Job ID = 1301879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,974,614 reads read : 23,974,614 reads written : 23,974,614 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: 00:12:43 23974614 reads; of these: 23974614 (100.00%) were unpaired; of these: 6163921 (25.71%) aligned 0 times 9194071 (38.35%) aligned exactly 1 time 8616622 (35.94%) aligned >1 times 74.29% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 12416421 / 17810693 = 0.6971 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 20:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.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 20:26:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:26:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.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 20:26:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:26:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.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 20:26:53: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:26:53: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:27:02: 1000000 INFO @ Mon, 03 Jun 2019 20:27:03: 1000000 INFO @ Mon, 03 Jun 2019 20:27:03: 1000000 INFO @ Mon, 03 Jun 2019 20:27:10: 2000000 INFO @ Mon, 03 Jun 2019 20:27:12: 2000000 INFO @ Mon, 03 Jun 2019 20:27:13: 2000000 INFO @ Mon, 03 Jun 2019 20:27:18: 3000000 INFO @ Mon, 03 Jun 2019 20:27:21: 3000000 INFO @ Mon, 03 Jun 2019 20:27:23: 3000000 INFO @ Mon, 03 Jun 2019 20:27:26: 4000000 INFO @ Mon, 03 Jun 2019 20:27:30: 4000000 INFO @ Mon, 03 Jun 2019 20:27:32: 4000000 INFO @ Mon, 03 Jun 2019 20:27:34: 5000000 INFO @ Mon, 03 Jun 2019 20:27:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:27:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:27:37: #1 total tags in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:37: #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 20:27:37: #1 tags after filtering in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:27:37: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:38: #2 number of paired peaks: 1589 INFO @ Mon, 03 Jun 2019 20:27:38: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:38: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:38: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:38: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:38: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 20:27:38: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 20:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05_model.r WARNING @ Mon, 03 Jun 2019 20:27:38: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:27:38: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 20:27:38: #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 20:27:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:39: 5000000 INFO @ Mon, 03 Jun 2019 20:27:41: 5000000 INFO @ Mon, 03 Jun 2019 20:27:43: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:27:43: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:27:43: #1 total tags in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:43: #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 20:27:43: #1 tags after filtering in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:27:43: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:44: #2 number of paired peaks: 1589 INFO @ Mon, 03 Jun 2019 20:27:44: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:44: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:44: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:44: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:44: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 20:27:44: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 20:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20_model.r WARNING @ Mon, 03 Jun 2019 20:27:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:27:44: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 20:27:44: #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 20:27:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:27:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:27:45: #1 total tags in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:27:45: #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 20:27:45: #1 tags after filtering in treatment: 5394272 INFO @ Mon, 03 Jun 2019 20:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:27:45: #1 finished! INFO @ Mon, 03 Jun 2019 20:27:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:27:45: #2 number of paired peaks: 1589 INFO @ Mon, 03 Jun 2019 20:27:45: start model_add_line... INFO @ Mon, 03 Jun 2019 20:27:45: start X-correlation... INFO @ Mon, 03 Jun 2019 20:27:45: end of X-cor INFO @ Mon, 03 Jun 2019 20:27:45: #2 finished! INFO @ Mon, 03 Jun 2019 20:27:45: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 20:27:45: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 20:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10_model.r WARNING @ Mon, 03 Jun 2019 20:27:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:27:45: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 20:27:45: #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 20:27:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:27:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:28:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:28:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.05_summits.bed INFO @ Mon, 03 Jun 2019 20:28:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2936 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.20_summits.bed INFO @ Mon, 03 Jun 2019 20:28:08: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1311 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:28:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:28:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:28:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933869/SRX4933869.10_summits.bed INFO @ Mon, 03 Jun 2019 20:28:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1671 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。