 11:07:40: #4 Write peak in narrowPeak format file... SRX3011237.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:07:40: #4 Write summits bed file... SRX3011237.10_summits.bed INFO @ Mon, 07 May 2018 11:07:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7190 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 11:07:41: #4 Write output xls file... SRX3011237.05_peaks.xls INFO @ Mon, 07 May 2018 11:07:41: #4 Write peak in narrowPeak format file... SRX3011237.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 11:07:41: #4 Write summits bed file... SRX3011237.05_summits.bed INFO @ Mon, 07 May 2018 11:07:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9110 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。