Job ID = 11158476 sra ファイルのダウンロード中... Completed: 3079322K bytes transferred in 40 seconds (627469K 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: PAIRED fastq に変換中... Read 46994018 spots for /home/okishinya/chipatlas/results/dm3/SRX4279653/SRR7408149.sra Written 46994018 spots for /home/okishinya/chipatlas/results/dm3/SRX4279653/SRR7408149.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: 13:41:16 46994018 reads; of these: 46994018 (100.00%) were paired; of these: 34866018 (74.19%) aligned concordantly 0 times 8770926 (18.66%) aligned concordantly exactly 1 time 3357074 (7.14%) aligned concordantly >1 times ---- 34866018 pairs aligned concordantly 0 times; of these: 37467 (0.11%) aligned discordantly 1 time ---- 34828551 pairs aligned 0 times concordantly or discordantly; of these: 69657102 mates make up the pairs; of these: 57956555 (83.20%) aligned 0 times 673670 (0.97%) aligned exactly 1 time 11026877 (15.83%) aligned >1 times 38.34% overall alignment rate Time searching: 13:41:16 Overall time: 13:41:16 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 9135833 / 12143297 = 0.7523 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 @ Tue, 04 Sep 2018 23:32:57: # Command line: callpeak -t SRX4279653.bam -f BAM -g dm -n SRX4279653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279653.05 # format = BAM # ChIP-seq file = ['SRX4279653.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 @ Tue, 04 Sep 2018 23:32:57: # Command line: callpeak -t SRX4279653.bam -f BAM -g dm -n SRX4279653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279653.10 # format = BAM # ChIP-seq file = ['SRX4279653.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 @ Tue, 04 Sep 2018 23:32:57: # Command line: callpeak -t SRX4279653.bam -f BAM -g dm -n SRX4279653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279653.20 # format = BAM # ChIP-seq file = ['SRX4279653.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 @ Tue, 04 Sep 2018 23:32:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 23:32:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 23:32:57: #1 read tag files... INFO @ Tue, 04 Sep 2018 23:32:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 23:32:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 23:32:57: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 23:33:04: 1000000 INFO @ Tue, 04 Sep 2018 23:33:05: 1000000 INFO @ Tue, 04 Sep 2018 23:33:05: 1000000 INFO @ Tue, 04 Sep 2018 23:33:11: 2000000 INFO @ Tue, 04 Sep 2018 23:33:12: 2000000 INFO @ Tue, 04 Sep 2018 23:33:12: 2000000 INFO @ Tue, 04 Sep 2018 23:33:18: 3000000 INFO @ Tue, 04 Sep 2018 23:33:19: 3000000 INFO @ Tue, 04 Sep 2018 23:33:19: 3000000 INFO @ Tue, 04 Sep 2018 23:33:24: 4000000 INFO @ Tue, 04 Sep 2018 23:33:26: 4000000 INFO @ Tue, 04 Sep 2018 23:33:26: 4000000 INFO @ Tue, 04 Sep 2018 23:33:30: 5000000 INFO @ Tue, 04 Sep 2018 23:33:33: 5000000 INFO @ Tue, 04 Sep 2018 23:33:33: 5000000 INFO @ Tue, 04 Sep 2018 23:33:36: 6000000 INFO @ Tue, 04 Sep 2018 23:33:39: 6000000 INFO @ Tue, 04 Sep 2018 23:33:39: 6000000 INFO @ Tue, 04 Sep 2018 23:33:41: 7000000 INFO @ Tue, 04 Sep 2018 23:33:45: 7000000 INFO @ Tue, 04 Sep 2018 23:33:45: 7000000 INFO @ Tue, 04 Sep 2018 23:33:47: 8000000 INFO @ Tue, 04 Sep 2018 23:33:51: 8000000 INFO @ Tue, 04 Sep 2018 23:33:51: 8000000 INFO @ Tue, 04 Sep 2018 23:33:52: 9000000 INFO @ Tue, 04 Sep 2018 23:33:57: 9000000 INFO @ Tue, 04 Sep 2018 23:33:57: 9000000 INFO @ Tue, 04 Sep 2018 23:33:58: 10000000 INFO @ Tue, 04 Sep 2018 23:34:04: 10000000 INFO @ Tue, 04 Sep 2018 23:34:04: 10000000 INFO @ Tue, 04 Sep 2018 23:34:05: 11000000 INFO @ Tue, 04 Sep 2018 23:34:11: 11000000 INFO @ Tue, 04 Sep 2018 23:34:11: 12000000 INFO @ Tue, 04 Sep 2018 23:34:11: 11000000 INFO @ Tue, 04 Sep 2018 23:34:17: 13000000 INFO @ Tue, 04 Sep 2018 23:34:17: 12000000 INFO @ Tue, 04 Sep 2018 23:34:17: 12000000 INFO @ Tue, 04 Sep 2018 23:34:22: 14000000 INFO @ Tue, 04 Sep 2018 23:34:24: 13000000 INFO @ Tue, 04 Sep 2018 23:34:24: 13000000 INFO @ Tue, 04 Sep 2018 23:34:28: 15000000 INFO @ Tue, 04 Sep 2018 23:34:30: 14000000 INFO @ Tue, 04 Sep 2018 23:34:30: 14000000 INFO @ Tue, 04 Sep 2018 23:34:33: 16000000 INFO @ Tue, 04 Sep 2018 23:34:36: 15000000 INFO @ Tue, 04 Sep 2018 23:34:37: 15000000 INFO @ Tue, 04 Sep 2018 23:34:39: 17000000 INFO @ Tue, 04 Sep 2018 23:34:43: 16000000 INFO @ Tue, 04 Sep 2018 23:34:43: 16000000 INFO @ Tue, 04 Sep 2018 23:34:44: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 23:34:44: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 23:34:44: #1 total tags in treatment: 3012468 INFO @ Tue, 04 Sep 2018 23:34:44: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 23:34:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 23:34:44: #1 tags after filtering in treatment: 2867199 INFO @ Tue, 04 Sep 2018 