Job ID = 1292522 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:05:51 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256451 (1.19%) aligned 0 times 17820575 (82.85%) aligned exactly 1 time 3432583 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 3667549 / 21253158 = 0.1726 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 19:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.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 19:28:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.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 19:28:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.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 19:28:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:38: 1000000 INFO @ Sun, 02 Jun 2019 19:28:39: 1000000 INFO @ Sun, 02 Jun 2019 19:28:40: 1000000 INFO @ Sun, 02 Jun 2019 19:28:47: 2000000 INFO @ Sun, 02 Jun 2019 19:28:47: 2000000 INFO @ Sun, 02 Jun 2019 19:28:49: 2000000 INFO @ Sun, 02 Jun 2019 19:28:55: 3000000 INFO @ Sun, 02 Jun 2019 19:28:56: 3000000 INFO @ Sun, 02 Jun 2019 19:28:59: 3000000 INFO @ Sun, 02 Jun 2019 19:29:03: 4000000 INFO @ Sun, 02 Jun 2019 19:29:04: 4000000 INFO @ Sun, 02 Jun 2019 19:29:08: 4000000 INFO @ Sun, 02 Jun 2019 19:29:11: 5000000 INFO @ Sun, 02 Jun 2019 19:29:12: 5000000 INFO @ Sun, 02 Jun 2019 19:29:17: 5000000 INFO @ Sun, 02 Jun 2019 19:29:19: 6000000 INFO @ Sun, 02 Jun 2019 19:29:20: 6000000 INFO @ Sun, 02 Jun 2019 19:29:26: 6000000 INFO @ Sun, 02 Jun 2019 19:29:27: 7000000 INFO @ Sun, 02 Jun 2019 19:29:29: 7000000 INFO @ Sun, 02 Jun 2019 19:29:35: 8000000 INFO @ Sun, 02 Jun 2019 19:29:36: 7000000 INFO @ Sun, 02 Jun 2019 19:29:37: 8000000 INFO @ Sun, 02 Jun 2019 19:29:43: 9000000 INFO @ Sun, 02 Jun 2019 19:29:45: 8000000 INFO @ Sun, 02 Jun 2019 19:29:45: 9000000 INFO @ Sun, 02 Jun 2019 19:29:52: 10000000 INFO @ Sun, 02 Jun 2019 19:29:54: 9000000 INFO @ Sun, 02 Jun 2019 19:29:54: 10000000 INFO @ Sun, 02 Jun 2019 19:30:00: 11000000 INFO @ Sun, 02 Jun 2019 19:30:02: 11000000 INFO @ Sun, 02 Jun 2019 19:30:03: 10000000 INFO @ Sun, 02 Jun 2019 19:30:07: 12000000 INFO @ Sun, 02 Jun 2019 19:30:11: 12000000 INFO @ Sun, 02 Jun 2019 19:30:12: 11000000 INFO @ Sun, 02 Jun 2019 19:30:15: 13000000 INFO @ Sun, 02 Jun 2019 19:30:19: 13000000 INFO @ Sun, 02 Jun 2019 19:30:20: 12000000 INFO @ Sun, 02 Jun 2019 19:30:23: 14000000 INFO @ Sun, 02 Jun 2019 19:30:27: 14000000 INFO @ Sun, 02 Jun 2019 19:30:29: 13000000 INFO @ Sun, 02 Jun 2019 19:30:31: 15000000 INFO @ Sun, 02 Jun 2019 19:30:35: 15000000 INFO @ Sun, 02 Jun 2019 19:30:38: 14000000 INFO @ Sun, 02 Jun 2019 19:30:39: 16000000 INFO @ Sun, 02 Jun 2019 19:30:44: 16000000 INFO @ Sun, 02 Jun 2019 19:30:46: 15000000 INFO @ Sun, 02 Jun 2019 19:30:47: 17000000 INFO @ Sun, 02 Jun 2019 19:30:52: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:30:52: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:30:52: #1 total tags in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:30:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:30:52: #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 19:30:52: 17000000 INFO @ Sun, 02 Jun 2019 19:30:52: #1 tags after filtering in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:30:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:30:52: #1 finished! INFO @ Sun, 02 Jun 2019 19:30:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:30:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:30:54: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 19:30:54: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 19:30:54: start model_add_line... INFO @ Sun, 02 Jun 2019 19:30:54: start X-correlation... INFO @ Sun, 02 Jun 2019 19:30:54: end of X-cor INFO @ Sun, 02 Jun 2019 19:30:54: #2 finished! INFO @ Sun, 02 Jun 2019 19:30:54: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:30:54: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Sun, 02 Jun 2019 19:30:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10_model.r WARNING @ Sun, 02 Jun 2019 19:30:54: #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 19:30:54: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Sun, 02 Jun 2019 19:30:54: #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 19:30:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:30:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:30:55: 16000000 INFO @ Sun, 02 Jun 2019 19:30:57: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:30:57: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:30:57: #1 total tags in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:30:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:30:57: #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 19:30:57: #1 tags after filtering in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:30:57: #1 finished! INFO @ Sun, 02 Jun 2019 19:30:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:30:59: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 19:30:59: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 19:30:59: start model_add_line... INFO @ Sun, 02 Jun 2019 19:30:59: start X-correlation... INFO @ Sun, 02 Jun 2019 19:30:59: end of X-cor INFO @ Sun, 02 Jun 2019 19:30:59: #2 finished! INFO @ Sun, 02 Jun 2019 19:30:59: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:30:59: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Sun, 02 Jun 2019 19:30:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05_model.r WARNING @ Sun, 02 Jun 2019 19:30:59: #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 19:30:59: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Sun, 02 Jun 2019 19:30:59: #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 19:30:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:30:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:31:04: 17000000 INFO @ Sun, 02 Jun 2019 19:31:09: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:31:09: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:31:09: #1 total tags in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:31:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:31:09: #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 19:31:09: #1 tags after filtering in treatment: 17585609 INFO @ Sun, 02 Jun 2019 19:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:31:09: #1 finished! INFO @ Sun, 02 Jun 2019 19:31:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:31:11: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 19:31:11: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 19:31:11: start model_add_line... INFO @ Sun, 02 Jun 2019 19:31:11: start X-correlation... INFO @ Sun, 02 Jun 2019 19:31:11: end of X-cor INFO @ Sun, 02 Jun 2019 19:31:11: #2 finished! INFO @ Sun, 02 Jun 2019 19:31:11: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:31:11: #2 alternative fragment length(s) may be 1,45,543 bps INFO @ Sun, 02 Jun 2019 19:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20_model.r WARNING @ Sun, 02 Jun 2019 19:31:11: #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 19:31:11: #2 You may need to consider one of the other alternative d(s): 1,45,543 WARNING @ Sun, 02 Jun 2019 19:31:11: #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 19:31:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:31:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:31:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:31:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.10_summits.bed INFO @ Sun, 02 Jun 2019 19:31:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.05_summits.bed INFO @ Sun, 02 Jun 2019 19:32:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466536/SRX466536.20_summits.bed INFO @ Sun, 02 Jun 2019 19:32:14: Done! pass1 - making usageList (0 chroms): 2 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。