Job ID = 2003690 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,709,077 reads read : 26,709,077 reads written : 26,709,077 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1103816.sra.cache’: 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: 00:22:21 26709077 reads; of these: 26709077 (100.00%) were unpaired; of these: 2190781 (8.20%) aligned 0 times 17160353 (64.25%) aligned exactly 1 time 7357943 (27.55%) aligned >1 times 91.80% overall alignment rate Time searching: 00:22:24 Overall time: 00:22:24 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] 1735345 / 24518296 = 0.0708 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 13:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.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 13:46:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:46:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.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 13:46:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:46:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.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 13:46:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:46:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:46:20: 1000000 INFO @ Fri, 05 Jul 2019 13:46:21: 1000000 INFO @ Fri, 05 Jul 2019 13:46:24: 1000000 INFO @ Fri, 05 Jul 2019 13:46:29: 2000000 INFO @ Fri, 05 Jul 2019 13:46:32: 2000000 INFO @ Fri, 05 Jul 2019 13:46:37: 2000000 INFO @ Fri, 05 Jul 2019 13:46:37: 3000000 INFO @ Fri, 05 Jul 2019 13:46:43: 3000000 INFO @ Fri, 05 Jul 2019 13:46:45: 4000000 INFO @ Fri, 05 Jul 2019 13:46:49: 3000000 INFO @ Fri, 05 Jul 2019 13:46:53: 5000000 INFO @ Fri, 05 Jul 2019 13:46:54: 4000000 INFO @ Fri, 05 Jul 2019 13:47:01: 4000000 INFO @ Fri, 05 Jul 2019 13:47:02: 6000000 INFO @ Fri, 05 Jul 2019 13:47:05: 5000000 INFO @ Fri, 05 Jul 2019 13:47:11: 7000000 INFO @ Fri, 05 Jul 2019 13:47:13: 5000000 INFO @ Fri, 05 Jul 2019 13:47:16: 6000000 INFO @ Fri, 05 Jul 2019 13:47:19: 8000000 INFO @ Fri, 05 Jul 2019 13:47:26: 7000000 INFO @ Fri, 05 Jul 2019 13:47:27: 6000000 INFO @ Fri, 05 Jul 2019 13:47:27: 9000000 INFO @ Fri, 05 Jul 2019 13:47:35: 10000000 INFO @ Fri, 05 Jul 2019 13:47:37: 8000000 INFO @ Fri, 05 Jul 2019 13:47:39: 7000000 INFO @ Fri, 05 Jul 2019 13:47:44: 11000000 INFO @ Fri, 05 Jul 2019 13:47:48: 9000000 INFO @ Fri, 05 Jul 2019 13:47:51: 8000000 INFO @ Fri, 05 Jul 2019 13:47:52: 12000000 INFO @ Fri, 05 Jul 2019 13:48:00: 13000000 INFO @ Fri, 05 Jul 2019 13:48:00: 10000000 INFO @ Fri, 05 Jul 2019 13:48:04: 9000000 INFO @ Fri, 05 Jul 2019 13:48:08: 14000000 INFO @ Fri, 05 Jul 2019 13:48:11: 11000000 INFO @ Fri, 05 Jul 2019 13:48:16: 15000000 INFO @ Fri, 05 Jul 2019 13:48:17: 10000000 INFO @ Fri, 05 Jul 2019 13:48:21: 12000000 INFO @ Fri, 05 Jul 2019 13:48:24: 16000000 INFO @ Fri, 05 Jul 2019 13:48:29: 11000000 INFO @ Fri, 05 Jul 2019 13:48:32: 17000000 INFO @ Fri, 05 Jul 2019 13:48:32: 13000000 INFO @ Fri, 05 Jul 2019 13:48:40: 18000000 INFO @ Fri, 05 Jul 2019 13:48:41: 12000000 INFO @ Fri, 05 Jul 2019 13:48:43: 14000000 INFO @ Fri, 05 Jul 2019 13:48:49: 19000000 INFO @ Fri, 05 Jul 2019 13:48:53: 13000000 INFO @ Fri, 05 Jul 2019 13:48:54: 15000000 INFO @ Fri, 05 Jul 2019 13:48:57: 20000000 INFO @ Fri, 05 Jul 2019 13:49:05: 16000000 INFO @ Fri, 05 Jul 2019 13:49:05: 14000000 INFO @ Fri, 05 Jul 2019 13:49:06: 21000000 INFO @ Fri, 05 Jul 2019 13:49:14: 22000000 INFO @ Fri, 05 Jul 2019 13:49:15: 17000000 INFO @ Fri, 05 Jul 2019 13:49:17: 15000000 INFO @ Fri, 05 Jul 2019 13:49:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:49:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:49:21: #1 total tags in treatment: 22782951 INFO @ Fri, 05 Jul 2019 13:49:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:49:21: #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 13:49:22: #1 tags after filtering in treatment: 22782834 INFO @ Fri, 05 Jul 2019 13:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:49:22: #1 finished! INFO @ Fri, 05 Jul 2019 13:49:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:49:25: #2 number of paired peaks: 5674 INFO @ Fri, 05 Jul 2019 13:49:25: start model_add_line... INFO @ Fri, 05 Jul 2019 13:49:25: start X-correlation... INFO @ Fri, 05 Jul 2019 13:49:25: end of X-cor INFO @ Fri, 05 Jul 2019 13:49:25: #2 finished! INFO @ Fri, 