23:34:44: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 23:34:44: #1 finished! INFO @ Tue, 04 Sep 2018 23:34:44: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 23:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 23:34:45: #2 number of paired peaks: 3369 INFO @ Tue, 04 Sep 2018 23:34:45: start model_add_line... INFO @ Tue, 04 Sep 2018 23:34:45: start X-correlation... INFO @ Tue, 04 Sep 2018 23:34:45: end of X-cor INFO @ Tue, 04 Sep 2018 23:34:45: #2 finished! INFO @ Tue, 04 Sep 2018 23:34:45: #2 predicted fragment length is 176 bps INFO @ Tue, 04 Sep 2018 23:34:45: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 04 Sep 2018 23:34:45: #2.2 Generate R script for model : SRX4279653.05_model.r INFO @ Tue, 04 Sep 2018 23:34:45: #3 Call peaks... INFO @ Tue, 04 Sep 2018 23:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 23:34:49: 17000000 INFO @ Tue, 04 Sep 2018 23:34:50: 17000000 INFO @ Tue, 04 Sep 2018 23:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 23:34:54: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 23:34:54: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 23:34:54: #1 total tags in treatment: 3012468 INFO @ Tue, 04 Sep 2018 23:34:54: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 23:34:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 23:34:54: #1 tags after filtering in treatment: 2867199 INFO @ Tue, 04 Sep 2018 23:34:54: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 23:34:54: #1 finished! INFO @ Tue, 04 Sep 2018 23:34:54: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 23:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 23:34:55: #2 number of paired peaks: 3369 INFO @ Tue, 04 Sep 2018 23:34:55: start model_add_line... INFO @ Tue, 04 Sep 2018 23:34:55: start X-correlation... INFO @ Tue, 04 Sep 2018 23:34:55: end of X-cor INFO @ Tue, 04 Sep 2018 23:34:55: #2 finished! INFO @ Tue, 04 Sep 2018 23:34:55: #2 predicted fragment length is 176 bps INFO @ Tue, 04 Sep 2018 23:34:55: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 04 Sep 2018 23:34:55: #2.2 Generate R script for model : SRX4279653.20_model.r INFO @ Tue, 04 Sep 2018 23:34:55: #3 Call peaks... INFO @ Tue, 04 Sep 2018 23:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 23:34:55: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 23:34:55: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 23:34:55: #1 total tags in treatment: 3012468 INFO @ Tue, 04 Sep 2018 23:34:55: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 23:34:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 23:34:55: #1 tags after filtering in treatment: 2867199 INFO @ Tue, 04 Sep 2018 23:34:55: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 04 Sep 2018 23:34:55: #1 finished! INFO @ Tue, 04 Sep 2018 23:34:55: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 23:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 23:34:56: #2 number of paired peaks: 3369 INFO @ Tue, 04 Sep 2018 23:34:56: start model_add_line... INFO @ Tue, 04 Sep 2018 23:34:56: start X-correlation... INFO @ Tue, 04 Sep 2018 23:34:56: end of X-cor INFO @ Tue, 04 Sep 2018 23:34:56: #2 finished! INFO @ Tue, 04 Sep 2018 23:34:56: #2 predicted fragment length is 176 bps INFO @ Tue, 04 Sep 2018 23:34:56: #2 alternative fragment length(s) may be 176 bps INFO @ Tue, 04 Sep 2018 23:34:56: #2.2 Generate R script for model : SRX4279653.10_model.r INFO @ Tue, 04 Sep 2018 23:34:56: #3 Call peaks... INFO @ Tue, 04 Sep 2018 23:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 23:34:58: #4 Write output xls file... SRX4279653.05_peaks.xls INFO @ Tue, 04 Sep 2018 23:34:58: #4 Write peak in narrowPeak format file... SRX4279653.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 23:34:58: #4 Write summits bed file... SRX4279653.05_summits.bed INFO @ Tue, 04 Sep 2018 23:34:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3821 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 23:35:03: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 23:35:04: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write output xls file... SRX4279653.20_peaks.xls INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write peak in narrowPeak format file... SRX4279653.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write summits bed file... SRX4279653.20_summits.bed INFO @ Tue, 04 Sep 2018 23:35:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write output xls file... SRX4279653.10_peaks.xls INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write peak in narrowPeak format file... SRX4279653.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 23:35:08: #4 Write summits bed file... SRX4279653.10_summits.bed INFO @ Tue, 04 Sep 2018 23:35:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1973 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。