Job ID = 9730420 sra ファイルのダウンロード中... Completed: 684034K bytes transferred in 10 seconds (554925K bits/sec), in 2 files, 3 directories. 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 16253253 spots for /home/okishinya/chipatlas/results/ce10/SRX2582954/SRR5279132.sra Written 16253253 spots total Written 16504724 spots for /home/okishinya/chipatlas/results/ce10/SRX2582954/SRR5279131.sra Written 16504724 spots total 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: 00:08:38 32757977 reads; of these: 32757977 (100.00%) were unpaired; of these: 343872 (1.05%) aligned 0 times 27271739 (83.25%) aligned exactly 1 time 5142366 (15.70%) aligned >1 times 98.95% overall alignment rate Time searching: 00:08:38 Overall time: 00:08:38 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 16 files... [bam_rmdupse_core] 7146662 / 32414105 = 0.2205 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 Sep 2017 01:10:51: # Command line: callpeak -t SRX2582954.bam -f BAM -g ce -n SRX2582954.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2582954.05 # format = BAM # ChIP-seq file = ['SRX2582954.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 Sep 2017 01:10:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:51: # Command line: callpeak -t SRX2582954.bam -f BAM -g ce -n SRX2582954.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2582954.10 # format = BAM # ChIP-seq file = ['SRX2582954.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 Sep 2017 01:10:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:51: # Command line: callpeak -t SRX2582954.bam -f BAM -g ce -n SRX2582954.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2582954.20 # format = BAM # ChIP-seq file = ['SRX2582954.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 Sep 2017 01:10:51: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:10:51: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:10:58: 1000000 INFO @ Sun, 03 Sep 2017 01:10:58: 1000000 INFO @ Sun, 03 Sep 2017 01:10:58: 1000000 INFO @ Sun, 03 Sep 2017 01:11:05: 2000000 INFO @ Sun, 03 Sep 2017 01:11:05: 2000000 INFO @ Sun, 03 Sep 2017 01:11:05: 2000000 INFO @ Sun, 03 Sep 2017 01:11:13: 3000000 INFO @ Sun, 03 Sep 2017 01:11:13: 3000000 INFO @ Sun, 03 Sep 2017 01:11:13: 3000000 INFO @ Sun, 03 Sep 2017 01:11:20: 4000000 INFO @ Sun, 03 Sep 2017 01:11:20: 4000000 INFO @ Sun, 03 Sep 2017 01:11:20: 4000000 INFO @ Sun, 03 Sep 2017 01:11:27: 5000000 INFO @ Sun, 03 Sep 2017 01:11:27: 5000000 INFO @ Sun, 03 Sep 2017 01:11:27: 5000000 INFO @ Sun, 03 Sep 2017 01:11:35: 6000000 INFO @ Sun, 03 Sep 2017 01:11:35: 6000000 INFO @ Sun, 03 Sep 2017 01:11:35: 6000000 INFO @ Sun, 03 Sep 2017 01:11:42: 7000000 INFO @ Sun, 03 Sep 2017 01:11:42: 7000000 INFO @ Sun, 03 Sep 2017 01:11:42: 7000000 INFO @ Sun, 03 Sep 2017 01:11:49: 8000000 INFO @ Sun, 03 Sep 2017 01:11:49: 8000000 INFO @ Sun, 03 Sep 2017 01:11:49: 8000000 INFO @ Sun, 03 Sep 2017 01:11:57: 9000000 INFO @ Sun, 03 Sep 2017 01:11:57: 9000000 INFO @ Sun, 03 Sep 2017 01:11:57: 9000000 INFO @ Sun, 03 Sep 2017 01:12:04: 10000000 INFO @ Sun, 03 Sep 2017 01:12:04: 10000000 INFO @ Sun, 03 Sep 2017 01:12:04: 10000000 INFO @ Sun, 03 Sep 2017 01:12:12: 11000000 INFO @ Sun, 03 Sep 2017 01:12:12: 11000000 INFO @ Sun, 03 Sep 2017 01:12:12: 11000000 INFO @ Sun, 03 Sep 2017 01:12:18: 12000000 INFO @ Sun, 03 Sep 2017 01:12:19: 12000000 INFO @ Sun, 03 Sep 2017 01:12:19: 12000000 INFO @ Sun, 03 Sep 2017 01:12:25: 13000000 INFO @ Sun, 03 Sep 2017 01:12:26: 13000000 INFO @ Sun, 03 Sep 2017 01:12:26: 13000000 INFO @ Sun, 03 Sep 2017 01:12:33: 14000000 INFO @ Sun, 03 Sep 2017 01:12:34: 14000000 INFO @ Sun, 03 Sep 2017 01:12:34: 14000000 INFO @ Sun, 03 Sep 2017 01:12:40: 15000000 INFO @ Sun, 03 Sep 2017 01:12:41: 15000000 INFO @ Sun, 03 Sep 2017 01:12:41: 15000000 INFO @ Sun, 03 Sep 2017 01:12:48: 16000000 INFO @ Sun, 03 Sep 2017 01:12:49: 16000000 INFO @ Sun, 03 Sep 2017 01:12:49: 16000000 INFO @ Sun, 03 Sep 2017 01:12:56: 17000000 INFO @ Sun, 03 Sep 2017 01:12:57: 17000000 INFO @ Sun, 03 Sep 2017 01:12:57: 17000000 INFO @ Sun, 03 Sep 2017 01:13:04: 18000000 INFO @ Sun, 03 Sep 2017 01:13:05: 18000000 INFO @ Sun, 03 Sep 2017 01:13:05: 18000000 INFO @ Sun, 03 Sep 2017 01:13:12: 19000000 INFO @ Sun, 03 Sep 2017 01:13:13: 19000000 INFO @ Sun, 03 Sep 2017 01:13:13: 19000000 INFO @ Sun, 03 Sep 2017 01:13:19: 20000000 INFO @ Sun, 03 Sep 2017 01:13:20: 20000000 INFO @ Sun, 03 Sep 2017 01:13:20: 20000000 INFO @ Sun, 03 Sep 2017 01:13:27: 21000000 INFO @ Sun, 03 Sep 2017 01:13:28: 21000000 INFO @ Sun, 03 Sep 2017 01:13:28: 21000000 INFO @ Sun, 03 Sep 2017 01:13:35: 22000000 INFO @ Sun, 03 Sep 2017 01:13:36: 22000000 INFO @ Sun, 03 Sep 2017 01:13:36: 22000000 INFO @ Sun, 03 Sep 2017 01:13:43: 23000000 INFO @ Sun, 03 Sep 2017 01:13:44: 23000000 INFO @ Sun, 03 Sep 2017 01:13:44: 23000000 INFO @ Sun, 03 Sep 2017 01:13:51: 24000000 INFO @ Sun, 03 Sep 2017 01:13:51: 24000000 INFO @ Sun, 03 Sep 2017 01:13:51: 24000000 INFO @ Sun, 03 Sep 2017 01:13:58: 25000000 INFO @ Sun, 03 Sep 2017 01:13:59: 25000000 INFO @ Sun, 03 Sep 2017 01:13:59: 25000000 INFO @ Sun, 03 Sep 2017 01:14:00: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:14:00: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:14:00: #1 total tags in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:00: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:14:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:14:01: #1 tags after filtering in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:14:01: #1 finished! INFO @ Sun, 03 Sep 2017 01:14:01: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:14:01: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:14:01: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:14:01: #1 total tags in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:01: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:14:01: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:14:01: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:14:01: #1 total tags in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:01: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:14:02: #1 tags after filtering in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:14:02: #1 finished! INFO @ Sun, 03 Sep 2017 01:14:02: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:14:02: #1 tags after filtering in treatment: 25267443 INFO @ Sun, 03 Sep 2017 01:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:14:02: #1 finished! INFO @ Sun, 03 Sep 2017 01:14:02: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:14:02: #2 number of paired peaks: 123 WARNING @ Sun, 03 Sep 2017 01:14:02: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 03 Sep 2017 01:14:02: start model_add_line... INFO @ Sun, 03 Sep 2017 01:14:03: start X-correlation... INFO @ Sun, 03 Sep 2017 01:14:03: end of X-cor INFO @ Sun, 03 Sep 2017 01:14:03: #2 finished! INFO @ Sun, 03 Sep 2017 01:14:03: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:14:03: #2 alternative fragment length(s) may be 1,47,521,549,581 bps INFO @ Sun, 03 Sep 2017 01:14:03: #2.2 