Job ID = 1292319 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,577,412 reads read : 30,577,412 reads written : 30,577,412 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:23 30577412 reads; of these: 30577412 (100.00%) were unpaired; of these: 2073733 (6.78%) aligned 0 times 22338828 (73.06%) aligned exactly 1 time 6164851 (20.16%) aligned >1 times 93.22% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 19011704 / 28503679 = 0.6670 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 @ Sun, 02 Jun 2019 18:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:04:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:04:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:04:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:04:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 18:04:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:04:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:04:34: 1000000 INFO @ Sun, 02 Jun 2019 18:04:35: 1000000 INFO @ Sun, 02 Jun 2019 18:04:36: 1000000 INFO @ Sun, 02 Jun 2019 18:04:41: 2000000 INFO @ Sun, 02 Jun 2019 18:04:43: 2000000 INFO @ Sun, 02 Jun 2019 18:04:44: 2000000 INFO @ Sun, 02 Jun 2019 18:04:47: 3000000 INFO @ Sun, 02 Jun 2019 18:04:50: 3000000 INFO @ Sun, 02 Jun 2019 18:04:50: 3000000 INFO @ Sun, 02 Jun 2019 18:04:54: 4000000 INFO @ Sun, 02 Jun 2019 18:04:57: 4000000 INFO @ Sun, 02 Jun 2019 18:04:58: 4000000 INFO @ Sun, 02 Jun 2019 18:05:00: 5000000 INFO @ Sun, 02 Jun 2019 18:05:04: 5000000 INFO @ Sun, 02 Jun 2019 18:05:05: 5000000 INFO @ Sun, 02 Jun 2019 18:05:06: 6000000 INFO @ Sun, 02 Jun 2019 18:05:10: 6000000 INFO @ Sun, 02 Jun 2019 18:05:12: 6000000 INFO @ Sun, 02 Jun 2019 18:05:13: 7000000 INFO @ Sun, 02 Jun 2019 18:05:17: 7000000 INFO @ Sun, 02 Jun 2019 18:05:19: 8000000 INFO @ Sun, 02 Jun 2019 18:05:20: 7000000 INFO @ Sun, 02 Jun 2019 18:05:24: 8000000 INFO @ Sun, 02 Jun 2019 18:05:25: 9000000 INFO @ Sun, 02 Jun 2019 18:05:27: 8000000 INFO @ Sun, 02 Jun 2019 18:05:29: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:05:29: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:05:29: #1 total tags in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:05:29: #1 tags after filtering in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:30: #2 number of paired peaks: 1327 INFO @ Sun, 02 Jun 2019 18:05:30: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:30: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:30: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:30: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:30: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:05:30: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Sun, 02 Jun 2019 18:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05_model.r WARNING @ Sun, 02 Jun 2019 18:05:30: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:05:30: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Sun, 02 Jun 2019 18:05:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:05:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:31: 9000000 INFO @ Sun, 02 Jun 2019 18:05:34: 9000000 INFO @ Sun, 02 Jun 2019 18:05:34: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:05:34: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:05:34: #1 total tags in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:05:34: #1 tags after filtering in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:34: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:35: #2 number of paired peaks: 1327 INFO @ Sun, 02 Jun 2019 18:05:35: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:35: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:35: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:35: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:35: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:05:35: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Sun, 02 Jun 2019 18:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20_model.r WARNING @ Sun, 02 Jun 2019 18:05:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:05:36: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Sun, 02 Jun 2019 18:05:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:05:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:37: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:05:37: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:05:37: #1 total tags in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:05:38: #1 tags after filtering in treatment: 9491975 INFO @ Sun, 02 Jun 2019 18:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:38: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:39: #2 number of paired peaks: 1327 INFO @ Sun, 02 Jun 2019 18:05:39: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:39: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:39: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:39: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:39: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:05:39: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Sun, 02 Jun 2019 18:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10_model.r WARNING @ Sun, 02 Jun 2019 18:05:39: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:05:39: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Sun, 02 Jun 2019 18:05:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:05:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:06:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:06:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.05_summits.bed INFO @ Sun, 02 Jun 2019 18:06:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4324 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.20_summits.bed INFO @ Sun, 02 Jun 2019 18:06:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:06:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331344/SRX331344.10_summits.bed INFO @ Sun, 02 Jun 2019 18:06:19: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1700 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。