Job ID = 10450986 sra ファイルのダウンロード中... Completed: 364928K bytes transferred in 33 seconds (89400K 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 18987942 spots for /home/okishinya/chipatlas/results/dm3/SRX3404043/SRR6303520.sra Written 18987942 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: 00:14:56 18987942 reads; of these: 18987942 (100.00%) were unpaired; of these: 491284 (2.59%) aligned 0 times 13407597 (70.61%) aligned exactly 1 time 5089061 (26.80%) aligned >1 times 97.41% overall alignment rate Time searching: 00:14:56 Overall time: 00:14:56 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] 3692152 / 18496658 = 0.1996 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 @ Wed, 07 Feb 2018 14:43:11: # Command line: callpeak -t SRX3404043.bam -f BAM -g dm -n SRX3404043.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404043.10 # format = BAM # ChIP-seq file = ['SRX3404043.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 @ Wed, 07 Feb 2018 14:43:11: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:43:11: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:43:11: # Command line: callpeak -t SRX3404043.bam -f BAM -g dm -n SRX3404043.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404043.20 # format = BAM # ChIP-seq file = ['SRX3404043.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 @ Wed, 07 Feb 2018 14:43:11: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:43:11: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:43:11: # Command line: callpeak -t SRX3404043.bam -f BAM -g dm -n SRX3404043.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404043.05 # format = BAM # ChIP-seq file = ['SRX3404043.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 @ Wed, 07 Feb 2018 14:43:11: #1 read tag files... INFO @ Wed, 07 Feb 2018 14:43:11: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 14:43:26: 1000000 INFO @ Wed, 07 Feb 2018 14:43:33: 1000000 INFO @ Wed, 07 Feb 2018 14:43:37: 1000000 INFO @ Wed, 07 Feb 2018 14:43:41: 2000000 INFO @ Wed, 07 Feb 2018 14:43:48: 2000000 INFO @ Wed, 07 Feb 2018 14:43:53: 2000000 INFO @ Wed, 07 Feb 2018 14:43:57: 3000000 INFO @ Wed, 07 Feb 2018 14:44:02: 3000000 INFO @ Wed, 07 Feb 2018 14:44:09: 3000000 INFO @ Wed, 07 Feb 2018 14:44:12: 4000000 INFO @ Wed, 07 Feb 2018 14:44:21: 4000000 INFO @ Wed, 07 Feb 2018 14:44:25: 5000000 INFO @ Wed, 07 Feb 2018 14:44:27: 4000000 INFO @ Wed, 07 Feb 2018 14:44:37: 6000000 INFO @ Wed, 07 Feb 2018 14:44:38: 5000000 INFO @ Wed, 07 Feb 2018 14:44:45: 5000000 INFO @ Wed, 07 Feb 2018 14:44:48: 7000000 INFO @ Wed, 07 Feb 2018 14:45:02: 8000000 INFO @ Wed, 07 Feb 2018 14:45:07: 6000000 INFO @ Wed, 07 Feb 2018 14:45:12: 6000000 INFO @ Wed, 07 Feb 2018 14:45:14: 9000000 INFO @ Wed, 07 Feb 2018 14:45:25: 7000000 INFO @ Wed, 07 Feb 2018 14:45:27: 10000000 INFO @ Wed, 07 Feb 2018 14:45:29: 7000000 INFO @ Wed, 07 Feb 2018 14:45:40: 11000000 INFO @ Wed, 07 Feb 2018 14:45:43: 8000000 INFO @ Wed, 07 Feb 2018 14:45:47: 8000000 INFO @ Wed, 07 Feb 2018 14:45:58: 12000000 INFO @ Wed, 07 Feb 2018 14:46:07: 9000000 INFO @ Wed, 07 Feb 2018 14:46:10: 9000000 INFO @ Wed, 07 Feb 2018 14:46:19: 13000000 INFO @ Wed, 07 Feb 2018 14:46:31: 10000000 INFO @ Wed, 07 Feb 2018 14:46:32: 10000000 INFO @ Wed, 07 Feb 2018 14:46:40: 14000000 INFO @ Wed, 07 Feb 2018 14:46:55: 11000000 INFO @ Wed, 07 Feb 2018 14:46:56: 11000000 INFO @ Wed, 07 Feb 2018 14:46:56: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:46:56: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:46:56: #1 total tags in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:46:56: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:46:56: #1 tags after filtering in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:46:56: #1 finished! INFO @ Wed, 07 Feb 2018 14:46:56: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:46:58: #2 number of paired peaks: 1797 INFO @ Wed, 07 Feb 2018 14:46:58: start model_add_line... INFO @ Wed, 07 Feb 2018 14:46:58: start X-correlation... INFO @ Wed, 07 Feb 2018 14:46:58: end of X-cor INFO @ Wed, 07 Feb 2018 14:46:58: #2 finished! INFO @ Wed, 07 Feb 2018 14:46:58: #2 predicted fragment length is 159 bps INFO @ Wed, 07 Feb 2018 14:46:58: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 07 Feb 2018 14:46:58: #2.2 Generate