Generate R script for model : SRX2582954.05_model.r WARNING @ Sun, 03 Sep 2017 01:14:03: #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 Sep 2017 01:14:03: #2 You may need to consider one of the other alternative d(s): 1,47,521,549,581 WARNING @ Sun, 03 Sep 2017 01:14:03: #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 Sep 2017 01:14:03: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:14:03: #2 number of paired peaks: 123 WARNING @ Sun, 03 Sep 2017 01:14:03: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 03 Sep 2017 01:14:03: start model_add_line... INFO @ Sun, 03 Sep 2017 01:14:03: #2 number of paired peaks: 123 WARNING @ Sun, 03 Sep 2017 01:14:03: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Sun, 03 Sep 2017 01:14:03: start model_add_line... INFO @ Sun, 03 Sep 2017 01:14:04: start X-correlation... INFO @ Sun, 03 Sep 2017 01:14:04: end of X-cor INFO @ Sun, 03 Sep 2017 01:14:04: #2 finished! INFO @ Sun, 03 Sep 2017 01:14:04: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:14:04: #2 alternative fragment length(s) may be 1,47,521,549,581 bps INFO @ Sun, 03 Sep 2017 01:14:04: #2.2 Generate R script for model : SRX2582954.20_model.r WARNING @ Sun, 03 Sep 2017 01:14:04: #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 Sep 2017 01:14:04: #2 You may need to consider one of the other alternative d(s): 1,47,521,549,581 WARNING @ Sun, 03 Sep 2017 01:14:04: #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 Sep 2017 01:14:04: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:14:04: start X-correlation... INFO @ Sun, 03 Sep 2017 01:14:04: end of X-cor INFO @ Sun, 03 Sep 2017 01:14:04: #2 finished! INFO @ Sun, 03 Sep 2017 01:14:04: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Sep 2017 01:14:04: #2 alternative fragment length(s) may be 1,47,521,549,581 bps INFO @ Sun, 03 Sep 2017 01:14:04: #2.2 Generate R script for model : SRX2582954.10_model.r WARNING @ Sun, 03 Sep 2017 01:14:04: #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 Sep 2017 01:14:04: #2 You may need to consider one of the other alternative d(s): 1,47,521,549,581 WARNING @ Sun, 03 Sep 2017 01:14:04: #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 Sep 2017 01:14:04: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:14:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:14:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:14:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:15:03: #4 Write output xls file... SRX2582954.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:15:03: #4 Write peak in narrowPeak format file... SRX2582954.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:15:03: #4 Write summits bed file... SRX2582954.05_summits.bed INFO @ Sun, 03 Sep 2017 01:15:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:15:04: #4 Write output xls file... SRX2582954.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:15:04: #4 Write peak in narrowPeak format file... SRX2582954.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:15:04: #4 Write summits bed file... SRX2582954.20_summits.bed INFO @ Sun, 03 Sep 2017 01:15:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:15:06: #4 Write output xls file... SRX2582954.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:15:06: #4 Write peak in narrowPeak format file... SRX2582954.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:15:06: #4 Write summits bed file... SRX2582954.10_summits.bed INFO @ Sun, 03 Sep 2017 01:15:06: 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。