Job ID = 9730417 sra ファイルのダウンロード中... Completed: 512750K bytes transferred in 9 seconds (452252K 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 12484521 spots for /home/okishinya/chipatlas/results/ce10/SRX2582951/SRR5279126.sra Written 12484521 spots total Written 12852280 spots for /home/okishinya/chipatlas/results/ce10/SRX2582951/SRR5279125.sra Written 12852280 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: 00:05:51 25336801 reads; of these: 25336801 (100.00%) were unpaired; of these: 3556709 (14.04%) aligned 0 times 18198837 (71.83%) aligned exactly 1 time 3581255 (14.13%) aligned >1 times 85.96% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 2264533 / 21780092 = 0.1040 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 01:04:49: # Command line: callpeak -t SRX2582951.bam -f BAM -g ce -n SRX2582951.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2582951.10 # format = BAM # ChIP-seq file = ['SRX2582951.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 01:04:49: # Command line: callpeak -t SRX2582951.bam -f BAM -g ce -n SRX2582951.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2582951.05 # format = BAM # ChIP-seq file = ['SRX2582951.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 01:04:49: # Command line: callpeak -t SRX2582951.bam -f BAM -g ce -n SRX2582951.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2582951.20 # format = BAM # ChIP-seq file = ['SRX2582951.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 01:04:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:49: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:04:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:04:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:04:49: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:04:56: 1000000 INFO @ Sun, 03 Sep 2017 01:04:56: 1000000 INFO @ Sun, 03 Sep 2017 01:04:56: 1000000 INFO @ Sun, 03 Sep 2017 01:05:03: 2000000 INFO @ Sun, 03 Sep 2017 01:05:03: 2000000 INFO @ Sun, 03 Sep 2017 01:05:03: 2000000 INFO @ Sun, 03 Sep 2017 01:05:11: 3000000 INFO @ Sun, 03 Sep 2017 01:05:11: 3000000 INFO @ Sun, 03 Sep 2017 01:05:12: 3000000 INFO @ Sun, 03 Sep 2017 01:05:20: 4000000 INFO @ Sun, 03 Sep 2017 01:05:20: 4000000 INFO @ Sun, 03 Sep 2017 01:05:21: 4000000 INFO @ Sun, 03 Sep 2017 01:05:29: 5000000 INFO @ Sun, 03 Sep 2017 01:05:29: 5000000 INFO @ Sun, 03 Sep 2017 01:05:29: 5000000 INFO @ Sun, 03 Sep 2017 01:05:37: 6000000 INFO @ Sun, 03 Sep 2017 01:05:37: 6000000 INFO @ Sun, 03 Sep 2017 01:05:38: 6000000 INFO @ Sun, 03 Sep 2017 01:05:46: 7000000 INFO @ Sun, 03 Sep 2017 01:05:46: 7000000 INFO @ Sun, 03 Sep 2017 01:05:46: 7000000 INFO @ Sun, 03 Sep 2017 01:05:54: 8000000 INFO @ Sun, 03 Sep 2017 01:05:54: 8000000 INFO @ Sun, 03 Sep 2017 01:05:54: 8000000 INFO @ Sun, 03 Sep 2017 01:06:03: 9000000 INFO @ Sun, 03 Sep 2017 01:06:03: 9000000 INFO @ Sun, 03 Sep 2017 01:06:03: 9000000 INFO @ Sun, 03 Sep 2017 01:06:11: 10000000 INFO @ Sun, 03 Sep 2017 01:06:11: 10000000 INFO @ Sun, 03 Sep 2017 01:06:11: 10000000 INFO @ Sun, 03 Sep 2017 01:06:20: 11000000 INFO @ Sun, 03 Sep 2017 01:06:20: 11000000 INFO @ Sun, 03 Sep 2017 01:06:20: 11000000 INFO @ Sun, 03 Sep 2017 01:06:28: 12000000 INFO @ Sun, 03 Sep 2017 01:06:28: 12000000 INFO @ Sun, 03 Sep 2017 01:06:28: 12000000 INFO @ Sun, 03 Sep 2017 01:06:36: 13000000 INFO @ Sun, 03 Sep 2017 01:06:36: 13000000 INFO @ Sun, 03 Sep 2017 01:06:37: 13000000 INFO @ Sun, 03 Sep 2017 01:06:44: 14000000 INFO @ Sun, 03 Sep 2017 01:06:44: 14000000 INFO @ Sun, 03 Sep 2017 01:06:47: 14000000 INFO @ Sun, 03 Sep 2017 01:06:52: 15000000 INFO @ Sun, 03 Sep 2017 01:06:52: 15000000 INFO @ Sun, 03 Sep 2017 01:06:56: 15000000 INFO @ Sun, 03 Sep 2017 01:07:00: 16000000 INFO @ Sun, 03 Sep 2017 01:07:00: 16000000 INFO @ Sun, 03 Sep 2017 01:07:06: 16000000 INFO @ Sun, 03 Sep 2017 01:07:08: 17000000 INFO @ Sun, 03 Sep 2017 01:07:08: 17000000 INFO @ Sun, 03 Sep 2017 01:07:15: 17000000 INFO @ Sun, 03 Sep 2017 01:07:16: 18000000 INFO @ Sun, 03 Sep 2017 01:07:16: 18000000 INFO @ Sun, 03 Sep 2017 01:07:24: 19000000 INFO @ Sun, 03 Sep 2017 01:07:24: 19000000 INFO @ Sun, 03 Sep 2017 01:07:25: 18000000 INFO @ Sun, 03 Sep 2017 01:07:28: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:07:28: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:07:28: #1 total tags in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:28: #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 01:07:28: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:07:28: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:07:28: #1 total tags in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:28: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:28: #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 01:07:28: #1 tags after filtering in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:28: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:28: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:28: #1 tags after filtering in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:28: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:28: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:29: #2 number of paired peaks: 146 WARNING @ Sun, 03 Sep 2017 01:07:29: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:29: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:29: #2 number of paired peaks: 146 WARNING @ Sun, 03 Sep 2017 01:07:29: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:29: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:30: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:30: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:30: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:30: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:30: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:30: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:30: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:07:30: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:07:30: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Sun, 03 Sep 2017 01:07:30: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Sun, 03 Sep 2017 01:07:30: #2.2 Generate R script for model : SRX2582951.10_model.r INFO @ Sun, 03 Sep 2017 01:07:30: #2.2 Generate R script for model : SRX2582951.05_model.r WARNING @ Sun, 03 Sep 2017 01:07:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:30: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Sun, 03 Sep 2017 01:07:30: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Sun, 03 Sep 2017 01:07:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 03 Sep 2017 01:07:30: #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 01:07:30: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:30: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:07:34: 19000000 INFO @ Sun, 03 Sep 2017 01:07:39: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:07:39: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:07:39: #1 total tags in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:39: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:07:39: #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 01:07:39: #1 tags after filtering in treatment: 19515559 INFO @ Sun, 03 Sep 2017 01:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:07:39: #1 finished! INFO @ Sun, 03 Sep 2017 01:07:39: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:07:41: #2 number of paired peaks: 146 WARNING @ Sun, 03 Sep 2017 01:07:41: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sun, 03 Sep 2017 01:07:41: start model_add_line... INFO @ Sun, 03 Sep 2017 01:07:41: start X-correlation... INFO @ Sun, 03 Sep 2017 01:07:41: end of X-cor INFO @ Sun, 03 Sep 2017 01:07:41: #2 finished! INFO @ Sun, 03 Sep 2017 01:07:41: #2 predicted fragment length is 45 bps INFO @ Sun, 03 Sep 2017 01:07:41: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Sun, 03 Sep 2017 01:07:41: #2.2 Generate R script for model : SRX2582951.20_model.r WARNING @ Sun, 03 Sep 2017 01:07:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:07:41: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Sun, 03 Sep 2017 01:07:41: #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 01:07:41: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:08:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:17: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:08:21: #4 Write output xls file... SRX2582951.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:22: #4 Write peak in narrowPeak format file... SRX2582951.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:22: #4 Write summits bed file... SRX2582951.05_summits.bed INFO @ Sun, 03 Sep 2017 01:08:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1554 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:08:25: #4 Write output xls file... SRX2582951.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:25: #4 Write peak in narrowPeak format file... SRX2582951.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:25: #4 Write summits bed file... SRX2582951.10_summits.bed INFO @ Sun, 03 Sep 2017 01:08:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:08:36: #4 Write output xls file... SRX2582951.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:08:36: #4 Write peak in narrowPeak format file... SRX2582951.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:08:36: #4 Write summits bed file... SRX2582951.20_summits.bed INFO @ Sun, 03 Sep 2017 01:08:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。