Job ID = 10201994 sra ファイルのダウンロード中... Completed: 754881K bytes transferred in 13 seconds (460401K 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... Written 23882510 spots for /home/okishinya/chipatlas/results/ce10/SRX2576663/SRR5272620.sra Written 23882510 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': 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: 00:12:52 23882510 reads; of these: 23882510 (100.00%) were unpaired; of these: 343241 (1.44%) aligned 0 times 19591163 (82.03%) aligned exactly 1 time 3948106 (16.53%) aligned >1 times 98.56% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:53 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] 3278243 / 23539269 = 0.1393 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 @ Mon, 13 Nov 2017 13:32:01: # Command line: callpeak -t SRX2576663.bam -f BAM -g ce -n SRX2576663.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576663.20 # format = BAM # ChIP-seq file = ['SRX2576663.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 @ Mon, 13 Nov 2017 13:32:01: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:32:01: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:32:01: # Command line: callpeak -t SRX2576663.bam -f BAM -g ce -n SRX2576663.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576663.10 # format = BAM # ChIP-seq file = ['SRX2576663.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 @ Mon, 13 Nov 2017 13:32:01: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:32:01: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:32:01: # Command line: callpeak -t SRX2576663.bam -f BAM -g ce -n SRX2576663.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576663.05 # format = BAM # ChIP-seq file = ['SRX2576663.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 @ Mon, 13 Nov 2017 13:32:01: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:32:01: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:32:14: 1000000 INFO @ Mon, 13 Nov 2017 13:32:16: 1000000 INFO @ Mon, 13 Nov 2017 13:32:17: 1000000 INFO @ Mon, 13 Nov 2017 13:32:27: 2000000 INFO @ Mon, 13 Nov 2017 13:32:31: 2000000 INFO @ Mon, 13 Nov 2017 13:32:32: 2000000 INFO @ Mon, 13 Nov 2017 13:32:39: 3000000 INFO @ Mon, 13 Nov 2017 13:32:45: 3000000 INFO @ Mon, 13 Nov 2017 13:32:47: 3000000 INFO @ Mon, 13 Nov 2017 13:32:53: 4000000 INFO @ Mon, 13 Nov 2017 13:33:00: 4000000 INFO @ Mon, 13 Nov 2017 13:33:02: 4000000 INFO @ Mon, 13 Nov 2017 13:33:06: 5000000 INFO @ Mon, 13 Nov 2017 13:33:15: 5000000 INFO @ Mon, 13 Nov 2017 13:33:18: 5000000 INFO @ Mon, 13 Nov 2017 13:33:25: 6000000 INFO @ Mon, 13 Nov 2017 13:33:30: 6000000 INFO @ Mon, 13 Nov 2017 13:33:33: 6000000 INFO @ Mon, 13 Nov 2017 13:33:44: 7000000 INFO @ Mon, 13 Nov 2017 13:33:45: 7000000 INFO @ Mon, 13 Nov 2017 13:33:49: 7000000 INFO @ Mon, 13 Nov 2017 13:33:59: 8000000 INFO @ Mon, 13 Nov 2017 13:34:04: 8000000 INFO @ Mon, 13 Nov 2017 13:34:05: 8000000 INFO @ Mon, 13 Nov 2017 13:34:13: 9000000 INFO @ Mon, 13 Nov 2017 13:34:17: 9000000 INFO @ Mon, 13 Nov 2017 13:34:20: 9000000 INFO @ Mon, 13 Nov 2017 13:34:26: 10000000 INFO @ Mon, 13 Nov 2017 13:34:27: 10000000 INFO @ Mon, 13 Nov 2017 13:34:35: 10000000 INFO @ Mon, 13 Nov 2017 13:34:36: 11000000 INFO @ Mon, 13 Nov 2017 13:34:41: 11000000 INFO @ Mon, 13 Nov 2017 13:34:46: 12000000 INFO @ Mon, 13 Nov 2017 13:34:48: 11000000 INFO @ Mon, 13 Nov 2017 13:34:55: 13000000 INFO @ Mon, 13 Nov 2017 13:34:56: 12000000 INFO @ Mon, 13 Nov 2017 13:35:02: 12000000 INFO @ Mon, 13 Nov 2017 13:35:05: 14000000 INFO @ Mon, 13 Nov 2017 13:35:10: 13000000 INFO @ Mon, 13 Nov 2017 13:35:14: 15000000 INFO @ Mon, 13 Nov 2017 13:35:15: 13000000 INFO @ Mon, 13 Nov 2017 13:35:24: 16000000 INFO @ Mon, 13 Nov 2017 13:35:24: 14000000 INFO @ Mon, 13 Nov 2017 13:35:29: 14000000 INFO @ Mon, 13 Nov 2017 13:35:34: 17000000 INFO @ Mon, 13 Nov 2017 13:35:39: 15000000 INFO @ Mon, 13 Nov 2017 13:35:43: 18000000 INFO @ Mon, 13 Nov 2017 13:35:46: 15000000 INFO @ Mon, 13 Nov 2017 13:35:53: 16000000 INFO @ Mon, 13 Nov 2017 13:35:53: 19000000 INFO @ Mon, 13 Nov 2017 13:36:03: 20000000 INFO @ Mon, 13 Nov 2017 13:36:04: 16000000 INFO @ Mon, 13 Nov 2017 13:36:06: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:36:06: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:36:06: #1 total tags in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:36:06: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:36:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:36:06: #1 tags after filtering in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:36:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:36:06: #1 finished! INFO @ Mon, 13 Nov 2017 13:36:06: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:36:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:36:07: 17000000 INFO @ Mon, 13 Nov 2017 13:36:08: #2 number of paired peaks: 191 WARNING @ Mon, 13 Nov 2017 13:36:08: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 13 Nov 