Job ID = 2590555 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,655,538 reads read : 15,311,076 reads written : 15,311,076 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: 00:19:03 7655538 reads; of these: 7655538 (100.00%) were paired; of these: 850799 (11.11%) aligned concordantly 0 times 4810841 (62.84%) aligned concordantly exactly 1 time 1993898 (26.05%) aligned concordantly >1 times ---- 850799 pairs aligned concordantly 0 times; of these: 32018 (3.76%) aligned discordantly 1 time ---- 818781 pairs aligned 0 times concordantly or discordantly; of these: 1637562 mates make up the pairs; of these: 1373643 (83.88%) aligned 0 times 168008 (10.26%) aligned exactly 1 time 95911 (5.86%) aligned >1 times 91.03% overall alignment rate Time searching: 00:19:03 Overall time: 00:19:03 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] 956417 / 6824469 = 0.1401 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 22:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.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 22:48:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.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 22:48:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.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 22:48:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:48:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:48:54: 1000000 INFO @ Mon, 12 Aug 2019 22:48:54: 1000000 INFO @ Mon, 12 Aug 2019 22:48:56: 1000000 INFO @ Mon, 12 Aug 2019 22:49:02: 2000000 INFO @ Mon, 12 Aug 2019 22:49:04: 2000000 INFO @ Mon, 12 Aug 2019 22:49:05: 2000000 INFO @ Mon, 12 Aug 2019 22:49:10: 3000000 INFO @ Mon, 12 Aug 2019 22:49:13: 3000000 INFO @ Mon, 12 Aug 2019 22:49:15: 3000000 INFO @ Mon, 12 Aug 2019 22:49:18: 4000000 INFO @ Mon, 12 Aug 2019 22:49:23: 4000000 INFO @ Mon, 12 Aug 2019 22:49:24: 4000000 INFO @ Mon, 12 Aug 2019 22:49:26: 5000000 INFO @ Mon, 12 Aug 2019 22:49:32: 5000000 INFO @ Mon, 12 Aug 2019 22:49:33: 5000000 INFO @ Mon, 12 Aug 2019 22:49:34: 6000000 INFO @ Mon, 12 Aug 2019 22:49:41: 7000000 INFO @ Mon, 12 Aug 2019 22:49:42: 6000000 INFO @ Mon, 12 Aug 2019 22:49:43: 6000000 INFO @ Mon, 12 Aug 2019 22:49:49: 8000000 INFO @ Mon, 12 Aug 2019 22:49:52: 7000000 INFO @ Mon, 12 Aug 2019 22:49:52: 7000000 INFO @ Mon, 12 Aug 2019 22:49:57: 9000000 INFO @ Mon, 12 Aug 2019 22:50:02: 8000000 INFO @ Mon, 12 Aug 2019 22:50:02: 8000000 INFO @ Mon, 12 Aug 2019 22:50:05: 10000000 INFO @ Mon, 12 Aug 2019 22:50:12: 9000000 INFO @ Mon, 12 Aug 2019 22:50:12: 9000000 INFO @ Mon, 12 Aug 2019 22:50:13: 11000000 INFO @ Mon, 12 Aug 2019 22:50:21: 12000000 INFO @ Mon, 12 Aug 2019 22:50:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:50:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:50:21: #1 total tags in treatment: 5849531 INFO @ Mon, 12 Aug 2019 22:50:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:50:21: #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 22:50:21: #1 tags after filtering in treatment: 5004905 INFO @ Mon, 12 Aug 2019 22:50:21: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 12 Aug 2019 22:50:21: #1 finished! INFO @ Mon, 12 Aug 2019 22:50:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:50:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:50:21: 10000000 INFO @ Mon, 12 Aug 2019 22:50:22: 10000000 INFO @ Mon, 12 Aug 2019 22:50:22: #2 number of paired peaks: 2696 INFO @ Mon, 12 Aug 2019 22:50:22: start model_add_line... INFO @ Mon, 12 Aug 2019 22:50:22: start X-correlation... INFO @ Mon, 12 Aug 2019 22:50:22: end of X-cor INFO @ Mon, 12 Aug 2019 22:50:22: #2 finished! INFO @ Mon, 12 Aug 2019 22:50:22: #2 predicted fragment length is 151 bps INFO @ Mon, 12 Aug 2019 22:50:22: #2 alternative fragment length(s) may be 151 bps INFO @ Mon, 12 Aug 2019 22:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10_model.r INFO @ Mon, 12 Aug 2019 22:50:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:29: 11000000 INFO @ Mon, 12 Aug 2019 22:50:31: 11000000 INFO @ Mon, 12 Aug 2019 22:50:37: 12000000 INFO @ Mon, 12 Aug 2019 22:50:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:50:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:50:37: #1 total tags in treatment: 5849531 INFO @ Mon, 12 Aug 2019 22:50:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:50:37: #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 22:50:37: #1 tags after filtering in treatment: 5004905 INFO @ Mon, 12 Aug 2019 22:50:37: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 12 Aug 2019 22:50:37: #1 finished! INFO @ Mon, 12 Aug 2019 22:50:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:50:38: #2 number of paired peaks: 2696 INFO @ Mon, 12 Aug 2019 22:50:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:50:38: start X-correlation... INFO @ Mon, 12 Aug 2019 22:50:38: end of X-cor INFO @ Mon, 12 Aug 2019 22:50:38: #2 finished! INFO @ Mon, 12 Aug 2019 22:50:38: #2 predicted fragment length is 151 bps INFO @ Mon, 12 Aug 2019 22:50:38: #2 alternative fragment length(s) may be 151 bps INFO @ Mon, 12 Aug 2019 22:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20_model.r INFO @ Mon, 12 Aug 2019 22:50:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:40: 12000000 INFO @ Mon, 12 Aug 2019 22:50:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:50:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:50:40: #1 total tags in treatment: 5849531 INFO @ Mon, 12 Aug 2019 22:50:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:50:40: #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 22:50:41: #1 tags after filtering in treatment: 5004905 INFO @ Mon, 12 Aug 2019 22:50:41: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 12 Aug 2019 22:50:41: #1 finished! INFO @ Mon, 12 Aug 2019 22:50:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:50:41: #2 number of paired peaks: 2696 INFO @ Mon, 12 Aug 2019 22:50:41: start model_add_line... INFO @ Mon, 12 Aug 2019 22:50:41: start X-correlation... INFO @ Mon, 12 Aug 2019 22:50:41: end of X-cor INFO @ Mon, 12 Aug 2019 22:50:41: #2 finished! INFO @ Mon, 12 Aug 2019 22:50:41: #2 predicted fragment length is 151 bps INFO @ Mon, 12 Aug 2019 22:50:41: #2 alternative fragment length(s) may be 151 bps INFO @ Mon, 12 Aug 2019 22:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05_model.r INFO @ Mon, 12 Aug 2019 22:50:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.10_summits.bed INFO @ Mon, 12 Aug 2019 22:50:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3213 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:50:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.20_summits.bed INFO @ Mon, 12 Aug 2019 22:51:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2015 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501947/SRX4501947.05_summits.bed INFO @ Mon, 12 Aug 2019 22:51:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5229 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。