Job ID = 4288849 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,619,896 reads read : 27,239,792 reads written : 13,619,896 reads 0-length : 13,619,896 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:21 13619896 reads; of these: 13619896 (100.00%) were unpaired; of these: 308115 (2.26%) aligned 0 times 9232634 (67.79%) aligned exactly 1 time 4079147 (29.95%) aligned >1 times 97.74% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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] 623830 / 13311781 = 0.0469 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.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 12:39:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:59: 1000000 INFO @ Tue, 10 Dec 2019 12:40:09: 2000000 INFO @ Tue, 10 Dec 2019 12:40:17: 3000000 INFO @ Tue, 10 Dec 2019 12:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.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 12:40:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:27: 4000000 INFO @ Tue, 10 Dec 2019 12:40:30: 1000000 INFO @ Tue, 10 Dec 2019 12:40:36: 5000000 INFO @ Tue, 10 Dec 2019 12:40:40: 2000000 INFO @ Tue, 10 Dec 2019 12:40:46: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.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 12:40:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:52: 3000000 INFO @ Tue, 10 Dec 2019 12:40:55: 7000000 INFO @ Tue, 10 Dec 2019 12:41:01: 1000000 INFO @ Tue, 10 Dec 2019 12:41:02: 4000000 INFO @ Tue, 10 Dec 2019 12:41:06: 8000000 INFO @ Tue, 10 Dec 2019 12:41:12: 2000000 INFO @ Tue, 10 Dec 2019 12:41:13: 5000000 INFO @ Tue, 10 Dec 2019 12:41:16: 9000000 INFO @ Tue, 10 Dec 2019 12:41:23: 3000000 INFO @ Tue, 10 Dec 2019 12:41:24: 6000000 INFO @ Tue, 10 Dec 2019 12:41:26: 10000000 INFO @ Tue, 10 Dec 2019 12:41:34: 4000000 INFO @ Tue, 10 Dec 2019 12:41:35: 7000000 INFO @ Tue, 10 Dec 2019 12:41:37: 11000000 INFO @ Tue, 10 Dec 2019 12:41:45: 5000000 INFO @ Tue, 10 Dec 2019 12:41:45: 8000000 INFO @ Tue, 10 Dec 2019 12:41:48: 12000000 INFO @ Tue, 10 Dec 2019 12:41:55: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:55: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:55: #1 total tags in treatment: 12687951 INFO @ Tue, 10 Dec 2019 12:41:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:55: #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 12:41:56: #1 tags after filtering in treatment: 12687768 INFO @ Tue, 10 Dec 2019 12:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:56: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:56: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:56: 9000000 INFO @ Tue, 10 Dec 2019 12:41:56: 6000000 INFO @ Tue, 10 Dec 2019 12:41:57: #2 number of paired peaks: 5286 INFO @ Tue, 10 Dec 2019 12:41:57: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:57: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:57: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:57: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:57: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:57: #2 alternative fragment length(s) may be 51,226,412,552,583 bps INFO @ Tue, 10 Dec 2019 12:41:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05_model.r WARNING @ Tue, 10 Dec 2019 12:41:57: #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 12:41:57: #2 You may need to consider one of the other alternative d(s): 51,226,412,552,583 WARNING @ Tue, 10 Dec 2019 12:41:57: #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 12:41:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:06: 10000000 INFO @ Tue, 10 Dec 2019 12:42:07: 7000000 INFO @ Tue, 10 Dec 2019 12:42:16: 11000000 INFO @ Tue, 10 Dec 2019 12:42:18: 8000000 INFO @ Tue, 10 Dec 2019 12:42:27: 12000000 INFO @ Tue, 10 Dec 2019 12:42:29: 9000000 INFO @ Tue, 10 Dec 2019 12:42:34: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:42:34: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:42:34: #1 total tags in treatment: 12687951 INFO @ Tue, 10 Dec 2019 12:42:34: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:42:34: #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 12:42:35: #1 tags after filtering in treatment: 12687768 INFO @ Tue, 10 Dec 2019 12:42:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:42:35: #1 finished! INFO @ Tue, 10 Dec 2019 12:42:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:42:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:42:36: #2 number of paired peaks: 5286 INFO @ Tue, 10 Dec 2019 12:42:36: start model_add_line... INFO @ Tue, 10 Dec 2019 12:42:36: start X-correlation... INFO @ Tue, 10 Dec 2019 12:42:36: end of X-cor INFO @ Tue, 10 Dec 2019 12:42:36: #2 finished! INFO @ Tue, 10 Dec 2019 12:42:36: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:42:36: #2 alternative fragment length(s) may be 51,226,412,552,583 bps INFO @ Tue, 10 Dec 2019 12:42:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10_model.r WARNING @ Tue, 10 Dec 2019 12:42:36: #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 12:42:36: #2 You may need to consider one of the other alternative d(s): 51,226,412,552,583 WARNING @ Tue, 10 Dec 2019 12:42:36: #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 12:42:36: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:42:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:38: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:40: 10000000 INFO @ Tue, 10 Dec 2019 12:42:51: 11000000 INFO @ Tue, 10 Dec 2019 12:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.05_summits.bed INFO @ Tue, 10 Dec 2019 12:42:58: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1021 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:43:02: 12000000 INFO @ Tue, 10 Dec 2019 12:43:10: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:43:10: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:43:10: #1 total tags in treatment: 12687951 INFO @ Tue, 10 Dec 2019 12:43:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:43:10: #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 12:43:10: #1 tags after filtering in treatment: 12687768 INFO @ Tue, 10 Dec 2019 12:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:43:10: #1 finished! INFO @ Tue, 10 Dec 2019 12:43:10: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:43:12: #2 number of paired peaks: 5286 INFO @ Tue, 10 Dec 2019 12:43:12: start model_add_line... INFO @ Tue, 10 Dec 2019 12:43:12: start X-correlation... INFO @ Tue, 10 Dec 2019 12:43:12: end of X-cor INFO @ Tue, 10 Dec 2019 12:43:12: #2 finished! INFO @ Tue, 10 Dec 2019 12:43:12: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:43:12: #2 alternative fragment length(s) may be 51,226,412,552,583 bps INFO @ Tue, 10 Dec 2019 12:43:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20_model.r WARNING @ Tue, 10 Dec 2019 12:43:12: #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 12:43:12: #2 You may need to consider one of the other alternative d(s): 51,226,412,552,583 WARNING @ Tue, 10 Dec 2019 12:43:12: #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 12:43:12: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:43:17: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.10_summits.bed INFO @ Tue, 10 Dec 2019 12:43:36: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:43:52: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654077/SRX4654077.20_summits.bed INFO @ Tue, 10 Dec 2019 12:44:13: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (258 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。