Job ID = 2002190 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,949,541 reads read : 34,949,541 reads written : 34,949,541 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:56 34949541 reads; of these: 34949541 (100.00%) were unpaired; of these: 10129943 (28.98%) aligned 0 times 17740760 (50.76%) aligned exactly 1 time 7078838 (20.25%) aligned >1 times 71.02% overall alignment rate Time searching: 00:23:58 Overall time: 00:23:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9609235 / 24819598 = 0.3872 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 @ Fri, 05 Jul 2019 12:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:09:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:09:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:09:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:09:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 12:09:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:09:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:09:38: 1000000 INFO @ Fri, 05 Jul 2019 12:09:38: 1000000 INFO @ Fri, 05 Jul 2019 12:09:39: 1000000 INFO @ Fri, 05 Jul 2019 12:09:49: 2000000 INFO @ Fri, 05 Jul 2019 12:09:49: 2000000 INFO @ Fri, 05 Jul 2019 12:09:50: 2000000 INFO @ Fri, 05 Jul 2019 12:09:58: 3000000 INFO @ Fri, 05 Jul 2019 12:09:58: 3000000 INFO @ Fri, 05 Jul 2019 12:10:00: 3000000 INFO @ Fri, 05 Jul 2019 12:10:07: 4000000 INFO @ Fri, 05 Jul 2019 12:10:08: 4000000 INFO @ Fri, 05 Jul 2019 12:10:09: 4000000 INFO @ Fri, 05 Jul 2019 12:10:16: 5000000 INFO @ Fri, 05 Jul 2019 12:10:17: 5000000 INFO @ Fri, 05 Jul 2019 12:10:19: 5000000 INFO @ Fri, 05 Jul 2019 12:10:26: 6000000 INFO @ Fri, 05 Jul 2019 12:10:28: 6000000 INFO @ Fri, 05 Jul 2019 12:10:30: 6000000 INFO @ Fri, 05 Jul 2019 12:10:35: 7000000 INFO @ Fri, 05 Jul 2019 12:10:37: 7000000 INFO @ Fri, 05 Jul 2019 12:10:39: 7000000 INFO @ Fri, 05 Jul 2019 12:10:44: 8000000 INFO @ Fri, 05 Jul 2019 12:10:47: 8000000 INFO @ Fri, 05 Jul 2019 12:10:49: 8000000 INFO @ Fri, 05 Jul 2019 12:10:53: 9000000 INFO @ Fri, 05 Jul 2019 12:10:57: 9000000 INFO @ Fri, 05 Jul 2019 12:10:58: 9000000 INFO @ Fri, 05 Jul 2019 12:11:02: 10000000 INFO @ Fri, 05 Jul 2019 12:11:06: 10000000 INFO @ Fri, 05 Jul 2019 12:11:07: 10000000 INFO @ Fri, 05 Jul 2019 12:11:11: 11000000 INFO @ Fri, 05 Jul 2019 12:11:15: 11000000 INFO @ Fri, 05 Jul 2019 12:11:17: 11000000 INFO @ Fri, 05 Jul 2019 12:11:21: 12000000 INFO @ Fri, 05 Jul 2019 12:11:26: 12000000 INFO @ Fri, 05 Jul 2019 12:11:26: 12000000 INFO @ Fri, 05 Jul 2019 12:11:31: 13000000 INFO @ Fri, 05 Jul 2019 12:11:35: 13000000 INFO @ Fri, 05 Jul 2019 12:11:36: 13000000 INFO @ Fri, 05 Jul 2019 12:11:40: 14000000 INFO @ Fri, 05 Jul 2019 12:11:45: 14000000 INFO @ Fri, 05 Jul 2019 12:11:46: 14000000 INFO @ Fri, 05 Jul 2019 12:11:50: 15000000 INFO @ Fri, 05 Jul 2019 12:11:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:11:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:11:52: #1 total tags in treatment: 15210363 INFO @ Fri, 05 Jul 2019 12:11:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:11:53: #1 tags after filtering in treatment: 15210211 INFO @ Fri, 05 Jul 2019 12:11:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:11:53: #1 finished! INFO @ Fri, 05 Jul 2019 12:11:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:11:54: 15000000 INFO @ Fri, 05 Jul 2019 12:11:55: 15000000 INFO @ Fri, 05 Jul 2019 12:11:55: #2 number of paired peaks: 6579 INFO @ Fri, 05 Jul 2019 12:11:55: start model_add_line... INFO @ Fri, 05 Jul 2019 12:11:56: start X-correlation... INFO @ Fri, 05 Jul 2019 12:11:56: end of X-cor INFO @ Fri, 05 Jul 2019 12:11:56: #2 finished! INFO @ Fri, 05 Jul 2019 12:11:56: #2 predicted fragment length is 51 bps INFO @ Fri, 05 Jul 2019 12:11:56: #2 alternative fragment length(s) may be 51,225,393,412 bps INFO @ Fri, 05 Jul 2019 12:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10_model.r WARNING @ Fri, 05 Jul 2019 12:11:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:11:56: #2 You may need to consider one of the other alternative d(s): 51,225,393,412 WARNING @ Fri, 05 Jul 2019 12:11:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:11:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:11:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:11:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:11:56: #1 total tags in treatment: 15210363 INFO @ Fri, 05 Jul 2019 12:11:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:11:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:11:57: #1 tags after filtering in treatment: 15210211 INFO @ Fri, 05 Jul 2019 12:11:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:11:57: #1 finished! INFO @ Fri, 05 Jul 2019 12:11:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:11:58: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:11:58: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:11:58: #1 total tags in treatment: 15210363 INFO @ Fri, 05 Jul 2019 12:11:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:11:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:11:58: #1 tags after filtering in treatment: 15210211 INFO @ Fri, 05 Jul 2019 12:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:11:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:11:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:11:59: #2 number of paired peaks: 6579 INFO @ Fri, 05 Jul 2019 12:11:59: start model_add_line... INFO @ Fri, 05 Jul 2019 12:11:59: start X-correlation... INFO @ Fri, 05 Jul 2019 12:11:59: end of X-cor INFO @ Fri, 05 Jul 2019 12:11:59: #2 finished! INFO @ Fri, 05 Jul 2019 12:11:59: #2 predicted fragment length is 51 bps INFO @ Fri, 05 Jul 2019 12:11:59: #2 alternative fragment length(s) may be 51,225,393,412 bps INFO @ Fri, 05 Jul 2019 12:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05_model.r WARNING @ Fri, 05 Jul 2019 12:11:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:11:59: #2 You may need to consider one of the other alternative d(s): 51,225,393,412 WARNING @ Fri, 05 Jul 2019 12:11:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:11:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:12:01: #2 number of paired peaks: 6579 INFO @ Fri, 05 Jul 2019 12:12:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:12:01: start X-correlation... INFO @ Fri, 05 Jul 2019 12:12:01: end of X-cor INFO @ Fri, 05 Jul 2019 12:12:01: #2 finished! INFO @ Fri, 05 Jul 2019 12:12:01: #2 predicted fragment length is 51 bps INFO @ Fri, 05 Jul 2019 12:12:01: #2 alternative fragment length(s) may be 51,225,393,412 bps INFO @ Fri, 05 Jul 2019 12:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20_model.r WARNING @ Fri, 05 Jul 2019 12:12:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:12:01: #2 You may need to consider one of the other alternative d(s): 51,225,393,412 WARNING @ Fri, 05 Jul 2019 12:12:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:12:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:12:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:12:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.10_summits.bed INFO @ Fri, 05 Jul 2019 12:13:16: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (961 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 12:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.05_summits.bed INFO @ Fri, 05 Jul 2019 12:13:19: Done! CompletedMACS2peakCalling pass1 - making usageList (46 chroms): 3 millis pass2 - checking and writing primary data (1663 records, 4 fields): 14 millis INFO @ Fri, 05 Jul 2019 12:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250259/ERX2250259.20_summits.bed INFO @ Fri, 05 Jul 2019 12:13:21: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。