R script for model : SRX3404043.10_model.r INFO @ Wed, 07 Feb 2018 14:46:58: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:47:19: 12000000 INFO @ Wed, 07 Feb 2018 14:47:19: 12000000 INFO @ Wed, 07 Feb 2018 14:47:43: 13000000 INFO @ Wed, 07 Feb 2018 14:47:44: 13000000 INFO @ Wed, 07 Feb 2018 14:47:54: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:48:05: 14000000 INFO @ Wed, 07 Feb 2018 14:48:08: 14000000 INFO @ Wed, 07 Feb 2018 14:48:24: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:48:24: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:48:24: #1 total tags in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:48:24: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:48:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:48:24: #4 Write output xls file... SRX3404043.10_peaks.xls INFO @ Wed, 07 Feb 2018 14:48:24: #4 Write peak in narrowPeak format file... SRX3404043.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:48:24: #4 Write summits bed file... SRX3404043.10_summits.bed INFO @ Wed, 07 Feb 2018 14:48:24: Done! INFO @ Wed, 07 Feb 2018 14:48:24: #1 tags after filtering in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:48:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:48:24: #1 finished! INFO @ Wed, 07 Feb 2018 14:48:24: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:48:24: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4420 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:48:26: #2 number of paired peaks: 1797 INFO @ Wed, 07 Feb 2018 14:48:26: start model_add_line... INFO @ Wed, 07 Feb 2018 14:48:26: start X-correlation... INFO @ Wed, 07 Feb 2018 14:48:26: end of X-cor INFO @ Wed, 07 Feb 2018 14:48:26: #2 finished! INFO @ Wed, 07 Feb 2018 14:48:26: #2 predicted fragment length is 159 bps INFO @ Wed, 07 Feb 2018 14:48:26: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 07 Feb 2018 14:48:26: #2.2 Generate R script for model : SRX3404043.20_model.r INFO @ Wed, 07 Feb 2018 14:48:26: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:48:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:48:27: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 14:48:27: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 14:48:27: #1 total tags in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:48:27: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 14:48:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 14:48:27: #1 tags after filtering in treatment: 14804506 INFO @ Wed, 07 Feb 2018 14:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 14:48:27: #1 finished! INFO @ Wed, 07 Feb 2018 14:48:27: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 14:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 14:48:29: #2 number of paired peaks: 1797 INFO @ Wed, 07 Feb 2018 14:48:29: start model_add_line... INFO @ Wed, 07 Feb 2018 14:48:30: start X-correlation... INFO @ Wed, 07 Feb 2018 14:48:30: end of X-cor INFO @ Wed, 07 Feb 2018 14:48:30: #2 finished! INFO @ Wed, 07 Feb 2018 14:48:30: #2 predicted fragment length is 159 bps INFO @ Wed, 07 Feb 2018 14:48:30: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 07 Feb 2018 14:48:30: #2.2 Generate R script for model : SRX3404043.05_model.r INFO @ Wed, 07 Feb 2018 14:48:30: #3 Call peaks... INFO @ Wed, 07 Feb 2018 14:48:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 14:49:19: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:49:30: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 14:49:46: #4 Write output xls file... SRX3404043.20_peaks.xls INFO @ Wed, 07 Feb 2018 14:49:46: #4 Write peak in narrowPeak format file... SRX3404043.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:49:46: #4 Write summits bed file... SRX3404043.20_summits.bed INFO @ Wed, 07 Feb 2018 14:49:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3352 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 14:50:02: #4 Write output xls file... SRX3404043.05_peaks.xls INFO @ Wed, 07 Feb 2018 14:50:02: #4 Write peak in narrowPeak format file... SRX3404043.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 14:50:02: #4 Write summits bed file... SRX3404043.05_summits.bed INFO @ Wed, 07 Feb 2018 14:50:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5618 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。