Job ID = 10487620 sra ファイルのダウンロード中... Completed: 993544K bytes transferred in 107 seconds (75575K 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 25791932 spots for /home/okishinya/chipatlas/results/rn6/SRX3358576/SRR6251635.sra Written 25791932 spots total 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:37 25791932 reads; of these: 25791932 (100.00%) were unpaired; of these: 958207 (3.72%) aligned 0 times 18279663 (70.87%) aligned exactly 1 time 6554062 (25.41%) aligned >1 times 96.28% overall alignment rate Time searching: 00:33:39 Overall time: 00:33:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1234474 / 24833725 = 0.0497 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, 18 Mar 2018 11:04:29: # Command line: callpeak -t SRX3358576.bam -f BAM -g 2.15e9 -n SRX3358576.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358576.20 # format = BAM # ChIP-seq file = ['SRX3358576.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 18 Mar 2018 11:04:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:04:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:04:29: # Command line: callpeak -t SRX3358576.bam -f BAM -g 2.15e9 -n SRX3358576.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358576.05 # format = BAM # ChIP-seq file = ['SRX3358576.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 18 Mar 2018 11:04:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:04:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:04:29: # Command line: callpeak -t SRX3358576.bam -f BAM -g 2.15e9 -n SRX3358576.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358576.10 # format = BAM # ChIP-seq file = ['SRX3358576.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 18 Mar 2018 11:04:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:04:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:04:37: 1000000 INFO @ Sun, 18 Mar 2018 11:04:38: 1000000 INFO @ Sun, 18 Mar 2018 11:04:38: 1000000 INFO @ Sun, 18 Mar 2018 11:04:45: 2000000 INFO @ Sun, 18 Mar 2018 11:04:45: 2000000 INFO @ Sun, 18 Mar 2018 11:04:45: 2000000 INFO @ Sun, 18 Mar 2018 11:04:53: 3000000 INFO @ Sun, 18 Mar 2018 11:04:53: 3000000 INFO @ Sun, 18 Mar 2018 11:04:53: 3000000 INFO @ Sun, 18 Mar 2018 11:05:01: 4000000 INFO @ Sun, 18 Mar 2018 11:05:01: 4000000 INFO @ Sun, 18 Mar 2018 11:05:01: 4000000 INFO @ Sun, 18 Mar 2018 11:05:09: 5000000 INFO @ Sun, 18 Mar 2018 11:05:09: 5000000 INFO @ Sun, 18 Mar 2018 11:05:09: 5000000 INFO @ Sun, 18 Mar 2018 11:05:17: 6000000 INFO @ Sun, 18 Mar 2018 11:05:17: 6000000 INFO @ Sun, 18 Mar 2018 11:05:17: 6000000 INFO @ Sun, 18 Mar 2018 11:05:25: 7000000 INFO @ Sun, 18 Mar 2018 11:05:25: 7000000 INFO @ Sun, 18 Mar 2018 11:05:25: 7000000 INFO @ Sun, 18 Mar 2018 11:05:33: 8000000 INFO @ Sun, 18 Mar 2018 11:05:33: 8000000 INFO @ Sun, 18 Mar 2018 11:05:33: 8000000 INFO @ Sun, 18 Mar 2018 11:05:40: 9000000 INFO @ Sun, 18 Mar 2018 11:05:41: 9000000 INFO @ Sun, 18 Mar 2018 11:05:41: 9000000 INFO @ Sun, 18 Mar 2018 11:05:48: 10000000 INFO @ Sun, 18 Mar 2018 11:05:49: 10000000 INFO @ Sun, 18 Mar 2018 11:05:49: 10000000 INFO @ Sun, 18 Mar 2018 11:05:56: 11000000 INFO @ Sun, 18 Mar 2018 11:05:57: 11000000 INFO @ Sun, 18 Mar 2018 11:05:57: 11000000 INFO @ Sun, 18 Mar 2018 11:06:04: 12000000 INFO @ Sun, 18 Mar 2018 11:06:05: 12000000 INFO @ Sun, 18 Mar 2018 11:06:05: 12000000 INFO @ Sun, 18 Mar 2018 11:06:12: 13000000 INFO @ Sun, 18 Mar 2018 11:06:13: 13000000 INFO @ Sun, 18 Mar 2018 11:06:13: 13000000 INFO @ Sun, 18 Mar 2018 11:06:20: 14000000 INFO @ Sun, 18 Mar 2018 11:06:21: 14000000 INFO @ Sun, 18 Mar 2018 11:06:21: 14000000 INFO @ Sun, 18 Mar 2018 11:06:28: 15000000 INFO @ Sun, 18 Mar 2018 11:06:29: 15000000 INFO @ Sun, 18 Mar 2018 11:06:29: 15000000 INFO @ Sun, 18 Mar 2018 11:06:36: 16000000 INFO @ Sun, 18 Mar 2018 11:06:37: 16000000 INFO @ Sun, 18 Mar 2018 11:06:37: 16000000 INFO @ Sun, 18 Mar 2018 11:06:44: 17000000 INFO @ Sun, 18 Mar 2018 11:06:45: 17000000 INFO @ Sun, 18 Mar 2018 11:06:45: 17000000 INFO @ Sun, 18 Mar 2018 11:06:52: 18000000 INFO @ Sun, 18 Mar 2018 11:06:53: 18000000 INFO @ Sun, 18 Mar 2018 11:06:53: 18000000 INFO @ Sun, 18 Mar 2018 11:06:59: 19000000 INFO @ Sun, 18 Mar 2018 11:07:01: 19000000 INFO @ Sun, 18 Mar 2018 11:07:01: 19000000 INFO @ Sun, 18 Mar 2018 11:07:07: 20000000 INFO @ Sun, 18 Mar 2018 11:07:09: 20000000 INFO @ Sun, 18 Mar 2018 11:07:09: 20000000 INFO @ Sun, 18 Mar 2018 11:07:15: 21000000 INFO @ Sun, 18 Mar 2018 11:07:17: 21000000 INFO @ Sun, 18 Mar 2018 11:07:17: 21000000 INFO @ Sun, 18 Mar 2018 11:07:23: 22000000 INFO @ Sun, 18 Mar 2018 11:07:25: 22000000 INFO @ Sun, 18 Mar 2018 11:07:25: 22000000 INFO @ Sun, 18 Mar 2018 11:07:31: 23000000 INFO @ Sun, 18 Mar 2018 11:07:33: 23000000 INFO @ Sun, 18 Mar 2018 11:07:33: 23000000 INFO @ Sun, 18 Mar 2018 11:07:36: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:07:36: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:07:36: #1 total tags in treatment: 23599251 INFO @ Sun, 18 Mar 2018 11:07:36: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:07:37: #1 tags after filtering in treatment: 23599117 INFO @ Sun, 18 Mar 2018 11:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:37: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:37: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:38: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:07:38: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:07:38: #1 total tags in treatment: 23599251 INFO @ Sun, 18 Mar 2018 11:07:38: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:07:38: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 11:07:38: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 11:07:38: #1 total tags in treatment: 23599251 INFO @ Sun, 18 Mar 2018 11:07:38: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:07:39: #1 tags after filtering in treatment: 23599117 INFO @ Sun, 18 Mar 2018 11:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:39: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:39: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:39: #1 tags after filtering in treatment: 23599117 INFO @ Sun, 18 Mar 2018 11:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:39: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:39: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:39: #2 number of paired peaks: 5449 INFO @ Sun, 18 Mar 2018 11:07:39: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:39: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:39: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:39: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:39: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 11:07:39: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 18 Mar 2018 11:07:39: #2.2 Generate R script for model : SRX3358576.05_model.r WARNING @ Sun, 18 Mar 2018 11:07:39: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:07:39: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 18 Mar 2018 11:07:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:07:39: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:07:41: #2 number of paired peaks: 5449 INFO @ Sun, 18 Mar 2018 11:07:41: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:41: #2 number of paired peaks: 5449 INFO @ Sun, 18 Mar 2018 11:07:41: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:41: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:41: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:41: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:41: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 11:07:41: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 18 Mar 2018 11:07:41: #2.2 Generate R script for model : SRX3358576.10_model.r WARNING @ Sun, 18 Mar 2018 11:07:41: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:07:41: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 18 Mar 2018 11:07:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:07:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:07:41: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:41: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:41: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:41: #2 predicted fragment length is 75 bps INFO @ Sun, 18 Mar 2018 11:07:41: #2 alternative fragment length(s) may be 75 bps INFO @ Sun, 18 Mar 2018 11:07:41: #2.2 Generate R script for model : SRX3358576.20_model.r WARNING @ Sun, 18 Mar 2018 11:07:41: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:07:41: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sun, 18 Mar 2018 11:07:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:07:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:08:32: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:08:34: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:08:35: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:09:04: #4 Write output xls file... SRX3358576.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:09:04: #4 Write peak in narrowPeak format file... SRX3358576.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:09:04: #4 Write summits bed file... SRX3358576.05_summits.bed INFO @ Sun, 18 Mar 2018 11:09:04: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (1309 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:09:07: #4 Write output xls file... SRX3358576.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:09:07: #4 Write peak in narrowPeak format file... SRX3358576.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:09:07: #4 Write summits bed file... SRX3358576.10_summits.bed INFO @ Sun, 18 Mar 2018 11:09:07: Done! pass1 - making usageList (42 chroms): 0 millis pass2 - checking and writing primary data (771 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:09:08: #4 Write output xls file... SRX3358576.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:09:08: #4 Write peak in narrowPeak format file... SRX3358576.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:09:08: #4 Write summits bed file... SRX3358576.20_summits.bed INFO @ Sun, 18 Mar 2018 11:09:08: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。