Job ID = 1293967 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,375,444 reads read : 26,375,444 reads written : 26,375,444 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:20:46 26375444 reads; of these: 26375444 (100.00%) were unpaired; of these: 2879317 (10.92%) aligned 0 times 12338541 (46.78%) aligned exactly 1 time 11157586 (42.30%) aligned >1 times 89.08% overall alignment rate Time searching: 00:20:46 Overall time: 00:20:46 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 12 files... [bam_rmdupse_core] 10893508 / 23496127 = 0.4636 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, 03 Jun 2019 04:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.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, 03 Jun 2019 04:04:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.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, 03 Jun 2019 04:04:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.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, 03 Jun 2019 04:04:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:11: 1000000 INFO @ Mon, 03 Jun 2019 04:04:14: 1000000 INFO @ Mon, 03 Jun 2019 04:04:14: 1000000 INFO @ Mon, 03 Jun 2019 04:04:20: 2000000 INFO @ Mon, 03 Jun 2019 04:04:24: 2000000 INFO @ Mon, 03 Jun 2019 04:04:24: 2000000 INFO @ Mon, 03 Jun 2019 04:04:28: 3000000 INFO @ Mon, 03 Jun 2019 04:04:35: 3000000 INFO @ Mon, 03 Jun 2019 04:04:35: 3000000 INFO @ Mon, 03 Jun 2019 04:04:37: 4000000 INFO @ Mon, 03 Jun 2019 04:04:46: 5000000 INFO @ Mon, 03 Jun 2019 04:04:46: 4000000 INFO @ Mon, 03 Jun 2019 04:04:46: 4000000 INFO @ Mon, 03 Jun 2019 04:04:54: 6000000 INFO @ Mon, 03 Jun 2019 04:04:57: 5000000 INFO @ Mon, 03 Jun 2019 04:04:57: 5000000 INFO @ Mon, 03 Jun 2019 04:05:03: 7000000 INFO @ Mon, 03 Jun 2019 04:05:08: 6000000 INFO @ Mon, 03 Jun 2019 04:05:08: 6000000 INFO @ Mon, 03 Jun 2019 04:05:12: 8000000 INFO @ Mon, 03 Jun 2019 04:05:18: 7000000 INFO @ Mon, 03 Jun 2019 04:05:18: 7000000 INFO @ Mon, 03 Jun 2019 04:05:21: 9000000 INFO @ Mon, 03 Jun 2019 04:05:29: 8000000 INFO @ Mon, 03 Jun 2019 04:05:29: 8000000 INFO @ Mon, 03 Jun 2019 04:05:29: 10000000 INFO @ Mon, 03 Jun 2019 04:05:38: 11000000 INFO @ Mon, 03 Jun 2019 04:05:40: 9000000 INFO @ Mon, 03 Jun 2019 04:05:40: 9000000 INFO @ Mon, 03 Jun 2019 04:05:47: 12000000 INFO @ Mon, 03 Jun 2019 04:05:51: 10000000 INFO @ Mon, 03 Jun 2019 04:05:51: 10000000 INFO @ Mon, 03 Jun 2019 04:05:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:05:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:05:52: #1 total tags in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:05:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:05:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:05:53: #1 tags after filtering in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:05:53: #1 finished! INFO @ Mon, 03 Jun 2019 04:05:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:05:54: #2 number of paired peaks: 1338 INFO @ Mon, 03 Jun 2019 04:05:54: start model_add_line... INFO @ Mon, 03 Jun 2019 04:05:54: start X-correlation... INFO @ Mon, 03 Jun 2019 04:05:54: end of X-cor INFO @ Mon, 03 Jun 2019 04:05:54: #2 finished! INFO @ Mon, 03 Jun 2019 04:05:54: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 04:05:54: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 04:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20_model.r WARNING @ Mon, 03 Jun 2019 04:05:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:05:54: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 04:05:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:05:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:01: 11000000 INFO @ Mon, 03 Jun 2019 04:06:01: 11000000 INFO @ Mon, 03 Jun 2019 04:06:11: 12000000 INFO @ Mon, 03 Jun 2019 04:06:11: 12000000 INFO @ Mon, 03 Jun 2019 04:06:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:06:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:06:16: #1 total tags in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:06:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:06:16: #1 tags after filtering in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:06:16: #1 finished! INFO @ Mon, 03 Jun 2019 04:06:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:06:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:06:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:06:17: #1 total tags in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:06:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:06:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:06:17: #1 tags after filtering in treatment: 12602619 INFO @ Mon, 03 Jun 2019 04:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:06:17: #1 finished! INFO @ Mon, 03 Jun 2019 04:06:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:06:18: #2 number of paired peaks: 1338 INFO @ Mon, 03 Jun 2019 04:06:18: start model_add_line... INFO @ Mon, 03 Jun 2019 04:06:18: start X-correlation... INFO @ Mon, 03 Jun 2019 04:06:18: end of X-cor INFO @ Mon, 03 Jun 2019 04:06:18: #2 finished! INFO @ Mon, 03 Jun 2019 04:06:18: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 04:06:18: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 04:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10_model.r WARNING @ Mon, 03 Jun 2019 04:06:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:06:18: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 04:06:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:06:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:18: #2 number of paired peaks: 1338 INFO @ Mon, 03 Jun 2019 04:06:18: start model_add_line... INFO @ Mon, 03 Jun 2019 04:06:18: start X-correlation... INFO @ Mon, 03 Jun 2019 04:06:18: end of X-cor INFO @ Mon, 03 Jun 2019 04:06:18: #2 finished! INFO @ Mon, 03 Jun 2019 04:06:18: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 04:06:18: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 04:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05_model.r WARNING @ Mon, 03 Jun 2019 04:06:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:06:18: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 04:06:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:06:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:06:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.20_summits.bed INFO @ Mon, 03 Jun 2019 04:06:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:06:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.10_summits.bed INFO @ Mon, 03 Jun 2019 04:07:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3816 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152099/SRX152099.05_summits.bed INFO @ Mon, 03 Jun 2019 04:07:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7341 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。