05 Jul 2019 13:49:25: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 13:49:25: #2 alternative fragment length(s) may be 58,96,588 bps INFO @ Fri, 05 Jul 2019 13:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20_model.r WARNING @ Fri, 05 Jul 2019 13:49:25: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:49:25: #2 You may need to consider one of the other alternative d(s): 58,96,588 WARNING @ Fri, 05 Jul 2019 13:49:25: #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 13:49:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:49:26: 18000000 INFO @ Fri, 05 Jul 2019 13:49:29: 16000000 INFO @ Fri, 05 Jul 2019 13:49:36: 19000000 INFO @ Fri, 05 Jul 2019 13:49:41: 17000000 INFO @ Fri, 05 Jul 2019 13:49:46: 20000000 INFO @ Fri, 05 Jul 2019 13:49:52: 18000000 INFO @ Fri, 05 Jul 2019 13:49:58: 21000000 INFO @ Fri, 05 Jul 2019 13:50:04: 19000000 INFO @ Fri, 05 Jul 2019 13:50:10: 22000000 INFO @ Fri, 05 Jul 2019 13:50:16: 20000000 INFO @ Fri, 05 Jul 2019 13:50:19: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:19: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:19: #1 total tags in treatment: 22782951 INFO @ Fri, 05 Jul 2019 13:50:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:19: #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 13:50:20: #1 tags after filtering in treatment: 22782834 INFO @ Fri, 05 Jul 2019 13:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:20: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:22: #2 number of paired peaks: 5674 INFO @ Fri, 05 Jul 2019 13:50:22: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:22: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:22: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:22: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:22: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 13:50:22: #2 alternative fragment length(s) may be 58,96,588 bps INFO @ Fri, 05 Jul 2019 13:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05_model.r WARNING @ Fri, 05 Jul 2019 13:50:23: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:50:23: #2 You may need to consider one of the other alternative d(s): 58,96,588 WARNING @ Fri, 05 Jul 2019 13:50:23: #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 13:50:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:50:29: 21000000 INFO @ Fri, 05 Jul 2019 13:50:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:50:42: 22000000 INFO @ Fri, 05 Jul 2019 13:50:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:50:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:50:53: #1 total tags in treatment: 22782951 INFO @ Fri, 05 Jul 2019 13:50:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:53: #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 13:50:53: #1 tags after filtering in treatment: 22782834 INFO @ Fri, 05 Jul 2019 13:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:53: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:56: #2 number of paired peaks: 5674 INFO @ Fri, 05 Jul 2019 13:50:56: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:56: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:56: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:56: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:56: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 13:50:56: #2 alternative fragment length(s) may be 58,96,588 bps INFO @ Fri, 05 Jul 2019 13:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10_model.r WARNING @ Fri, 05 Jul 2019 13:50:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:50:56: #2 You may need to consider one of the other alternative d(s): 58,96,588 WARNING @ Fri, 05 Jul 2019 13:50:56: #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 13:50:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.20_summits.bed INFO @ Fri, 05 Jul 2019 13:51:14: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:51:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:52:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.05_summits.bed INFO @ Fri, 05 Jul 2019 13:52:11: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1280 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX423107/SRX423107.10_summits.bed INFO @ Fri, 05 Jul 2019 13:52:46: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (533 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。