Job ID = 10714415 sra ファイルのダウンロード中... Completed: 426622K bytes transferred in 35 seconds (99528K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 19591062 spots for /home/okishinya/chipatlas/results/ce10/SRX4082375/SRR7164193.sra Written 19591062 spots for /home/okishinya/chipatlas/results/ce10/SRX4082375/SRR7164193.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:05:40 19591062 reads; of these: 19591062 (100.00%) were unpaired; of these: 245092 (1.25%) aligned 0 times 14611013 (74.58%) aligned exactly 1 time 4734957 (24.17%) aligned >1 times 98.75% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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 8 files... [bam_rmdupse_core] 3390381 / 19345970 = 0.1752 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, 03 Jun 2018 12:41:30: # Command line: callpeak -t SRX4082375.bam -f BAM -g ce -n SRX4082375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082375.20 # format = BAM # ChIP-seq file = ['SRX4082375.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, 03 Jun 2018 12:41:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:41:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:41:30: # Command line: callpeak -t SRX4082375.bam -f BAM -g ce -n SRX4082375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082375.05 # format = BAM # ChIP-seq file = ['SRX4082375.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, 03 Jun 2018 12:41:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:41:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:41:30: # Command line: callpeak -t SRX4082375.bam -f BAM -g ce -n SRX4082375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082375.10 # format = BAM # ChIP-seq file = ['SRX4082375.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, 03 Jun 2018 12:41:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:41:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:41:36: 1000000 INFO @ Sun, 03 Jun 2018 12:41:36: 1000000 INFO @ Sun, 03 Jun 2018 12:41:37: 1000000 INFO @ Sun, 03 Jun 2018 12:41:43: 2000000 INFO @ Sun, 03 Jun 2018 12:41:43: 2000000 INFO @ Sun, 03 Jun 2018 12:41:44: 2000000 INFO @ Sun, 03 Jun 2018 12:41:50: 3000000 INFO @ Sun, 03 Jun 2018 12:41:50: 3000000 INFO @ Sun, 03 Jun 2018 12:41:51: 3000000 INFO @ Sun, 03 Jun 2018 12:41:57: 4000000 INFO @ Sun, 03 Jun 2018 12:41:57: 4000000 INFO @ Sun, 03 Jun 2018 12:41:58: 4000000 INFO @ Sun, 03 Jun 2018 12:42:04: 5000000 INFO @ Sun, 03 Jun 2018 12:42:04: 5000000 INFO @ Sun, 03 Jun 2018 12:42:06: 5000000 INFO @ Sun, 03 Jun 2018 12:42:11: 6000000 INFO @ Sun, 03 Jun 2018 12:42:11: 6000000 INFO @ Sun, 03 Jun 2018 12:42:13: 6000000 INFO @ Sun, 03 Jun 2018 12:42:18: 7000000 INFO @ Sun, 03 Jun 2018 12:42:19: 7000000 INFO @ Sun, 03 Jun 2018 12:42:21: 7000000 INFO @ Sun, 03 Jun 2018 12:42:25: 8000000 INFO @ Sun, 03 Jun 2018 12:42:26: 8000000 INFO @ Sun, 03 Jun 2018 12:42:28: 8000000 INFO @ Sun, 03 Jun 2018 12:42:32: 9000000 INFO @ Sun, 03 Jun 2018 12:42:33: 9000000 INFO @ Sun, 03 Jun 2018 12:42:36: 9000000 INFO @ Sun, 03 Jun 2018 12:42:39: 10000000 INFO @ Sun, 03 Jun 2018 12:42:41: 10000000 INFO @ Sun, 03 Jun 2018 12:42:43: 10000000 INFO @ Sun, 03 Jun 2018 12:42:46: 11000000 INFO @ Sun, 03 Jun 2018 12:42:48: 11000000 INFO @ Sun, 03 Jun 2018 12:42:51: 11000000 INFO @ Sun, 03 Jun 2018 12:42:54: 12000000 INFO @ Sun, 03 Jun 2018 12:42:56: 12000000 INFO @ Sun, 03 Jun 2018 12:42:59: 12000000 INFO @ Sun, 03 Jun 2018 12:43:02: 13000000 INFO @ Sun, 03 Jun 2018 12:43:04: 13000000 INFO @ Sun, 03 Jun 2018 12:43:07: 13000000 INFO @ Sun, 03 Jun 2018 12:43:09: 14000000 INFO @ Sun, 03 Jun 2018 12:43:12: 14000000 INFO @ Sun, 03 Jun 2018 12:43:15: 14000000 INFO @ Sun, 03 Jun 2018 12:43:17: 15000000 INFO @ Sun, 03 Jun 2018 12:43:20: 15000000 INFO @ Sun, 03 Jun 2018 12:43:23: 15000000 INFO @ Sun, 03 Jun 2018 12:43:24: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:43:24: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:43:24: #1 total tags in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:24: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:43:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:43:25: #1 tags after filtering in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:43:25: #1 finished! INFO @ Sun, 03 Jun 2018 12:43:25: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:43:26: #2 number of paired peaks: 393 WARNING @ Sun, 03 Jun 2018 12:43:26: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 03 Jun 2018 12:43:26: start model_add_line... INFO @ Sun, 03 Jun 2018 12:43:26: start X-correlation... INFO @ Sun, 03 Jun 2018 12:43:26: end of X-cor INFO @ Sun, 03 Jun 2018 12:43:26: #2 finished! INFO @ Sun, 03 Jun 2018 12:43:26: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:43:26: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Sun, 03 Jun 2018 12:43:26: #2.2 Generate R script for model : SRX4082375.05_model.r WARNING @ Sun, 03 Jun 2018 12:43:26: #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, 03 Jun 2018 12:43:26: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Sun, 03 Jun 2018 12:43:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:43:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:43:27: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:43:27: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:43:27: #1 total tags in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:27: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:43:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:43:27: #1 tags after filtering in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:43:27: #1 finished! INFO @ Sun, 03 Jun 2018 12:43:27: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:43:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:43:29: #2 number of paired peaks: 393 WARNING @ Sun, 03 Jun 2018 12:43:29: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 03 Jun 2018 12:43:29: start model_add_line... INFO @ Sun, 03 Jun 2018 12:43:29: start X-correlation... INFO @ Sun, 03 Jun 2018 12:43:29: end of X-cor INFO @ Sun, 03 Jun 2018 12:43:29: #2 finished! INFO @ Sun, 03 Jun 2018 12:43:29: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:43:29: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Sun, 03 Jun 2018 12:43:29: #2.2 Generate R script for model : SRX4082375.20_model.r WARNING @ Sun, 03 Jun 2018 12:43:29: #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, 03 Jun 2018 12:43:29: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Sun, 03 Jun 2018 12:43:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:43:29: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:43:30: #1 tag size is determined as 49 bps INFO @ Sun, 03 Jun 2018 12:43:30: #1 tag size = 49 INFO @ Sun, 03 Jun 2018 12:43:30: #1 total tags in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:30: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:43:31: #1 tags after filtering in treatment: 15955589 INFO @ Sun, 03 Jun 2018 12:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:43:31: #1 finished! INFO @ Sun, 03 Jun 2018 12:43:31: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:43:32: #2 number of paired peaks: 393 WARNING @ Sun, 03 Jun 2018 12:43:32: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 03 Jun 2018 12:43:32: start model_add_line... INFO @ Sun, 03 Jun 2018 12:43:32: start X-correlation... INFO @ Sun, 03 Jun 2018 12:43:32: end of X-cor INFO @ Sun, 03 Jun 2018 12:43:32: #2 finished! INFO @ Sun, 03 Jun 2018 12:43:32: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:43:32: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Sun, 03 Jun 2018 12:43:32: #2.2 Generate R script for model : SRX4082375.10_model.r WARNING @ Sun, 03 Jun 2018 12:43:32: #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, 03 Jun 2018 12:43:32: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Sun, 03 Jun 2018 12:43:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 12:43:32: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:43:54: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:43:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:43:58: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:44:08: #4 Write output xls file... SRX4082375.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:08: #4 Write peak in narrowPeak format file... SRX4082375.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:08: #4 Write summits bed file... SRX4082375.05_summits.bed INFO @ Sun, 03 Jun 2018 12:44:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:44:10: #4 Write output xls file... SRX4082375.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:10: #4 Write peak in narrowPeak format file... SRX4082375.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:10: #4 Write summits bed file... SRX4082375.20_summits.bed INFO @ Sun, 03 Jun 2018 12:44:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:44:13: #4 Write output xls file... SRX4082375.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:44:13: #4 Write peak in narrowPeak format file... SRX4082375.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:44:13: #4 Write summits bed file... SRX4082375.10_summits.bed INFO @ Sun, 03 Jun 2018 12:44:13: 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。