Job ID = 11293695 sra ファイルのダウンロード中... Completed: 451345K bytes transferred in 17 seconds (206544K 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 13485141 spots for /home/okishinya/chipatlas/results/dm3/SRX4375856/SRR7506510.sra Written 13485141 spots for /home/okishinya/chipatlas/results/dm3/SRX4375856/SRR7506510.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: 00:03:41 13485141 reads; of these: 13485141 (100.00%) were unpaired; of these: 2066582 (15.32%) aligned 0 times 9426064 (69.90%) aligned exactly 1 time 1992495 (14.78%) aligned >1 times 84.68% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 3839302 / 11418559 = 0.3362 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 @ Sun, 04 Nov 2018 17:55:08: # Command line: callpeak -t SRX4375856.bam -f BAM -g dm -n SRX4375856.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375856.05 # format = BAM # ChIP-seq file = ['SRX4375856.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 @ Sun, 04 Nov 2018 17:55:08: # Command line: callpeak -t SRX4375856.bam -f BAM -g dm -n SRX4375856.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375856.20 # format = BAM # ChIP-seq file = ['SRX4375856.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 @ Sun, 04 Nov 2018 17:55:08: # Command line: callpeak -t SRX4375856.bam -f BAM -g dm -n SRX4375856.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375856.10 # format = BAM # ChIP-seq file = ['SRX4375856.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 @ Sun, 04 Nov 2018 17:55:08: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:08: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:08: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:08: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:08: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:08: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:15: 1000000 INFO @ Sun, 04 Nov 2018 17:55:15: 1000000 INFO @ Sun, 04 Nov 2018 17:55:15: 1000000 INFO @ Sun, 04 Nov 2018 17:55:22: 2000000 INFO @ Sun, 04 Nov 2018 17:55:22: 2000000 INFO @ Sun, 04 Nov 2018 17:55:23: 2000000 INFO @ Sun, 04 Nov 2018 17:55:29: 3000000 INFO @ Sun, 04 Nov 2018 17:55:30: 3000000 INFO @ Sun, 04 Nov 2018 17:55:30: 3000000 INFO @ Sun, 04 Nov 2018 17:55:36: 4000000 INFO @ Sun, 04 Nov 2018 17:55:38: 4000000 INFO @ Sun, 04 Nov 2018 17:55:38: 4000000 INFO @ Sun, 04 Nov 2018 17:55:43: 5000000 INFO @ Sun, 04 Nov 2018 17:55:46: 5000000 INFO @ Sun, 04 Nov 2018 17:55:47: 5000000 INFO @ Sun, 04 Nov 2018 17:55:50: 6000000 INFO @ Sun, 04 Nov 2018 17:55:54: 6000000 INFO @ Sun, 04 Nov 2018 17:55:56: 6000000 INFO @ Sun, 04 Nov 2018 17:55:58: 7000000 INFO @ Sun, 04 Nov 2018 17:56:02: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:02: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:02: #1 total tags in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:02: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:02: #1 tags after filtering in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:02: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:02: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:03: 7000000 INFO @ Sun, 04 Nov 2018 17:56:03: #2 number of paired peaks: 8314 INFO @ Sun, 04 Nov 2018 17:56:03: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:03: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:04: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:04: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:04: #2 predicted fragment length is 197 bps INFO @ Sun, 04 Nov 2018 17:56:04: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 04 Nov 2018 17:56:04: #2.2 Generate R script for model : SRX4375856.10_model.r INFO @ Sun, 04 Nov 2018 17:56:04: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:05: 7000000 INFO @ Sun, 04 Nov 2018 17:56:08: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:08: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:08: #1 total tags in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:08: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:08: #1 tags after filtering in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:08: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:08: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:09: #2 number of paired peaks: 8314 INFO @ Sun, 04 Nov 2018 17:56:09: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:09: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:09: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:09: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:09: #2 predicted fragment length is 197 bps INFO @ Sun, 04 Nov 2018 17:56:09: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 04 Nov 2018 17:56:09: #2.2 Generate R script for model : SRX4375856.05_model.r INFO @ Sun, 04 Nov 2018 17:56:09: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:10: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:56:10: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:56:10: #1 total tags in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:10: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:10: #1 tags after filtering in treatment: 7579257 INFO @ Sun, 04 Nov 2018 17:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:10: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:10: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:11: #2 number of paired peaks: 8314 INFO @ Sun, 04 Nov 2018 17:56:11: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:12: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:12: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:12: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:12: #2 predicted fragment length is 197 bps INFO @ Sun, 04 Nov 2018 17:56:12: #2 alternative fragment length(s) may be 197 bps INFO @ Sun, 04 Nov 2018 17:56:12: #2.2 Generate R script for model : SRX4375856.20_model.r INFO @ Sun, 04 Nov 2018 17:56:12: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:32: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:43: #4 Write output xls file... SRX4375856.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:43: #4 Write peak in narrowPeak format file... SRX4375856.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:44: #4 Write summits bed file... SRX4375856.10_summits.bed INFO @ Sun, 04 Nov 2018 17:56:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7639 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write output xls file... SRX4375856.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write peak in narrowPeak format file... SRX4375856.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write summits bed file... SRX4375856.05_summits.bed INFO @ Sun, 04 Nov 2018 17:56:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9382 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:52: #4 Write output xls file... SRX4375856.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:52: #4 Write peak in narrowPeak format file... SRX4375856.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:52: #4 Write summits bed file... SRX4375856.20_summits.bed INFO @ Sun, 04 Nov 2018 17:56:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5748 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。