Job ID = 2002187 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,304,205 reads read : 32,304,205 reads written : 32,304,205 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:58 32304205 reads; of these: 32304205 (100.00%) were unpaired; of these: 6589737 (20.40%) aligned 0 times 18439462 (57.08%) aligned exactly 1 time 7275006 (22.52%) aligned >1 times 79.60% overall alignment rate Time searching: 00:23:01 Overall time: 00:23:01 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] 13612772 / 25714468 = 0.5294 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 11:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.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 11:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.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 11:53:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.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 11:53:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:53:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:53:58: 1000000 INFO @ Fri, 05 Jul 2019 11:54:00: 1000000 INFO @ Fri, 05 Jul 2019 11:54:01: 1000000 INFO @ Fri, 05 Jul 2019 11:54:06: 2000000 INFO @ Fri, 05 Jul 2019 11:54:08: 2000000 INFO @ Fri, 05 Jul 2019 11:54:11: 2000000 INFO @ Fri, 05 Jul 2019 11:54:14: 3000000 INFO @ Fri, 05 Jul 2019 11:54:17: 3000000 INFO @ Fri, 05 Jul 2019 11:54:20: 3000000 INFO @ Fri, 05 Jul 2019 11:54:22: 4000000 INFO @ Fri, 05 Jul 2019 11:54:25: 4000000 INFO @ Fri, 05 Jul 2019 11:54:30: 4000000 INFO @ Fri, 05 Jul 2019 11:54:30: 5000000 INFO @ Fri, 05 Jul 2019 11:54:33: 5000000 INFO @ Fri, 05 Jul 2019 11:54:38: 6000000 INFO @ Fri, 05 Jul 2019 11:54:39: 5000000 INFO @ Fri, 05 Jul 2019 11:54:41: 6000000 INFO @ Fri, 05 Jul 2019 11:54:46: 7000000 INFO @ Fri, 05 Jul 2019 11:54:48: 6000000 INFO @ Fri, 05 Jul 2019 11:54:49: 7000000 INFO @ Fri, 05 Jul 2019 11:54:54: 8000000 INFO @ Fri, 05 Jul 2019 11:54:57: 8000000 INFO @ Fri, 05 Jul 2019 11:54:58: 7000000 INFO @ Fri, 05 Jul 2019 11:55:02: 9000000 INFO @ Fri, 05 Jul 2019 11:55:06: 9000000 INFO @ Fri, 05 Jul 2019 11:55:08: 8000000 INFO @ Fri, 05 Jul 2019 11:55:10: 10000000 INFO @ Fri, 05 Jul 2019 11:55:14: 10000000 INFO @ Fri, 05 Jul 2019 11:55:17: 11000000 INFO @ Fri, 05 Jul 2019 11:55:18: 9000000 INFO @ Fri, 05 Jul 2019 11:55:22: 11000000 INFO @ Fri, 05 Jul 2019 11:55:25: 12000000 INFO @ Fri, 05 Jul 2019 11:55:26: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:55:26: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:55:26: #1 total tags in treatment: 12101696 INFO @ Fri, 05 Jul 2019 11:55:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:55:26: #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 11:55:27: #1 tags after filtering in treatment: 12101540 INFO @ Fri, 05 Jul 2019 11:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:55:27: #1 finished! INFO @ Fri, 05 Jul 2019 11:55:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:55:27: 10000000 INFO @ Fri, 05 Jul 2019 11:55:29: #2 number of paired peaks: 18357 INFO @ Fri, 05 Jul 2019 11:55:29: start model_add_line... INFO @ Fri, 05 Jul 2019 11:55:29: start X-correlation... INFO @ Fri, 05 Jul 2019 11:55:29: end of X-cor INFO @ Fri, 05 Jul 2019 11:55:29: #2 finished! INFO @ Fri, 05 Jul 2019 11:55:29: #2 predicted fragment length is 54 bps INFO @ Fri, 05 Jul 2019 11:55:29: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 05 Jul 2019 11:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10_model.r WARNING @ Fri, 05 Jul 2019 11:55:29: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:55:29: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 05 Jul 2019 11:55:29: #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 11:55:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:55:31: 12000000 INFO @ Fri, 05 Jul 2019 11:55:32: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:55:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:55:32: #1 total tags in treatment: 12101696 INFO @ Fri, 05 Jul 2019 11:55:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:55:32: #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 11:55:32: #1 tags after filtering in treatment: 12101540 INFO @ Fri, 05 Jul 2019 11:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:55:32: #1 finished! INFO @ Fri, 05 Jul 2019 11:55:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:55:34: #2 number of paired peaks: 18357 INFO @ Fri, 05 Jul 2019 11:55:34: start model_add_line... INFO @ Fri, 05 Jul 2019 11:55:34: start X-correlation... INFO @ Fri, 05 Jul 2019 11:55:34: end of X-cor INFO @ Fri, 05 Jul 2019 11:55:34: #2 finished! INFO @ Fri, 05 Jul 2019 11:55:34: #2 predicted fragment length is 54 bps INFO @ Fri, 05 Jul 2019 11:55:34: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 05 Jul 2019 11:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20_model.r WARNING @ Fri, 05 Jul 2019 11:55:34: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:55:34: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 05 Jul 2019 11:55:34: #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 11:55:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:55:37: 11000000 INFO @ Fri, 05 Jul 2019 11:55:47: 12000000 INFO @ Fri, 05 Jul 2019 11:55:48: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:55:48: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:55:48: #1 total tags in treatment: 12101696 INFO @ Fri, 05 Jul 2019 11:55:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:55:48: #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 11:55:48: #1 tags after filtering in treatment: 12101540 INFO @ Fri, 05 Jul 2019 11:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:55:48: #1 finished! INFO @ Fri, 05 Jul 2019 11:55:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:55:51: #2 number of paired peaks: 18357 INFO @ Fri, 05 Jul 2019 11:55:51: start model_add_line... INFO @ Fri, 05 Jul 2019 11:55:51: start X-correlation... INFO @ Fri, 05 Jul 2019 11:55:51: end of X-cor INFO @ Fri, 05 Jul 2019 11:55:51: #2 finished! INFO @ Fri, 05 Jul 2019 11:55:51: #2 predicted fragment length is 54 bps INFO @ Fri, 05 Jul 2019 11:55:51: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 05 Jul 2019 11:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05_model.r WARNING @ Fri, 05 Jul 2019 11:55:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:55:51: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 05 Jul 2019 11:55:51: #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 11:55:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:56:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:56:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.10_summits.bed INFO @ Fri, 05 Jul 2019 11:56:27: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (906 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:56:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.20_summits.bed INFO @ Fri, 05 Jul 2019 11:56:31: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (423 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:56:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:56:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:56:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2250257/ERX2250257.05_summits.bed INFO @ Fri, 05 Jul 2019 11:56:48: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1664 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。