Job ID = 4288828 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,652,451 reads read : 39,304,902 reads written : 19,652,451 reads 0-length : 19,652,451 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:43 19652451 reads; of these: 19652451 (100.00%) were unpaired; of these: 882248 (4.49%) aligned 0 times 12956585 (65.93%) aligned exactly 1 time 5813618 (29.58%) aligned >1 times 95.51% overall alignment rate Time searching: 00:16:47 Overall time: 00:16:47 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] 865624 / 18770203 = 0.0461 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.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 12:39:20: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:20: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:27: 1000000 INFO @ Tue, 10 Dec 2019 12:39:33: 2000000 INFO @ Tue, 10 Dec 2019 12:39:39: 3000000 INFO @ Tue, 10 Dec 2019 12:39:46: 4000000 INFO @ Tue, 10 Dec 2019 12:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.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 12:39:50: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:50: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:52: 5000000 INFO @ Tue, 10 Dec 2019 12:39:57: 1000000 INFO @ Tue, 10 Dec 2019 12:39:58: 6000000 INFO @ Tue, 10 Dec 2019 12:40:04: 2000000 INFO @ Tue, 10 Dec 2019 12:40:05: 7000000 INFO @ Tue, 10 Dec 2019 12:40:11: 8000000 INFO @ Tue, 10 Dec 2019 12:40:11: 3000000 INFO @ Tue, 10 Dec 2019 12:40:17: 9000000 INFO @ Tue, 10 Dec 2019 12:40:18: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.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 12:40:20: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:20: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:23: 10000000 INFO @ Tue, 10 Dec 2019 12:40:25: 5000000 INFO @ Tue, 10 Dec 2019 12:40:27: 1000000 INFO @ Tue, 10 Dec 2019 12:40:30: 11000000 INFO @ Tue, 10 Dec 2019 12:40:31: 6000000 INFO @ Tue, 10 Dec 2019 12:40:33: 2000000 INFO @ Tue, 10 Dec 2019 12:40:36: 12000000 INFO @ Tue, 10 Dec 2019 12:40:38: 7000000 INFO @ Tue, 10 Dec 2019 12:40:40: 3000000 INFO @ Tue, 10 Dec 2019 12:40:42: 13000000 INFO @ Tue, 10 Dec 2019 12:40:45: 8000000 INFO @ Tue, 10 Dec 2019 12:40:46: 4000000 INFO @ Tue, 10 Dec 2019 12:40:49: 14000000 INFO @ Tue, 10 Dec 2019 12:40:51: 9000000 INFO @ Tue, 10 Dec 2019 12:40:53: 5000000 INFO @ Tue, 10 Dec 2019 12:40:55: 15000000 INFO @ Tue, 10 Dec 2019 12:40:58: 10000000 INFO @ Tue, 10 Dec 2019 12:40:59: 6000000 INFO @ Tue, 10 Dec 2019 12:41:01: 16000000 INFO @ Tue, 10 Dec 2019 12:41:05: 11000000 INFO @ Tue, 10 Dec 2019 12:41:06: 7000000 INFO @ Tue, 10 Dec 2019 12:41:08: 17000000 INFO @ Tue, 10 Dec 2019 12:41:12: 12000000 INFO @ Tue, 10 Dec 2019 12:41:12: 8000000 INFO @ Tue, 10 Dec 2019 12:41:14: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:14: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:14: #1 total tags in treatment: 17904579 INFO @ Tue, 10 Dec 2019 12:41:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:14: #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 12:41:14: #1 tags after filtering in treatment: 17904433 INFO @ Tue, 10 Dec 2019 12:41:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:14: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:17: #2 number of paired peaks: 6630 INFO @ Tue, 10 Dec 2019 12:41:17: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:17: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:17: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:17: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:17: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:17: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05_model.r WARNING @ Tue, 10 Dec 2019 12:41:17: #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 12:41:17: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:41:17: #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 12:41:17: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:18: 9000000 INFO @ Tue, 10 Dec 2019 12:41:18: 13000000 INFO @ Tue, 10 Dec 2019 12:41:24: 10000000 INFO @ Tue, 10 Dec 2019 12:41:25: 14000000 INFO @ Tue, 10 Dec 2019 12:41:31: 11000000 INFO @ Tue, 10 Dec 2019 12:41:32: 15000000 INFO @ Tue, 10 Dec 2019 12:41:37: 12000000 INFO @ Tue, 10 Dec 2019 12:41:39: 16000000 INFO @ Tue, 10 Dec 2019 12:41:43: 13000000 INFO @ Tue, 10 Dec 2019 12:41:45: 17000000 INFO @ Tue, 10 Dec 2019 12:41:50: 14000000 INFO @ Tue, 10 Dec 2019 12:41:52: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:52: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:52: #1 total tags in treatment: 17904579 INFO @ Tue, 10 Dec 2019 12:41:52: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:52: #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 12:41:52: #1 tags after filtering in treatment: 17904433 INFO @ Tue, 10 Dec 2019 12:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:52: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:54: #2 number of paired peaks: 6630 INFO @ Tue, 10 Dec 2019 12:41:54: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:55: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:55: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:55: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:55: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:55: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:41:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10_model.r WARNING @ Tue, 10 Dec 2019 12:41:55: #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 12:41:55: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:41:55: #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 12:41:55: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:56: 15000000 INFO @ Tue, 10 Dec 2019 12:42:02: 16000000 INFO @ Tue, 10 Dec 2019 12:42:09: 17000000 INFO @ Tue, 10 Dec 2019 12:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:15: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:42:15: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:42:15: #1 total tags in treatment: 17904579 INFO @ Tue, 10 Dec 2019 12:42:15: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:42:15: #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 12:42:15: #1 tags after filtering in treatment: 17904433 INFO @ Tue, 10 Dec 2019 12:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:42:15: #1 finished! INFO @ Tue, 10 Dec 2019 12:42:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:42:17: #2 number of paired peaks: 6630 INFO @ Tue, 10 Dec 2019 12:42:17: start model_add_line... INFO @ Tue, 10 Dec 2019 12:42:18: start X-correlation... INFO @ Tue, 10 Dec 2019 12:42:18: end of X-cor INFO @ Tue, 10 Dec 2019 12:42:18: #2 finished! INFO @ Tue, 10 Dec 2019 12:42:18: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:42:18: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 10 Dec 2019 12:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20_model.r WARNING @ Tue, 10 Dec 2019 12:42:18: #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 12:42:18: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 10 Dec 2019 12:42:18: #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 12:42:18: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.05_summits.bed INFO @ Tue, 10 Dec 2019 12:42:40: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (1861 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:42:51: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.10_summits.bed INFO @ Tue, 10 Dec 2019 12:43:18: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (907 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654073/SRX4654073.20_summits.bed INFO @ Tue, 10 Dec 2019 12:43:41: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (397 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。