Job ID = 1292407 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,403,813 reads read : 10,807,626 reads written : 5,403,813 reads 0-length : 5,403,813 spots read : 5,276,157 reads read : 10,552,314 reads written : 5,276,157 reads 0-length : 5,276,157 spots read : 5,397,633 reads read : 10,795,266 reads written : 5,397,633 reads 0-length : 5,397,633 spots read : 5,220,958 reads read : 10,441,916 reads written : 5,220,958 reads 0-length : 5,220,958 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: 00:09:23 21298561 reads; of these: 21298561 (100.00%) were unpaired; of these: 814532 (3.82%) aligned 0 times 15584888 (73.17%) aligned exactly 1 time 4899141 (23.00%) aligned >1 times 96.18% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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 12 files... [bam_rmdupse_core] 3980909 / 20484029 = 0.1943 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 18:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.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 18:48:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.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 18:48:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.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 18:48:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:48:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:49:07: 1000000 INFO @ Sun, 02 Jun 2019 18:49:07: 1000000 INFO @ Sun, 02 Jun 2019 18:49:08: 1000000 INFO @ Sun, 02 Jun 2019 18:49:16: 2000000 INFO @ Sun, 02 Jun 2019 18:49:16: 2000000 INFO @ Sun, 02 Jun 2019 18:49:17: 2000000 INFO @ Sun, 02 Jun 2019 18:49:24: 3000000 INFO @ Sun, 02 Jun 2019 18:49:24: 3000000 INFO @ Sun, 02 Jun 2019 18:49:27: 3000000 INFO @ Sun, 02 Jun 2019 18:49:33: 4000000 INFO @ Sun, 02 Jun 2019 18:49:33: 4000000 INFO @ Sun, 02 Jun 2019 18:49:36: 4000000 INFO @ Sun, 02 Jun 2019 18:49:41: 5000000 INFO @ Sun, 02 Jun 2019 18:49:41: 5000000 INFO @ Sun, 02 Jun 2019 18:49:45: 5000000 INFO @ Sun, 02 Jun 2019 18:49:49: 6000000 INFO @ Sun, 02 Jun 2019 18:49:50: 6000000 INFO @ Sun, 02 Jun 2019 18:49:54: 6000000 INFO @ Sun, 02 Jun 2019 18:49:58: 7000000 INFO @ Sun, 02 Jun 2019 18:49:58: 7000000 INFO @ Sun, 02 Jun 2019 18:50:03: 7000000 INFO @ Sun, 02 Jun 2019 18:50:06: 8000000 INFO @ Sun, 02 Jun 2019 18:50:06: 8000000 INFO @ Sun, 02 Jun 2019 18:50:12: 8000000 INFO @ Sun, 02 Jun 2019 18:50:15: 9000000 INFO @ Sun, 02 Jun 2019 18:50:15: 9000000 INFO @ Sun, 02 Jun 2019 18:50:21: 9000000 INFO @ Sun, 02 Jun 2019 18:50:23: 10000000 INFO @ Sun, 02 Jun 2019 18:50:23: 10000000 INFO @ Sun, 02 Jun 2019 18:50:31: 10000000 INFO @ Sun, 02 Jun 2019 18:50:32: 11000000 INFO @ Sun, 02 Jun 2019 18:50:32: 11000000 INFO @ Sun, 02 Jun 2019 18:50:40: 11000000 INFO @ Sun, 02 Jun 2019 18:50:40: 12000000 INFO @ Sun, 02 Jun 2019 18:50:40: 12000000 INFO @ Sun, 02 Jun 2019 18:50:48: 13000000 INFO @ Sun, 02 Jun 2019 18:50:48: 13000000 INFO @ Sun, 02 Jun 2019 18:50:49: 12000000 INFO @ Sun, 02 Jun 2019 18:50:57: 14000000 INFO @ Sun, 02 Jun 2019 18:50:57: 14000000 INFO @ Sun, 02 Jun 2019 18:50:58: 13000000 INFO @ Sun, 02 Jun 2019 18:51:05: 15000000 INFO @ Sun, 02 Jun 2019 18:51:05: 15000000 INFO @ Sun, 02 Jun 2019 18:51:07: 14000000 INFO @ Sun, 02 Jun 2019 18:51:13: 16000000 INFO @ Sun, 02 Jun 2019 18:51:13: 16000000 INFO @ Sun, 02 Jun 2019 18:51:16: 15000000 INFO @ Sun, 02 Jun 2019 18:51:17: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:51:17: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:51:17: #1 total tags in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:51:17: #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 18:51:17: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:51:17: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:51:17: #1 total tags in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:51:17: #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 18:51:18: #1 tags after filtering in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:51:18: #1 finished! INFO @ Sun, 02 Jun 2019 18:51:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:51:18: #1 tags after filtering in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:51:18: #1 finished! INFO @ Sun, 02 Jun 2019 18:51:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:51:19: #2 number of paired peaks: 472 WARNING @ Sun, 02 Jun 2019 18:51:19: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 02 Jun 2019 18:51:19: start model_add_line... INFO @ Sun, 02 Jun 2019 18:51:19: #2 number of paired peaks: 472 WARNING @ Sun, 02 Jun 2019 18:51:19: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 02 Jun 2019 18:51:19: start model_add_line... INFO @ Sun, 02 Jun 2019 18:51:19: start X-correlation... INFO @ Sun, 02 Jun 2019 18:51:19: end of X-cor INFO @ Sun, 02 Jun 2019 18:51:19: #2 finished! INFO @ Sun, 02 Jun 2019 18:51:19: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:51:19: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 02 Jun 2019 18:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10_model.r INFO @ Sun, 02 Jun 2019 18:51:19: start X-correlation... WARNING @ Sun, 02 Jun 2019 18:51:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:51:19: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 02 Jun 2019 18:51:19: #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 18:51:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:51:19: end of X-cor INFO @ Sun, 02 Jun 2019 18:51:19: #2 finished! INFO @ Sun, 02 Jun 2019 18:51:19: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:51:19: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 02 Jun 2019 18:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20_model.r WARNING @ Sun, 02 Jun 2019 18:51:19: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:51:19: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 02 Jun 2019 18:51:19: #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 18:51:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:51:24: 16000000 INFO @ Sun, 02 Jun 2019 18:51:29: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:51:29: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:51:29: #1 total tags in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:51:29: #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 18:51:29: #1 tags after filtering in treatment: 16503120 INFO @ Sun, 02 Jun 2019 18:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:51:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:51:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:51:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:51:31: #2 number of paired peaks: 472 WARNING @ Sun, 02 Jun 2019 18:51:31: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sun, 02 Jun 2019 18:51:31: start model_add_line... INFO @ Sun, 02 Jun 2019 18:51:31: start X-correlation... INFO @ Sun, 02 Jun 2019 18:51:31: end of X-cor INFO @ Sun, 02 Jun 2019 18:51:31: #2 finished! INFO @ Sun, 02 Jun 2019 18:51:31: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:51:31: #2 alternative fragment length(s) may be 1,47 bps INFO @ Sun, 02 Jun 2019 18:51:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05_model.r WARNING @ Sun, 02 Jun 2019 18:51:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:51:31: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Sun, 02 Jun 2019 18:51:31: #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 18:51:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:51:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:52:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:52:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.10_summits.bed INFO @ Sun, 02 Jun 2019 18:52:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.20_summits.bed INFO @ Sun, 02 Jun 2019 18:52:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194190/SRX4194190.05_summits.bed INFO @ Sun, 02 Jun 2019 18:52:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (942 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。