Job ID = 1293088 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,870,480 reads read : 55,740,960 reads written : 27,870,480 reads 0-length : 27,870,480 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: 00:07:56 27870480 reads; of these: 27870480 (100.00%) were unpaired; of these: 404142 (1.45%) aligned 0 times 22572738 (80.99%) aligned exactly 1 time 4893600 (17.56%) aligned >1 times 98.55% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 9067068 / 27466338 = 0.3301 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 22:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.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 22:02:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:02:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.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 22:02:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:02:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.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 22:02:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:02:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:02:49: 1000000 INFO @ Sun, 02 Jun 2019 22:02:52: 1000000 INFO @ Sun, 02 Jun 2019 22:02:52: 1000000 INFO @ Sun, 02 Jun 2019 22:02:56: 2000000 INFO @ Sun, 02 Jun 2019 22:03:02: 2000000 INFO @ Sun, 02 Jun 2019 22:03:02: 2000000 INFO @ Sun, 02 Jun 2019 22:03:04: 3000000 INFO @ Sun, 02 Jun 2019 22:03:11: 4000000 INFO @ Sun, 02 Jun 2019 22:03:12: 3000000 INFO @ Sun, 02 Jun 2019 22:03:12: 3000000 INFO @ Sun, 02 Jun 2019 22:03:19: 5000000 INFO @ Sun, 02 Jun 2019 22:03:22: 4000000 INFO @ Sun, 02 Jun 2019 22:03:22: 4000000 INFO @ Sun, 02 Jun 2019 22:03:27: 6000000 INFO @ Sun, 02 Jun 2019 22:03:34: 5000000 INFO @ Sun, 02 Jun 2019 22:03:34: 5000000 INFO @ Sun, 02 Jun 2019 22:03:34: 7000000 INFO @ Sun, 02 Jun 2019 22:03:42: 8000000 INFO @ Sun, 02 Jun 2019 22:03:44: 6000000 INFO @ Sun, 02 Jun 2019 22:03:45: 6000000 INFO @ Sun, 02 Jun 2019 22:03:50: 9000000 INFO @ Sun, 02 Jun 2019 22:03:55: 7000000 INFO @ Sun, 02 Jun 2019 22:03:56: 7000000 INFO @ Sun, 02 Jun 2019 22:03:57: 10000000 INFO @ Sun, 02 Jun 2019 22:04:05: 11000000 INFO @ Sun, 02 Jun 2019 22:04:06: 8000000 INFO @ Sun, 02 Jun 2019 22:04:06: 8000000 INFO @ Sun, 02 Jun 2019 22:04:13: 12000000 INFO @ Sun, 02 Jun 2019 22:04:17: 9000000 INFO @ Sun, 02 Jun 2019 22:04:17: 9000000 INFO @ Sun, 02 Jun 2019 22:04:20: 13000000 INFO @ Sun, 02 Jun 2019 22:04:27: 14000000 INFO @ Sun, 02 Jun 2019 22:04:28: 10000000 INFO @ Sun, 02 Jun 2019 22:04:28: 10000000 INFO @ Sun, 02 Jun 2019 22:04:34: 15000000 INFO @ Sun, 02 Jun 2019 22:04:39: 11000000 INFO @ Sun, 02 Jun 2019 22:04:39: 11000000 INFO @ Sun, 02 Jun 2019 22:04:41: 16000000 INFO @ Sun, 02 Jun 2019 22:04:48: 17000000 INFO @ Sun, 02 Jun 2019 22:04:49: 12000000 INFO @ Sun, 02 Jun 2019 22:04:50: 12000000 INFO @ Sun, 02 Jun 2019 22:04:55: 18000000 INFO @ Sun, 02 Jun 2019 22:04:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:04:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:04:58: #1 total tags in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:04:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:58: #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 22:04:59: #1 tags after filtering in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:59: 13000000 INFO @ Sun, 02 Jun 2019 22:05:00: #2 number of paired peaks: 224 WARNING @ Sun, 02 Jun 2019 22:05:00: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:00: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:00: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:00: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:00: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:00: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:05:00: #2 alternative fragment length(s) may be 1,45,596 bps INFO @ Sun, 02 Jun 2019 22:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20_model.r WARNING @ Sun, 02 Jun 2019 22:05:00: #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 22:05:00: #2 You may need to consider one of the other alternative d(s): 1,45,596 WARNING @ Sun, 02 Jun 2019 22:05:00: #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 22:05:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:01: 13000000 INFO @ Sun, 02 Jun 2019 22:05:11: 14000000 INFO @ Sun, 02 Jun 2019 22:05:11: 14000000 INFO @ Sun, 02 Jun 2019 22:05:21: 15000000 INFO @ Sun, 02 Jun 2019 22:05:21: 15000000 INFO @ Sun, 02 Jun 2019 22:05:31: 16000000 INFO @ Sun, 02 Jun 2019 22:05:32: 16000000 INFO @ Sun, 02 Jun 2019 22:05:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:41: 17000000 INFO @ Sun, 02 Jun 2019 22:05:43: 17000000 INFO @ Sun, 02 Jun 2019 22:05:51: 18000000 INFO @ Sun, 02 Jun 2019 22:05:53: 18000000 INFO @ Sun, 02 Jun 2019 22:05:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:05:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:05:55: #1 total tags in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:05:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:55: #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 22:05:55: #1 tags after filtering in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:05:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:55: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:57: #2 number of paired peaks: 224 WARNING @ Sun, 02 Jun 2019 22:05:57: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:05:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:05:57: #1 total tags in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:05:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:57: #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 22:05:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:05:57: #2 alternative fragment length(s) may be 1,45,596 bps INFO @ Sun, 02 Jun 2019 22:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10_model.r WARNING @ Sun, 02 Jun 2019 22:05:57: #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 22:05:57: #2 You may need to consider one of the other alternative d(s): 1,45,596 WARNING @ Sun, 02 Jun 2019 22:05:57: #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 22:05:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:57: #1 tags after filtering in treatment: 18399270 INFO @ Sun, 02 Jun 2019 22:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:57: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:59: #2 number of paired peaks: 224 WARNING @ Sun, 02 Jun 2019 22:05:59: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:59: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:05:59: #2 alternative fragment length(s) may be 1,45,596 bps INFO @ Sun, 02 Jun 2019 22:05:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05_model.r WARNING @ Sun, 02 Jun 2019 22:05:59: #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 22:05:59: #2 You may need to consider one of the other alternative d(s): 1,45,596 WARNING @ Sun, 02 Jun 2019 22:05:59: #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 22:05:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.10_summits.bed INFO @ Sun, 02 Jun 2019 22:06:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5073496/SRX5073496.05_summits.bed INFO @ Sun, 02 Jun 2019 22:06:58: 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。