Job ID = 10194817 sra ファイルのダウンロード中... Completed: 2016910K bytes transferred in 44 seconds (368627K 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 29730656 spots for /home/okishinya/chipatlas/results/rn6/SRX1926707/SRR3829898.sra Written 29730656 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:52:45 29730656 reads; of these: 29730656 (100.00%) were unpaired; of these: 1264797 (4.25%) aligned 0 times 21556288 (72.51%) aligned exactly 1 time 6909571 (23.24%) aligned >1 times 95.75% overall alignment rate Time searching: 01:52:49 Overall time: 01:52:49 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] 15815543 / 28465859 = 0.5556 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 @ Sat, 11 Nov 2017 00:06:25: # Command line: callpeak -t SRX1926707.bam -f BAM -g 2.15e9 -n SRX1926707.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1926707.10 # format = BAM # ChIP-seq file = ['SRX1926707.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 @ Sat, 11 Nov 2017 00:06:25: # Command line: callpeak -t SRX1926707.bam -f BAM -g 2.15e9 -n SRX1926707.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1926707.20 # format = BAM # ChIP-seq file = ['SRX1926707.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 @ Sat, 11 Nov 2017 00:06:25: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:06:25: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:06:25: # Command line: callpeak -t SRX1926707.bam -f BAM -g 2.15e9 -n SRX1926707.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1926707.05 # format = BAM # ChIP-seq file = ['SRX1926707.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 @ Sat, 11 Nov 2017 00:06:25: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:06:25: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:06:25: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:06:25: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:06:35: 1000000 INFO @ Sat, 11 Nov 2017 00:06:43: 1000000 INFO @ Sat, 11 Nov 2017 00:06:46: 1000000 INFO @ Sat, 11 Nov 2017 00:06:46: 2000000 INFO @ Sat, 11 Nov 2017 00:06:57: 3000000 INFO @ Sat, 11 Nov 2017 00:07:00: 2000000 INFO @ Sat, 11 Nov 2017 00:07:07: 4000000 INFO @ Sat, 11 Nov 2017 00:07:08: 2000000 INFO @ Sat, 11 Nov 2017 00:07:17: 3000000 INFO @ Sat, 11 Nov 2017 00:07:18: 5000000 INFO @ Sat, 11 Nov 2017 00:07:28: 6000000 INFO @ Sat, 11 Nov 2017 00:07:29: 3000000 INFO @ Sat, 11 Nov 2017 00:07:33: 4000000 INFO @ Sat, 11 Nov 2017 00:07:39: 7000000 INFO @ Sat, 11 Nov 2017 00:07:49: 5000000 INFO @ Sat, 11 Nov 2017 00:07:49: 8000000 INFO @ Sat, 11 Nov 2017 00:07:51: 4000000 INFO @ Sat, 11 Nov 2017 00:08:00: 9000000 INFO @ Sat, 11 Nov 2017 00:08:08: 6000000 INFO @ Sat, 11 Nov 2017 00:08:10: 10000000 INFO @ Sat, 11 Nov 2017 00:08:12: 5000000 INFO @ Sat, 11 Nov 2017 00:08:21: 11000000 INFO @ Sat, 11 Nov 2017 00:08:31: 12000000 INFO @ Sat, 11 Nov 2017 00:08:33: 6000000 INFO @ Sat, 11 Nov 2017 00:08:34: 7000000 INFO @ Sat, 11 Nov 2017 00:08:39: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:08:39: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:08:39: #1 total tags in treatment: 12650316 INFO @ Sat, 11 Nov 2017 00:08:39: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:08:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:08:39: #1 tags after filtering in treatment: 12650120 INFO @ Sat, 11 Nov 2017 00:08:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:08:39: #1 finished! INFO @ Sat, 11 Nov 2017 00:08:39: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:08:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:08:42: #2 number of paired peaks: 30124 INFO @ Sat, 11 Nov 2017 00:08:42: start model_add_line... INFO @ Sat, 11 Nov 2017 00:08:43: start X-correlation... INFO @ Sat, 11 Nov 2017 00:08:43: end of X-cor INFO @ Sat, 11 Nov 2017 00:08:43: #2 finished! INFO @ Sat, 11 Nov 2017 00:08:43: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:08:43: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:08:43: #2.2 Generate R script for model : SRX1926707.05_model.r WARNING @ Sat, 11 Nov 2017 00:08:43: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:08:43: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 11 Nov 2017 00:08:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:08:43: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:08:58: 7000000 INFO @ Sat, 11 Nov 2017 00:08:59: 8000000 INFO @ Sat, 11 Nov 2017 00:09:20: 9000000 INFO @ Sat, 11 Nov 2017 00:09:21: 8000000 INFO @ Sat, 11 Nov 2017 00:09:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:09:39: 10000000 INFO @ Sat, 11 Nov 2017 00:09:41: 9000000 INFO @ Sat, 11 Nov 2017 00:09:48: #4 Write output xls file... SRX1926707.