Job ID = 1292414 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,916,715 reads read : 13,833,430 reads written : 6,916,715 reads 0-length : 6,916,715 spots read : 6,787,209 reads read : 13,574,418 reads written : 6,787,209 reads 0-length : 6,787,209 spots read : 6,916,548 reads read : 13,833,096 reads written : 6,916,548 reads 0-length : 6,916,548 spots read : 6,701,121 reads read : 13,402,242 reads written : 6,701,121 reads 0-length : 6,701,121 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: 00:10:58 27321593 reads; of these: 27321593 (100.00%) were unpaired; of these: 1033747 (3.78%) aligned 0 times 21413964 (78.38%) aligned exactly 1 time 4873882 (17.84%) aligned >1 times 96.22% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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] 6817278 / 26287846 = 0.2593 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 18:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.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 18:56:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.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 18:56:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.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 18:56:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:12: 1000000 INFO @ Sun, 02 Jun 2019 18:56:13: 1000000 INFO @ Sun, 02 Jun 2019 18:56:13: 1000000 INFO @ Sun, 02 Jun 2019 18:56:18: 2000000 INFO @ Sun, 02 Jun 2019 18:56:22: 2000000 INFO @ Sun, 02 Jun 2019 18:56:23: 2000000 INFO @ Sun, 02 Jun 2019 18:56:25: 3000000 INFO @ Sun, 02 Jun 2019 18:56:30: 3000000 INFO @ Sun, 02 Jun 2019 18:56:32: 4000000 INFO @ Sun, 02 Jun 2019 18:56:32: 3000000 INFO @ Sun, 02 Jun 2019 18:56:39: 4000000 INFO @ Sun, 02 Jun 2019 18:56:39: 5000000 INFO @ Sun, 02 Jun 2019 18:56:42: 4000000 INFO @ Sun, 02 Jun 2019 18:56:46: 6000000 INFO @ Sun, 02 Jun 2019 18:56:47: 5000000 INFO @ Sun, 02 Jun 2019 18:56:50: 5000000 INFO @ Sun, 02 Jun 2019 18:56:53: 7000000 INFO @ Sun, 02 Jun 2019 18:56:55: 6000000 INFO @ Sun, 02 Jun 2019 18:56:59: 6000000 INFO @ Sun, 02 Jun 2019 18:56:59: 8000000 INFO @ Sun, 02 Jun 2019 18:57:03: 7000000 INFO @ Sun, 02 Jun 2019 18:57:06: 9000000 INFO @ Sun, 02 Jun 2019 18:57:08: 7000000 INFO @ Sun, 02 Jun 2019 18:57:11: 8000000 INFO @ Sun, 02 Jun 2019 18:57:13: 10000000 INFO @ Sun, 02 Jun 2019 18:57:16: 8000000 INFO @ Sun, 02 Jun 2019 18:57:19: 9000000 INFO @ Sun, 02 Jun 2019 18:57:19: 11000000 INFO @ Sun, 02 Jun 2019 18:57:25: 9000000 INFO @ Sun, 02 Jun 2019 18:57:26: 12000000 INFO @ Sun, 02 Jun 2019 18:57:27: 10000000 INFO @ Sun, 02 Jun 2019 18:57:33: 13000000 INFO @ Sun, 02 Jun 2019 18:57:34: 10000000 INFO @ Sun, 02 Jun 2019 18:57:35: 11000000 INFO @ Sun, 02 Jun 2019 18:57:39: 14000000 INFO @ Sun, 02 Jun 2019 18:57:42: 11000000 INFO @ Sun, 02 Jun 2019 18:57:43: 12000000 INFO @ Sun, 02 Jun 2019 18:57:46: 15000000 INFO @ Sun, 02 Jun 2019 18:57:51: 12000000 INFO @ Sun, 02 Jun 2019 18:57:51: 13000000 INFO @ Sun, 02 Jun 2019 18:57:52: 16000000 INFO @ Sun, 02 Jun 2019 18:57:59: 14000000 INFO @ Sun, 02 Jun 2019 18:57:59: 17000000 INFO @ Sun, 02 Jun 2019 18:57:59: 13000000 INFO @ Sun, 02 Jun 2019 18:58:05: 18000000 INFO @ Sun, 02 Jun 2019 18:58:06: 15000000 INFO @ Sun, 02 Jun 2019 18:58:07: 14000000 INFO @ Sun, 02 Jun 2019 18:58:12: 19000000 INFO @ Sun, 02 Jun 2019 18:58:15: 16000000 INFO @ Sun, 02 Jun 2019 18:58:15: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:15: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:15: #1 total tags in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:15: #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 18:58:16: 15000000 INFO @ Sun, 02 Jun 2019 18:58:16: #1 tags after filtering in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:16: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:17: #2 number of paired peaks: 347 WARNING @ Sun, 02 Jun 2019 18:58:17: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:17: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:18: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:18: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:18: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:18: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:58:18: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 18:58:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10_model.r WARNING @ Sun, 02 Jun 2019 18:58:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:18: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 18:58:18: #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 18:58:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:22: 17000000 INFO @ Sun, 02 Jun 2019 18:58:24: 16000000 INFO @ Sun, 02 Jun 2019 18:58:30: 18000000 INFO @ Sun, 02 Jun 2019 18:58:32: 17000000 INFO @ Sun, 02 Jun 2019 18:58:38: 19000000 INFO @ Sun, 02 Jun 2019 18:58:41: 18000000 INFO @ Sun, 02 Jun 2019 18:58:42: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:42: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:42: #1 total tags in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:42: #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 18:58:42: #1 tags after filtering in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:42: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:44: #2 number of paired peaks: 347 WARNING @ Sun, 02 Jun 2019 18:58:44: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:44: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:44: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:44: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:44: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:58:44: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 18:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05_model.r WARNING @ Sun, 02 Jun 2019 18:58:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:44: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 18:58:44: #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 18:58:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:49: 19000000 INFO @ Sun, 02 Jun 2019 18:58:53: #1 tag size is determined as 70 bps INFO @ Sun, 02 Jun 2019 18:58:53: #1 tag size = 70 INFO @ Sun, 02 Jun 2019 18:58:53: #1 total tags in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:53: #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 18:58:53: #1 tags after filtering in treatment: 19470568 INFO @ Sun, 02 Jun 2019 18:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:53: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:55: #2 number of paired peaks: 347 WARNING @ Sun, 02 Jun 2019 18:58:55: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:55: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:55: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:55: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:55: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:55: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:58:55: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 18:58:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20_model.r WARNING @ Sun, 02 Jun 2019 18:58:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:55: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 18:58:55: #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 18:58:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.10_summits.bed INFO @ Sun, 02 Jun 2019 18:59:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.05_summits.bed INFO @ Sun, 02 Jun 2019 18:59:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194199/SRX4194199.20_summits.bed INFO @ Sun, 02 Jun 2019 18:59:58: 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。