Job ID = 1293197 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,897,440 reads read : 30,897,440 reads written : 30,897,440 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:00 30897440 reads; of these: 30897440 (100.00%) were unpaired; of these: 4444139 (14.38%) aligned 0 times 17055541 (55.20%) aligned exactly 1 time 9397760 (30.42%) aligned >1 times 85.62% overall alignment rate Time searching: 00:14:01 Overall time: 00:14:01 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 12 files... [bam_rmdupse_core] 7684452 / 26453301 = 0.2905 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 22:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.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 22:51:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.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 22:51:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.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 22:51:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:34: 1000000 INFO @ Sun, 02 Jun 2019 22:51:34: 1000000 INFO @ Sun, 02 Jun 2019 22:51:35: 1000000 INFO @ Sun, 02 Jun 2019 22:51:47: 2000000 INFO @ Sun, 02 Jun 2019 22:51:47: 2000000 INFO @ Sun, 02 Jun 2019 22:51:47: 2000000 INFO @ Sun, 02 Jun 2019 22:51:59: 3000000 INFO @ Sun, 02 Jun 2019 22:52:00: 3000000 INFO @ Sun, 02 Jun 2019 22:52:00: 3000000 INFO @ Sun, 02 Jun 2019 22:52:11: 4000000 INFO @ Sun, 02 Jun 2019 22:52:12: 4000000 INFO @ Sun, 02 Jun 2019 22:52:13: 4000000 INFO @ Sun, 02 Jun 2019 22:52:24: 5000000 INFO @ Sun, 02 Jun 2019 22:52:24: 5000000 INFO @ Sun, 02 Jun 2019 22:52:25: 5000000 INFO @ Sun, 02 Jun 2019 22:52:37: 6000000 INFO @ Sun, 02 Jun 2019 22:52:37: 6000000 INFO @ Sun, 02 Jun 2019 22:52:38: 6000000 INFO @ Sun, 02 Jun 2019 22:52:50: 7000000 INFO @ Sun, 02 Jun 2019 22:52:51: 7000000 INFO @ Sun, 02 Jun 2019 22:52:52: 7000000 INFO @ Sun, 02 Jun 2019 22:53:03: 8000000 INFO @ Sun, 02 Jun 2019 22:53:04: 8000000 INFO @ Sun, 02 Jun 2019 22:53:05: 8000000 INFO @ Sun, 02 Jun 2019 22:53:16: 9000000 INFO @ Sun, 02 Jun 2019 22:53:18: 9000000 INFO @ Sun, 02 Jun 2019 22:53:18: 9000000 INFO @ Sun, 02 Jun 2019 22:53:30: 10000000 INFO @ Sun, 02 Jun 2019 22:53:32: 10000000 INFO @ Sun, 02 Jun 2019 22:53:33: 10000000 INFO @ Sun, 02 Jun 2019 22:53:44: 11000000 INFO @ Sun, 02 Jun 2019 22:53:45: 11000000 INFO @ Sun, 02 Jun 2019 22:53:47: 11000000 INFO @ Sun, 02 Jun 2019 22:53:57: 12000000 INFO @ Sun, 02 Jun 2019 22:53:58: 12000000 INFO @ Sun, 02 Jun 2019 22:54:02: 12000000 INFO @ Sun, 02 Jun 2019 22:54:11: 13000000 INFO @ Sun, 02 Jun 2019 22:54:11: 13000000 INFO @ Sun, 02 Jun 2019 22:54:17: 13000000 INFO @ Sun, 02 Jun 2019 22:54:24: 14000000 INFO @ Sun, 02 Jun 2019 22:54:24: 14000000 INFO @ Sun, 02 Jun 2019 22:54:31: 14000000 INFO @ Sun, 02 Jun 2019 22:54:37: 15000000 INFO @ Sun, 02 Jun 2019 22:54:37: 15000000 INFO @ Sun, 02 Jun 2019 22:54:44: 15000000 INFO @ Sun, 02 Jun 2019 22:54:49: 16000000 INFO @ Sun, 02 Jun 2019 22:54:50: 16000000 INFO @ Sun, 02 Jun 2019 22:54:58: 16000000 INFO @ Sun, 02 Jun 2019 22:55:02: 17000000 INFO @ Sun, 02 Jun 2019 22:55:04: 17000000 INFO @ Sun, 02 Jun 2019 22:55:13: 17000000 INFO @ Sun, 02 Jun 2019 22:55:14: 18000000 INFO @ Sun, 02 Jun 2019 22:55:18: 18000000 INFO @ Sun, 02 Jun 2019 22:55:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:55:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:55:25: #1 total tags in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:55:25: #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 22:55:26: #1 tags after filtering in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:55:26: #1 finished! INFO @ Sun, 02 Jun 2019 22:55:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:55:27: 18000000 INFO @ Sun, 02 Jun 2019 22:55:28: #2 number of paired peaks: 1544 INFO @ Sun, 02 Jun 2019 22:55:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:55:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:55:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:55:28: #1 total tags in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:55:28: #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 22:55:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:55:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:55:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:55:29: #2 predicted fragment length is 75 bps INFO @ Sun, 02 Jun 2019 22:55:29: #2 alternative fragment length(s) may be 3,75 bps INFO @ Sun, 02 Jun 2019 22:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20_model.r WARNING @ Sun, 02 Jun 2019 22:55:29: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:55:29: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Sun, 02 Jun 2019 22:55:29: #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 22:55:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:55:29: #1 tags after filtering in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:55:29: #1 finished! INFO @ Sun, 02 Jun 2019 22:55:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:55:32: #2 number of paired peaks: 1544 INFO @ Sun, 02 Jun 2019 22:55:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:55:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:55:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:55:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:55:32: #2 predicted fragment length is 75 bps INFO @ Sun, 02 Jun 2019 22:55:32: #2 alternative fragment length(s) may be 3,75 bps INFO @ Sun, 02 Jun 2019 22:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05_model.r WARNING @ Sun, 02 Jun 2019 22:55:32: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:55:32: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Sun, 02 Jun 2019 22:55:32: #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 22:55:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:55:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:55:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:55:38: #1 total tags in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:55:38: #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 22:55:39: #1 tags after filtering in treatment: 18768849 INFO @ Sun, 02 Jun 2019 22:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:55:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:55:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:55:41: #2 number of paired peaks: 1544 INFO @ Sun, 02 Jun 2019 22:55:41: start model_add_line... INFO @ Sun, 02 Jun 2019 22:55:42: start X-correlation... INFO @ Sun, 02 Jun 2019 22:55:42: end of X-cor INFO @ Sun, 02 Jun 2019 22:55:42: #2 finished! INFO @ Sun, 02 Jun 2019 22:55:42: #2 predicted fragment length is 75 bps INFO @ Sun, 02 Jun 2019 22:55:42: #2 alternative fragment length(s) may be 3,75 bps INFO @ Sun, 02 Jun 2019 22:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10_model.r WARNING @ Sun, 02 Jun 2019 22:55:42: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:55:42: #2 You may need to consider one of the other alternative d(s): 3,75 WARNING @ Sun, 02 Jun 2019 22:55:42: #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 22:55:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:56:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:56:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:56:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.20_summits.bed INFO @ Sun, 02 Jun 2019 22:57:18: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (2567 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:57:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:57:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:57:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.05_summits.bed INFO @ Sun, 02 Jun 2019 22:57:22: Done! pass1 - making usageList (7 chroms): 10 millis pass2 - checking and writing primary data (10190 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402751/SRX5402751.10_summits.bed INFO @ Sun, 02 Jun 2019 22:57:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6255 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。