Job ID = 1292404 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,955,677 reads read : 11,911,354 reads written : 5,955,677 reads 0-length : 5,955,677 spots read : 5,805,692 reads read : 11,611,384 reads written : 5,805,692 reads 0-length : 5,805,692 spots read : 5,954,642 reads read : 11,909,284 reads written : 5,954,642 reads 0-length : 5,954,642 spots read : 5,752,810 reads read : 11,505,620 reads written : 5,752,810 reads 0-length : 5,752,810 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: 00:12:40 23468821 reads; of these: 23468821 (100.00%) were unpaired; of these: 828188 (3.53%) aligned 0 times 15441855 (65.80%) aligned exactly 1 time 7198778 (30.67%) aligned >1 times 96.47% overall alignment rate Time searching: 00:12:40 Overall time: 00:12:40 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] 6351545 / 22640633 = 0.2805 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 18:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.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 18:53:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.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 18:53:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.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 18:53:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:19: 1000000 INFO @ Sun, 02 Jun 2019 18:53:20: 1000000 INFO @ Sun, 02 Jun 2019 18:53:20: 1000000 INFO @ Sun, 02 Jun 2019 18:53:27: 2000000 INFO @ Sun, 02 Jun 2019 18:53:27: 2000000 INFO @ Sun, 02 Jun 2019 18:53:29: 2000000 INFO @ Sun, 02 Jun 2019 18:53:35: 3000000 INFO @ Sun, 02 Jun 2019 18:53:35: 3000000 INFO @ Sun, 02 Jun 2019 18:53:38: 3000000 INFO @ Sun, 02 Jun 2019 18:53:43: 4000000 INFO @ Sun, 02 Jun 2019 18:53:43: 4000000 INFO @ Sun, 02 Jun 2019 18:53:47: 4000000 INFO @ Sun, 02 Jun 2019 18:53:51: 5000000 INFO @ Sun, 02 Jun 2019 18:53:51: 5000000 INFO @ Sun, 02 Jun 2019 18:53:55: 5000000 INFO @ Sun, 02 Jun 2019 18:53:59: 6000000 INFO @ Sun, 02 Jun 2019 18:53:59: 6000000 INFO @ Sun, 02 Jun 2019 18:54:04: 6000000 INFO @ Sun, 02 Jun 2019 18:54:06: 7000000 INFO @ Sun, 02 Jun 2019 18:54:07: 7000000 INFO @ Sun, 02 Jun 2019 18:54:13: 7000000 INFO @ Sun, 02 Jun 2019 18:54:14: 8000000 INFO @ Sun, 02 Jun 2019 18:54:15: 8000000 INFO @ Sun, 02 Jun 2019 18:54:22: 8000000 INFO @ Sun, 02 Jun 2019 18:54:22: 9000000 INFO @ Sun, 02 Jun 2019 18:54:23: 9000000 INFO @ Sun, 02 Jun 2019 18:54:31: 10000000 INFO @ Sun, 02 Jun 2019 18:54:31: 9000000 INFO @ Sun, 02 Jun 2019 18:54:31: 10000000 INFO @ Sun, 02 Jun 2019 18:54:39: 11000000 INFO @ Sun, 02 Jun 2019 18:54:40: 10000000 INFO @ Sun, 02 Jun 2019 18:54:40: 11000000 INFO @ Sun, 02 Jun 2019 18:54:48: 12000000 INFO @ Sun, 02 Jun 2019 18:54:48: 12000000 INFO @ Sun, 02 Jun 2019 18:54:48: 11000000 INFO @ Sun, 02 Jun 2019 18:54:55: 13000000 INFO @ Sun, 02 Jun 2019 18:54:57: 13000000 INFO @ Sun, 02 Jun 2019 18:54:57: 12000000 INFO @ Sun, 02 Jun 2019 18:55:03: 14000000 INFO @ Sun, 02 Jun 2019 18:55:06: 13000000 INFO @ Sun, 02 Jun 2019 18:55:06: 14000000 INFO @ Sun, 02 Jun 2019 18:55:11: 15000000 INFO @ Sun, 02 Jun 2019 18:55:15: 14000000 INFO @ Sun, 02 Jun 2019 18:55:15: 15000000 INFO @ Sun, 02 Jun 2019 18:55:19: 16000000 INFO @ Sun, 02 Jun 2019 18:55:21: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:55:21: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:55:21: #1 total tags in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:21: #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 18:55:21: #1 tags after filtering in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:21: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:23: #2 number of paired peaks: 1158 INFO @ Sun, 02 Jun 2019 18:55:23: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:23: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:23: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:23: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:23: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:55:23: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Sun, 02 Jun 2019 18:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10_model.r WARNING @ Sun, 02 Jun 2019 18:55:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:55:23: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Sun, 02 Jun 2019 18:55:23: #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 18:55:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:24: 15000000 INFO @ Sun, 02 Jun 2019 18:55:24: 16000000 INFO @ Sun, 02 Jun 2019 18:55:27: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:55:27: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:55:27: #1 total tags in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:27: #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 18:55:27: #1 tags after filtering in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:27: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:29: #2 number of paired peaks: 1158 INFO @ Sun, 02 Jun 2019 18:55:29: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:29: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:29: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:29: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:29: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:55:29: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Sun, 02 Jun 2019 18:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20_model.r WARNING @ Sun, 02 Jun 2019 18:55:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:55:29: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Sun, 02 Jun 2019 18:55:29: #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 18:55:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:32: 16000000 INFO @ Sun, 02 Jun 2019 18:55:35: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:55:35: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:55:35: #1 total tags in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:55:35: #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 18:55:35: #1 tags after filtering in treatment: 16289088 INFO @ Sun, 02 Jun 2019 18:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:55:35: #1 finished! INFO @ Sun, 02 Jun 2019 18:55:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:55:37: #2 number of paired peaks: 1158 INFO @ Sun, 02 Jun 2019 18:55:37: start model_add_line... INFO @ Sun, 02 Jun 2019 18:55:37: start X-correlation... INFO @ Sun, 02 Jun 2019 18:55:37: end of X-cor INFO @ Sun, 02 Jun 2019 18:55:37: #2 finished! INFO @ Sun, 02 Jun 2019 18:55:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 18:55:37: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Sun, 02 Jun 2019 18:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05_model.r WARNING @ Sun, 02 Jun 2019 18:55:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:55:37: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Sun, 02 Jun 2019 18:55:37: #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 18:55:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:55:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.10_summits.bed INFO @ Sun, 02 Jun 2019 18:56:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.20_summits.bed INFO @ Sun, 02 Jun 2019 18:56:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194186/SRX4194186.05_summits.bed INFO @ Sun, 02 Jun 2019 18:56:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。