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:09:48: #4 Write peak in narrowPeak format file... SRX1926707.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:09:48: #4 Write summits bed file... SRX1926707.05_summits.bed INFO @ Sat, 11 Nov 2017 00:09:48: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (1059 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:09:58: 11000000 INFO @ Sat, 11 Nov 2017 00:10:01: 10000000 INFO @ Sat, 11 Nov 2017 00:10:16: 12000000 INFO @ Sat, 11 Nov 2017 00:10:23: 11000000 INFO @ Sat, 11 Nov 2017 00:10:28: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:10:28: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:10:28: #1 total tags in treatment: 12650316 INFO @ Sat, 11 Nov 2017 00:10:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:10:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:10:29: #1 tags after filtering in treatment: 12650120 INFO @ Sat, 11 Nov 2017 00:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:10:29: #1 finished! INFO @ Sat, 11 Nov 2017 00:10:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:10:32: #2 number of paired peaks: 30124 INFO @ Sat, 11 Nov 2017 00:10:32: start model_add_line... INFO @ Sat, 11 Nov 2017 00:10:32: start X-correlation... INFO @ Sat, 11 Nov 2017 00:10:33: end of X-cor INFO @ Sat, 11 Nov 2017 00:10:33: #2 finished! INFO @ Sat, 11 Nov 2017 00:10:33: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:10:33: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:10:33: #2.2 Generate R script for model : SRX1926707.20_model.r WARNING @ Sat, 11 Nov 2017 00:10:33: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:10:33: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 11 Nov 2017 00:10:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:10:33: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:10:41: 12000000 INFO @ Sat, 11 Nov 2017 00:10:55: #1 tag size is determined as 101 bps INFO @ Sat, 11 Nov 2017 00:10:55: #1 tag size = 101 INFO @ Sat, 11 Nov 2017 00:10:55: #1 total tags in treatment: 12650316 INFO @ Sat, 11 Nov 2017 00:10:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:10:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:10:56: #1 tags after filtering in treatment: 12650120 INFO @ Sat, 11 Nov 2017 00:10:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:10:56: #1 finished! INFO @ Sat, 11 Nov 2017 00:10:56: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:10:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:10:59: #2 number of paired peaks: 30124 INFO @ Sat, 11 Nov 2017 00:10:59: start model_add_line... INFO @ Sat, 11 Nov 2017 00:10:59: start X-correlation... INFO @ Sat, 11 Nov 2017 00:10:59: end of X-cor INFO @ Sat, 11 Nov 2017 00:10:59: #2 finished! INFO @ Sat, 11 Nov 2017 00:10:59: #2 predicted fragment length is 127 bps INFO @ Sat, 11 Nov 2017 00:10:59: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 11 Nov 2017 00:10:59: #2.2 Generate R script for model : SRX1926707.10_model.r WARNING @ Sat, 11 Nov 2017 00:10:59: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:10:59: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 11 Nov 2017 00:10:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:10:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:11:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:39: #4 Write output xls file... SRX1926707.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:39: #4 Write peak in narrowPeak format file... SRX1926707.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:39: #4 Write summits bed file... SRX1926707.20_summits.bed INFO @ Sat, 11 Nov 2017 00:11:39: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:11:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:12:04: #4 Write output xls file... SRX1926707.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:12:04: #4 Write peak in narrowPeak format file... SRX1926707.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:12:04: #4 Write summits bed file... SRX1926707.10_summits.bed INFO @ Sat, 11 Nov 2017 00:12:04: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。