Job ID = 1293973 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,620,125 reads read : 23,620,125 reads written : 23,620,125 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: 00:07:00 23620125 reads; of these: 23620125 (100.00%) were unpaired; of these: 4012055 (16.99%) aligned 0 times 13962760 (59.11%) aligned exactly 1 time 5645310 (23.90%) aligned >1 times 83.01% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 2086730 / 19608070 = 0.1064 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 03:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.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 03:58:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:58:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.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 03:58:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:58:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.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 03:58:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:58:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:59:01: 1000000 INFO @ Mon, 03 Jun 2019 03:59:01: 1000000 INFO @ Mon, 03 Jun 2019 03:59:01: 1000000 INFO @ Mon, 03 Jun 2019 03:59:08: 2000000 INFO @ Mon, 03 Jun 2019 03:59:08: 2000000 INFO @ Mon, 03 Jun 2019 03:59:09: 2000000 INFO @ Mon, 03 Jun 2019 03:59:15: 3000000 INFO @ Mon, 03 Jun 2019 03:59:15: 3000000 INFO @ Mon, 03 Jun 2019 03:59:17: 3000000 INFO @ Mon, 03 Jun 2019 03:59:22: 4000000 INFO @ Mon, 03 Jun 2019 03:59:23: 4000000 INFO @ Mon, 03 Jun 2019 03:59:24: 4000000 INFO @ Mon, 03 Jun 2019 03:59:29: 5000000 INFO @ Mon, 03 Jun 2019 03:59:30: 5000000 INFO @ Mon, 03 Jun 2019 03:59:32: 5000000 INFO @ Mon, 03 Jun 2019 03:59:35: 6000000 INFO @ Mon, 03 Jun 2019 03:59:37: 6000000 INFO @ Mon, 03 Jun 2019 03:59:39: 6000000 INFO @ Mon, 03 Jun 2019 03:59:42: 7000000 INFO @ Mon, 03 Jun 2019 03:59:44: 7000000 INFO @ Mon, 03 Jun 2019 03:59:47: 7000000 INFO @ Mon, 03 Jun 2019 03:59:49: 8000000 INFO @ Mon, 03 Jun 2019 03:59:51: 8000000 INFO @ Mon, 03 Jun 2019 03:59:54: 8000000 INFO @ Mon, 03 Jun 2019 03:59:56: 9000000 INFO @ Mon, 03 Jun 2019 03:59:57: 9000000 INFO @ Mon, 03 Jun 2019 04:00:02: 9000000 INFO @ Mon, 03 Jun 2019 04:00:02: 10000000 INFO @ Mon, 03 Jun 2019 04:00:04: 10000000 INFO @ Mon, 03 Jun 2019 04:00:09: 10000000 INFO @ Mon, 03 Jun 2019 04:00:09: 11000000 INFO @ Mon, 03 Jun 2019 04:00:11: 11000000 INFO @ Mon, 03 Jun 2019 04:00:16: 12000000 INFO @ Mon, 03 Jun 2019 04:00:16: 11000000 INFO @ Mon, 03 Jun 2019 04:00:18: 12000000 INFO @ Mon, 03 Jun 2019 04:00:22: 13000000 INFO @ Mon, 03 Jun 2019 04:00:23: 12000000 INFO @ Mon, 03 Jun 2019 04:00:25: 13000000 INFO @ Mon, 03 Jun 2019 04:00:29: 14000000 INFO @ Mon, 03 Jun 2019 04:00:31: 13000000 INFO @ Mon, 03 Jun 2019 04:00:32: 14000000 INFO @ Mon, 03 Jun 2019 04:00:36: 15000000 INFO @ Mon, 03 Jun 2019 04:00:38: 14000000 INFO @ Mon, 03 Jun 2019 04:00:39: 15000000 INFO @ Mon, 03 Jun 2019 04:00:43: 16000000 INFO @ Mon, 03 Jun 2019 04:00:45: 16000000 INFO @ Mon, 03 Jun 2019 04:00:46: 15000000 INFO @ Mon, 03 Jun 2019 04:00:50: 17000000 INFO @ Mon, 03 Jun 2019 04:00:52: 17000000 INFO @ Mon, 03 Jun 2019 04:00:53: 16000000 INFO @ Mon, 03 Jun 2019 04:00:54: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 04:00:54: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 04:00:54: #1 total tags in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:00:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:00:54: #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 04:00:54: #1 tags after filtering in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:00:54: #1 finished! INFO @ Mon, 03 Jun 2019 04:00:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:00:56: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 04:00:56: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 04:00:56: #1 total tags in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:00:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:00:56: #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 04:00:56: #2 number of paired peaks: 519 WARNING @ Mon, 03 Jun 2019 04:00:56: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Mon, 03 Jun 2019 04:00:56: start model_add_line... INFO @ Mon, 03 Jun 2019 04:00:56: start X-correlation... INFO @ Mon, 03 Jun 2019 04:00:56: end of X-cor INFO @ Mon, 03 Jun 2019 04:00:56: #2 finished! INFO @ Mon, 03 Jun 2019 04:00:56: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 04:00:56: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 04:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10_model.r WARNING @ Mon, 03 Jun 2019 04:00:56: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:00:56: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 04:00:56: #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 04:00:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:00:56: #1 tags after filtering in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:00:56: #1 finished! INFO @ Mon, 03 Jun 2019 04:00:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:00:58: #2 number of paired peaks: 519 WARNING @ Mon, 03 Jun 2019 04:00:58: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Mon, 03 Jun 2019 04:00:58: start model_add_line... INFO @ Mon, 03 Jun 2019 04:00:58: start X-correlation... INFO @ Mon, 03 Jun 2019 04:00:58: end of X-cor INFO @ Mon, 03 Jun 2019 04:00:58: #2 finished! INFO @ Mon, 03 Jun 2019 04:00:58: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 04:00:58: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 04:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05_model.r WARNING @ Mon, 03 Jun 2019 04:00:58: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:00:58: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 04:00:58: #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 04:00:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:01:01: 17000000 INFO @ Mon, 03 Jun 2019 04:01:05: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 04:01:05: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 04:01:05: #1 total tags in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:01:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:01:05: #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 04:01:05: #1 tags after filtering in treatment: 17521340 INFO @ Mon, 03 Jun 2019 04:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:01:05: #1 finished! INFO @ Mon, 03 Jun 2019 04:01:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:01:07: #2 number of paired peaks: 519 WARNING @ Mon, 03 Jun 2019 04:01:07: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Mon, 03 Jun 2019 04:01:07: start model_add_line... INFO @ Mon, 03 Jun 2019 04:01:07: start X-correlation... INFO @ Mon, 03 Jun 2019 04:01:07: end of X-cor INFO @ Mon, 03 Jun 2019 04:01:07: #2 finished! INFO @ Mon, 03 Jun 2019 04:01:07: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 04:01:07: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 04:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20_model.r WARNING @ Mon, 03 Jun 2019 04:01:07: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:01:07: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 04:01:07: #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 04:01:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:01:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:01:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:01:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.10_summits.bed INFO @ Mon, 03 Jun 2019 04:02:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2408 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.05_summits.bed INFO @ Mon, 03 Jun 2019 04:02:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4921 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152113/SRX152113.20_summits.bed INFO @ Mon, 03 Jun 2019 04:02:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (915 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。