2017 13:36:08: start model_add_line... INFO @ Mon, 13 Nov 2017 13:36:08: start X-correlation... INFO @ Mon, 13 Nov 2017 13:36:09: end of X-cor INFO @ Mon, 13 Nov 2017 13:36:09: #2 finished! INFO @ Mon, 13 Nov 2017 13:36:09: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:36:09: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Mon, 13 Nov 2017 13:36:09: #2.2 Generate R script for model : SRX2576663.05_model.r WARNING @ Mon, 13 Nov 2017 13:36:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:36:09: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Mon, 13 Nov 2017 13:36:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:36:09: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:36:21: 17000000 INFO @ Mon, 13 Nov 2017 13:36:22: 18000000 INFO @ Mon, 13 Nov 2017 13:36:36: 19000000 INFO @ Mon, 13 Nov 2017 13:36:38: 18000000 INFO @ Mon, 13 Nov 2017 13:36:50: 20000000 INFO @ Mon, 13 Nov 2017 13:36:55: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:36:55: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:36:55: #1 total tags in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:36:55: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:36:55: 19000000 INFO @ Mon, 13 Nov 2017 13:36:55: #1 tags after filtering in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:36:55: #1 finished! INFO @ Mon, 13 Nov 2017 13:36:55: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:36:56: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:57: #2 number of paired peaks: 191 WARNING @ Mon, 13 Nov 2017 13:36:57: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 13 Nov 2017 13:36:57: start model_add_line... INFO @ Mon, 13 Nov 2017 13:36:57: start X-correlation... INFO @ Mon, 13 Nov 2017 13:36:57: end of X-cor INFO @ Mon, 13 Nov 2017 13:36:57: #2 finished! INFO @ Mon, 13 Nov 2017 13:36:57: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:36:57: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Mon, 13 Nov 2017 13:36:57: #2.2 Generate R script for model : SRX2576663.10_model.r WARNING @ Mon, 13 Nov 2017 13:36:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:36:57: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Mon, 13 Nov 2017 13:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:36:57: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:37:14: 20000000 INFO @ Mon, 13 Nov 2017 13:37:18: #4 Write output xls file... SRX2576663.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:37:18: #4 Write peak in narrowPeak format file... SRX2576663.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:37:18: #4 Write summits bed file... SRX2576663.05_summits.bed INFO @ Mon, 13 Nov 2017 13:37:18: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:37:19: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:37:19: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:37:19: #1 total tags in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:37:19: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:37:20: #1 tags after filtering in treatment: 20261026 INFO @ Mon, 13 Nov 2017 13:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:37:20: #1 finished! INFO @ Mon, 13 Nov 2017 13:37:20: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:37:21: #2 number of paired peaks: 191 WARNING @ Mon, 13 Nov 2017 13:37:21: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Mon, 13 Nov 2017 13:37:21: start model_add_line... INFO @ Mon, 13 Nov 2017 13:37:22: start X-correlation... INFO @ Mon, 13 Nov 2017 13:37:22: end of X-cor INFO @ Mon, 13 Nov 2017 13:37:22: #2 finished! INFO @ Mon, 13 Nov 2017 13:37:22: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:37:22: #2 alternative fragment length(s) may be 1,49,577 bps INFO @ Mon, 13 Nov 2017 13:37:22: #2.2 Generate R script for model : SRX2576663.20_model.r WARNING @ Mon, 13 Nov 2017 13:37:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:37:22: #2 You may need to consider one of the other alternative d(s): 1,49,577 WARNING @ Mon, 13 Nov 2017 13:37:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:37:22: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:37:40: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:38:01: #4 Write output xls file... SRX2576663.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:38:01: #4 Write peak in narrowPeak format file... SRX2576663.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:38:01: #4 Write summits bed file... SRX2576663.10_summits.bed INFO @ Mon, 13 Nov 2017 13:38:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:38:05: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:38:26: #4 Write output xls file... SRX2576663.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:38:26: #4 Write peak in narrowPeak format file... SRX2576663.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:38:26: #4 Write summits bed file... SRX2576663.20_summits.bed INFO @ Mon, 13 Nov 2017 13:38:26: 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。