Job ID = 4287356 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,021,160 reads read : 32,042,320 reads written : 16,021,160 reads 0-length : 16,021,160 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:17:19 16021160 reads; of these: 16021160 (100.00%) were unpaired; of these: 359362 (2.24%) aligned 0 times 10767850 (67.21%) aligned exactly 1 time 4893948 (30.55%) aligned >1 times 97.76% overall alignment rate Time searching: 00:17:25 Overall time: 00:17:25 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 8 files... [bam_rmdupse_core] 738217 / 15661798 = 0.0471 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.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 @ Tue, 10 Dec 2019 12:24:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:32: 1000000 INFO @ Tue, 10 Dec 2019 12:24:39: 2000000 INFO @ Tue, 10 Dec 2019 12:24:47: 3000000 INFO @ Tue, 10 Dec 2019 12:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.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 @ Tue, 10 Dec 2019 12:24:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:55: 4000000 INFO @ Tue, 10 Dec 2019 12:25:02: 5000000 INFO @ Tue, 10 Dec 2019 12:25:03: 1000000 INFO @ Tue, 10 Dec 2019 12:25:10: 6000000 INFO @ Tue, 10 Dec 2019 12:25:12: 2000000 INFO @ Tue, 10 Dec 2019 12:25:17: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:25:21: 3000000 INFO @ Tue, 10 Dec 2019 12:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.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 @ Tue, 10 Dec 2019 12:25:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:25:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:25:24: 8000000 INFO @ Tue, 10 Dec 2019 12:25:31: 4000000 INFO @ Tue, 10 Dec 2019 12:25:31: 1000000 INFO @ Tue, 10 Dec 2019 12:25:32: 9000000 INFO @ Tue, 10 Dec 2019 12:25:39: 2000000 INFO @ Tue, 10 Dec 2019 12:25:40: 10000000 INFO @ Tue, 10 Dec 2019 12:25:40: 5000000 INFO @ Tue, 10 Dec 2019 12:25:46: 3000000 INFO @ Tue, 10 Dec 2019 12:25:47: 11000000 INFO @ Tue, 10 Dec 2019 12:25:50: 6000000 INFO @ Tue, 10 Dec 2019 12:25:53: 4000000 INFO @ Tue, 10 Dec 2019 12:25:55: 12000000 INFO @ Tue, 10 Dec 2019 12:26:00: 7000000 INFO @ Tue, 10 Dec 2019 12:26:01: 5000000 INFO @ Tue, 10 Dec 2019 12:26:03: 13000000 INFO @ Tue, 10 Dec 2019 12:26:08: 6000000 INFO @ Tue, 10 Dec 2019 12:26:10: 8000000 INFO @ Tue, 10 Dec 2019 12:26:11: 14000000 INFO @ Tue, 10 Dec 2019 12:26:15: 7000000 INFO @ Tue, 10 Dec 2019 12:26:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:26:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:26:18: #1 total tags in treatment: 14923581 INFO @ Tue, 10 Dec 2019 12:26:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:26:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:26:19: #1 tags after filtering in treatment: 14923402 INFO @ Tue, 10 Dec 2019 12:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:26:19: #1 finished! INFO @ Tue, 10 Dec 2019 12:26:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:26:19: 9000000 INFO @ Tue, 10 Dec 2019 12:26:20: #2 number of paired peaks: 6077 INFO @ Tue, 10 Dec 2019 12:26:20: start model_add_line... INFO @ Tue, 10 Dec 2019 12:26:21: start X-correlation... INFO @ Tue, 10 Dec 2019 12:26:21: end of X-cor INFO @ Tue, 10 Dec 2019 12:26:21: #2 finished! INFO @ Tue, 10 Dec 2019 12:26:21: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:26:21: #2 alternative fragment length(s) may be 51,224,416,504 bps INFO @ Tue, 10 Dec 2019 12:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05_model.r WARNING @ Tue, 10 Dec 2019 12:26:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:26:21: #2 You may need to consider one of the other alternative d(s): 51,224,416,504 WARNING @ Tue, 10 Dec 2019 12:26:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:26:21: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:26:23: 8000000 INFO @ Tue, 10 Dec 2019 12:26:29: 10000000 INFO @ Tue, 10 Dec 2019 12:26:30: 9000000 INFO @ Tue, 10 Dec 2019 12:26:37: 10000000 INFO @ Tue, 10 Dec 2019 12:26:39: 11000000 INFO @ Tue, 10 Dec 2019 12:26:45: 11000000 INFO @ Tue, 10 Dec 2019 12:26:48: 12000000 INFO @ Tue, 10 Dec 2019 12:26:52: 12000000 INFO @ Tue, 10 Dec 2019 12:26:58: 13000000 INFO @ Tue, 10 Dec 2019 12:26:59: 13000000 INFO @ Tue, 10 Dec 2019 12:27:06: 14000000 INFO @ Tue, 10 Dec 2019 12:27:08: 14000000 INFO @ Tue, 10 Dec 2019 12:27:08: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:27:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:27:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:27:14: #1 total tags in treatment: 14923581 INFO @ Tue, 10 Dec 2019 12:27:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:27:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:27:14: #1 tags after filtering in treatment: 14923402 INFO @ Tue, 10 Dec 2019 12:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:27:14: #1 finished! INFO @ Tue, 10 Dec 2019 12:27:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:27:16: #2 number of paired peaks: 6077 INFO @ Tue, 10 Dec 2019 12:27:16: start model_add_line... INFO @ Tue, 10 Dec 2019 12:27:16: start X-correlation... INFO @ Tue, 10 Dec 2019 12:27:16: end of X-cor INFO @ Tue, 10 Dec 2019 12:27:16: #2 finished! INFO @ Tue, 10 Dec 2019 12:27:16: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:27:16: #2 alternative fragment length(s) may be 51,224,416,504 bps INFO @ Tue, 10 Dec 2019 12:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20_model.r WARNING @ Tue, 10 Dec 2019 12:27:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:27:16: #2 You may need to consider one of the other alternative d(s): 51,224,416,504 WARNING @ Tue, 10 Dec 2019 12:27:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:27:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:27:18: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:27:18: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:27:18: #1 total tags in treatment: 14923581 INFO @ Tue, 10 Dec 2019 12:27:18: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:27:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:27:19: #1 tags after filtering in treatment: 14923402 INFO @ Tue, 10 Dec 2019 12:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:27:19: #1 finished! INFO @ Tue, 10 Dec 2019 12:27:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:27:21: #2 number of paired peaks: 6077 INFO @ Tue, 10 Dec 2019 12:27:21: start model_add_line... INFO @ Tue, 10 Dec 2019 12:27:21: start X-correlation... INFO @ Tue, 10 Dec 2019 12:27:21: end of X-cor INFO @ Tue, 10 Dec 2019 12:27:21: #2 finished! INFO @ Tue, 10 Dec 2019 12:27:21: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:27:21: #2 alternative fragment length(s) may be 51,224,416,504 bps INFO @ Tue, 10 Dec 2019 12:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10_model.r WARNING @ Tue, 10 Dec 2019 12:27:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:27:21: #2 You may need to consider one of the other alternative d(s): 51,224,416,504 WARNING @ Tue, 10 Dec 2019 12:27:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:27:21: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.05_summits.bed INFO @ Tue, 10 Dec 2019 12:27:31: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (1201 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:28:04: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:28:09: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.20_summits.bed INFO @ Tue, 10 Dec 2019 12:28:27: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654061/SRX4654061.10_summits.bed INFO @ Tue, 10 Dec 2019 12:28:32: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。