Job ID = 4288791 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,853,404 reads read : 35,706,808 reads written : 17,853,404 reads 0-length : 17,853,404 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: 00:00:00 Multiseed full-index search: 00:17:09 17853404 reads; of these: 17853404 (100.00%) were unpaired; of these: 410404 (2.30%) aligned 0 times 12114552 (67.86%) aligned exactly 1 time 5328448 (29.85%) aligned >1 times 97.70% overall alignment rate Time searching: 00:17:12 Overall time: 00:17:12 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] 738716 / 17443000 = 0.0424 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.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 12:33:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:33:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:33:28: 1000000 INFO @ Tue, 10 Dec 2019 12:33:37: 2000000 INFO @ Tue, 10 Dec 2019 12:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.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 12:33:48: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:33:48: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:33:48: 3000000 INFO @ Tue, 10 Dec 2019 12:33:59: 1000000 INFO @ Tue, 10 Dec 2019 12:33:59: 4000000 INFO @ Tue, 10 Dec 2019 12:34:11: 2000000 INFO @ Tue, 10 Dec 2019 12:34:12: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.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 12:34:18: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:34:18: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:34:24: 3000000 INFO @ Tue, 10 Dec 2019 12:34:24: 6000000 INFO @ Tue, 10 Dec 2019 12:34:28: 1000000 INFO @ Tue, 10 Dec 2019 12:34:36: 4000000 INFO @ Tue, 10 Dec 2019 12:34:36: 7000000 INFO @ Tue, 10 Dec 2019 12:34:38: 2000000 INFO @ Tue, 10 Dec 2019 12:34:47: 5000000 INFO @ Tue, 10 Dec 2019 12:34:47: 8000000 INFO @ Tue, 10 Dec 2019 12:34:48: 3000000 INFO @ Tue, 10 Dec 2019 12:34:59: 4000000 INFO @ Tue, 10 Dec 2019 12:34:59: 6000000 INFO @ Tue, 10 Dec 2019 12:34:59: 9000000 INFO @ Tue, 10 Dec 2019 12:35:09: 5000000 INFO @ Tue, 10 Dec 2019 12:35:10: 10000000 INFO @ Tue, 10 Dec 2019 12:35:10: 7000000 INFO @ Tue, 10 Dec 2019 12:35:19: 6000000 INFO @ Tue, 10 Dec 2019 12:35:22: 8000000 INFO @ Tue, 10 Dec 2019 12:35:22: 11000000 INFO @ Tue, 10 Dec 2019 12:35:30: 7000000 INFO @ Tue, 10 Dec 2019 12:35:34: 12000000 INFO @ Tue, 10 Dec 2019 12:35:34: 9000000 INFO @ Tue, 10 Dec 2019 12:35:40: 8000000 INFO @ Tue, 10 Dec 2019 12:35:45: 13000000 INFO @ Tue, 10 Dec 2019 12:35:45: 10000000 INFO @ Tue, 10 Dec 2019 12:35:50: 9000000 INFO @ Tue, 10 Dec 2019 12:35:57: 14000000 INFO @ Tue, 10 Dec 2019 12:35:57: 11000000 INFO @ Tue, 10 Dec 2019 12:36:00: 10000000 INFO @ Tue, 10 Dec 2019 12:36:08: 15000000 INFO @ Tue, 10 Dec 2019 12:36:09: 12000000 INFO @ Tue, 10 Dec 2019 12:36:11: 11000000 INFO @ Tue, 10 Dec 2019 12:36:20: 16000000 INFO @ Tue, 10 Dec 2019 12:36:20: 13000000 INFO @ Tue, 10 Dec 2019 12:36:21: 12000000 INFO @ Tue, 10 Dec 2019 12:36:28: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:36:28: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:36:28: #1 total tags in treatment: 16704284 INFO @ Tue, 10 Dec 2019 12:36:28: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:36:28: #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 12:36:28: #1 tags after filtering in treatment: 16704108 INFO @ Tue, 10 Dec 2019 12:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:36:28: #1 finished! INFO @ Tue, 10 Dec 2019 12:36:28: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:36:30: #2 number of paired peaks: 5355 INFO @ Tue, 10 Dec 2019 12:36:30: start model_add_line... INFO @ Tue, 10 Dec 2019 12:36:30: start X-correlation... INFO @ Tue, 10 Dec 2019 12:36:30: end of X-cor INFO @ Tue, 10 Dec 2019 12:36:30: #2 finished! INFO @ Tue, 10 Dec 2019 12:36:30: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:36:30: #2 alternative fragment length(s) may be 51,223,403,499,544 bps INFO @ Tue, 10 Dec 2019 12:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05_model.r WARNING @ Tue, 10 Dec 2019 12:36:30: #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 12:36:30: #2 You may need to consider one of the other alternative d(s): 51,223,403,499,544 WARNING @ Tue, 10 Dec 2019 12:36:30: #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 12:36:30: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:36:31: 13000000 INFO @ Tue, 10 Dec 2019 12:36:31: 14000000 INFO @ Tue, 10 Dec 2019 12:36:41: 14000000 INFO @ Tue, 10 Dec 2019 12:36:42: 15000000 INFO @ Tue, 10 Dec 2019 12:36:51: 15000000 INFO @ Tue, 10 Dec 2019 12:36:53: 16000000 INFO @ Tue, 10 Dec 2019 12:37:00: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:37:00: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:37:00: #1 total tags in treatment: 16704284 INFO @ Tue, 10 Dec 2019 12:37:00: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:37:00: #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 12:37:01: #1 tags after filtering in treatment: 16704108 INFO @ Tue, 10 Dec 2019 12:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:37:01: #1 finished! INFO @ Tue, 10 Dec 2019 12:37:01: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:37:02: 16000000 INFO @ Tue, 10 Dec 2019 12:37:03: #2 number of paired peaks: 5355 INFO @ Tue, 10 Dec 2019 12:37:03: start model_add_line... INFO @ Tue, 10 Dec 2019 12:37:03: start X-correlation... INFO @ Tue, 10 Dec 2019 12:37:03: end of X-cor INFO @ Tue, 10 Dec 2019 12:37:03: #2 finished! INFO @ Tue, 10 Dec 2019 12:37:03: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:37:03: #2 alternative fragment length(s) may be 51,223,403,499,544 bps INFO @ Tue, 10 Dec 2019 12:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10_model.r WARNING @ Tue, 10 Dec 2019 12:37:03: #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 12:37:03: #2 You may need to consider one of the other alternative d(s): 51,223,403,499,544 WARNING @ Tue, 10 Dec 2019 12:37:03: #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 12:37:03: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:37:09: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:37:09: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:37:09: #1 total tags in treatment: 16704284 INFO @ Tue, 10 Dec 2019 12:37:09: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:37:09: #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 12:37:09: #1 tags after filtering in treatment: 16704108 INFO @ Tue, 10 Dec 2019 12:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:37:09: #1 finished! INFO @ Tue, 10 Dec 2019 12:37:09: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:37:11: #2 number of paired peaks: 5355 INFO @ Tue, 10 Dec 2019 12:37:11: start model_add_line... INFO @ Tue, 10 Dec 2019 12:37:11: start X-correlation... INFO @ Tue, 10 Dec 2019 12:37:11: end of X-cor INFO @ Tue, 10 Dec 2019 12:37:11: #2 finished! INFO @ Tue, 10 Dec 2019 12:37:11: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:37:11: #2 alternative fragment length(s) may be 51,223,403,499,544 bps INFO @ Tue, 10 Dec 2019 12:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20_model.r WARNING @ Tue, 10 Dec 2019 12:37:12: #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 12:37:12: #2 You may need to consider one of the other alternative d(s): 51,223,403,499,544 WARNING @ Tue, 10 Dec 2019 12:37:12: #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 12:37:12: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:37:23: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.05_summits.bed INFO @ Tue, 10 Dec 2019 12:37:50: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (1276 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:37:56: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:38:04: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.10_summits.bed INFO @ Tue, 10 Dec 2019 12:38:22: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (707 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:38:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654065/SRX4654065.20_summits.bed INFO @ Tue, 10 Dec 2019 12:38:30: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (338 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。