Job ID = 2590553 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,866,614 reads read : 19,733,228 reads written : 19,733,228 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:23:38 9866614 reads; of these: 9866614 (100.00%) were paired; of these: 1758838 (17.83%) aligned concordantly 0 times 5419490 (54.93%) aligned concordantly exactly 1 time 2688286 (27.25%) aligned concordantly >1 times ---- 1758838 pairs aligned concordantly 0 times; of these: 79274 (4.51%) aligned discordantly 1 time ---- 1679564 pairs aligned 0 times concordantly or discordantly; of these: 3359128 mates make up the pairs; of these: 2915850 (86.80%) aligned 0 times 250882 (7.47%) aligned exactly 1 time 192396 (5.73%) aligned >1 times 85.22% overall alignment rate Time searching: 00:23:38 Overall time: 00:23:38 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_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] 2692877 / 8170728 = 0.3296 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, 12 Aug 2019 22:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.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, 12 Aug 2019 22:53:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:53:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.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, 12 Aug 2019 22:53:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:53:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.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, 12 Aug 2019 22:53:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:53:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:53:23: 1000000 INFO @ Mon, 12 Aug 2019 22:53:24: 1000000 INFO @ Mon, 12 Aug 2019 22:53:26: 1000000 INFO @ Mon, 12 Aug 2019 22:53:29: 2000000 INFO @ Mon, 12 Aug 2019 22:53:30: 2000000 INFO @ Mon, 12 Aug 2019 22:53:33: 2000000 INFO @ Mon, 12 Aug 2019 22:53:36: 3000000 INFO @ Mon, 12 Aug 2019 22:53:37: 3000000 INFO @ Mon, 12 Aug 2019 22:53:41: 3000000 INFO @ Mon, 12 Aug 2019 22:53:43: 4000000 INFO @ Mon, 12 Aug 2019 22:53:44: 4000000 INFO @ Mon, 12 Aug 2019 22:53:48: 4000000 INFO @ Mon, 12 Aug 2019 22:53:50: 5000000 INFO @ Mon, 12 Aug 2019 22:53:51: 5000000 INFO @ Mon, 12 Aug 2019 22:53:56: 5000000 INFO @ Mon, 12 Aug 2019 22:53:57: 6000000 INFO @ Mon, 12 Aug 2019 22:53:58: 6000000 INFO @ Mon, 12 Aug 2019 22:54:04: 6000000 INFO @ Mon, 12 Aug 2019 22:54:04: 7000000 INFO @ Mon, 12 Aug 2019 22:54:05: 7000000 INFO @ Mon, 12 Aug 2019 22:54:11: 8000000 INFO @ Mon, 12 Aug 2019 22:54:11: 7000000 INFO @ Mon, 12 Aug 2019 22:54:12: 8000000 INFO @ Mon, 12 Aug 2019 22:54:17: 9000000 INFO @ Mon, 12 Aug 2019 22:54:18: 9000000 INFO @ Mon, 12 Aug 2019 22:54:19: 8000000 INFO @ Mon, 12 Aug 2019 22:54:24: 10000000 INFO @ Mon, 12 Aug 2019 22:54:25: 10000000 INFO @ Mon, 12 Aug 2019 22:54:27: 9000000 INFO @ Mon, 12 Aug 2019 22:54:31: 11000000 INFO @ Mon, 12 Aug 2019 22:54:32: 11000000 INFO @ Mon, 12 Aug 2019 22:54:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:54:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:54:34: #1 total tags in treatment: 5426603 INFO @ Mon, 12 Aug 2019 22:54:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:54:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:54:34: #1 tags after filtering in treatment: 4977826 INFO @ Mon, 12 Aug 2019 22:54:34: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 12 Aug 2019 22:54:34: #1 finished! INFO @ Mon, 12 Aug 2019 22:54:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:54:34: 10000000 INFO @ Mon, 12 Aug 2019 22:54:35: #2 number of paired peaks: 1850 INFO @ Mon, 12 Aug 2019 22:54:35: start model_add_line... INFO @ Mon, 12 Aug 2019 22:54:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:54:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:54:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:54:35: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:54:35: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05_model.r INFO @ Mon, 12 Aug 2019 22:54:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:54:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:54:35: #1 total tags in treatment: 5426603 INFO @ Mon, 12 Aug 2019 22:54:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:54:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:54:35: #1 tags after filtering in treatment: 4977826 INFO @ Mon, 12 Aug 2019 22:54:35: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 12 Aug 2019 22:54:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:54:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:54:35: #2 number of paired peaks: 1850 INFO @ Mon, 12 Aug 2019 22:54:35: start model_add_line... INFO @ Mon, 12 Aug 2019 22:54:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:54:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:54:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:54:35: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:54:35: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10_model.r INFO @ Mon, 12 Aug 2019 22:54:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:54:41: 11000000 INFO @ Mon, 12 Aug 2019 22:54:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:54:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:54:44: #1 total tags in treatment: 5426603 INFO @ Mon, 12 Aug 2019 22:54:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:54:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:54:44: #1 tags after filtering in treatment: 4977826 INFO @ Mon, 12 Aug 2019 22:54:44: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 12 Aug 2019 22:54:44: #1 finished! INFO @ Mon, 12 Aug 2019 22:54:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:54:45: #2 number of paired peaks: 1850 INFO @ Mon, 12 Aug 2019 22:54:45: start model_add_line... INFO @ Mon, 12 Aug 2019 22:54:45: start X-correlation... INFO @ Mon, 12 Aug 2019 22:54:45: end of X-cor INFO @ Mon, 12 Aug 2019 22:54:45: #2 finished! INFO @ Mon, 12 Aug 2019 22:54:45: #2 predicted fragment length is 130 bps INFO @ Mon, 12 Aug 2019 22:54:45: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 12 Aug 2019 22:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20_model.r INFO @ Mon, 12 Aug 2019 22:54:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:54:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:54:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.05_summits.bed INFO @ Mon, 12 Aug 2019 22:54:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3461 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.10_summits.bed INFO @ Mon, 12 Aug 2019 22:54:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2075 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:55:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501945/SRX4501945.20_summits.bed INFO @ Mon, 12 Aug 2019 22:55:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1201 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。