Job ID = 10194788 sra ファイルのダウンロード中... Completed: 448125K bytes transferred in 6 seconds (525284K 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 19675533 spots for /home/okishinya/chipatlas/results/rn6/SRX1774920/SRR3544955.sra Written 19675533 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: 00:00:01 Multiseed full-index search: 00:14:10 19675533 reads; of these: 19675533 (100.00%) were unpaired; of these: 956746 (4.86%) aligned 0 times 14158187 (71.96%) aligned exactly 1 time 4560600 (23.18%) aligned >1 times 95.14% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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 8 files... [bam_rmdupse_core] 1561044 / 18718787 = 0.0834 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 @ Fri, 10 Nov 2017 17:27:08: # Command line: callpeak -t SRX1774920.bam -f BAM -g 2.15e9 -n SRX1774920.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774920.20 # format = BAM # ChIP-seq file = ['SRX1774920.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 @ Fri, 10 Nov 2017 17:27:08: # Command line: callpeak -t SRX1774920.bam -f BAM -g 2.15e9 -n SRX1774920.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774920.05 # format = BAM # ChIP-seq file = ['SRX1774920.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 @ Fri, 10 Nov 2017 17:27:08: # Command line: callpeak -t SRX1774920.bam -f BAM -g 2.15e9 -n SRX1774920.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774920.10 # format = BAM # ChIP-seq file = ['SRX1774920.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 @ Fri, 10 Nov 2017 17:27:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:27:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:27:08: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:27:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:27:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:27:08: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:27:16: 1000000 INFO @ Fri, 10 Nov 2017 17:27:17: 1000000 INFO @ Fri, 10 Nov 2017 17:27:17: 1000000 INFO @ Fri, 10 Nov 2017 17:27:23: 2000000 INFO @ Fri, 10 Nov 2017 17:27:26: 2000000 INFO @ Fri, 10 Nov 2017 17:27:26: 2000000 INFO @ Fri, 10 Nov 2017 17:27:29: 3000000 INFO @ Fri, 10 Nov 2017 17:27:35: 3000000 INFO @ Fri, 10 Nov 2017 17:27:35: 3000000 INFO @ Fri, 10 Nov 2017 17:27:36: 4000000 INFO @ Fri, 10 Nov 2017 17:27:43: 5000000 INFO @ Fri, 10 Nov 2017 17:27:44: 4000000 INFO @ Fri, 10 Nov 2017 17:27:44: 4000000 INFO @ Fri, 10 Nov 2017 17:27:50: 6000000 INFO @ Fri, 10 Nov 2017 17:27:53: 5000000 INFO @ Fri, 10 Nov 2017 17:27:53: 5000000 INFO @ Fri, 10 Nov 2017 17:27:57: 7000000 INFO @ Fri, 10 Nov 2017 17:28:01: 6000000 INFO @ Fri, 10 Nov 2017 17:28:01: 6000000 INFO @ Fri, 10 Nov 2017 17:28:04: 8000000 INFO @ Fri, 10 Nov 2017 17:28:10: 7000000 INFO @ Fri, 10 Nov 2017 17:28:10: 7000000 INFO @ Fri, 10 Nov 2017 17:28:11: 9000000 INFO @ Fri, 10 Nov 2017 17:28:18: 10000000 INFO @ Fri, 10 Nov 2017 17:28:19: 8000000 INFO @ Fri, 10 Nov 2017 17:28:19: 8000000 INFO @ Fri, 10 Nov 2017 17:28:25: 11000000 INFO @ Fri, 10 Nov 2017 17:28:28: 9000000 INFO @ Fri, 10 Nov 2017 17:28:28: 9000000 INFO @ Fri, 10 Nov 2017 17:28:32: 12000000 INFO @ Fri, 10 Nov 2017 17:28:37: 10000000 INFO @ Fri, 10 Nov 2017 17:28:37: 10000000 INFO @ Fri, 10 Nov 2017 17:28:38: 13000000 INFO @ Fri, 10 Nov 2017 17:28:45: 14000000 INFO @ Fri, 10 Nov 2017 17:28:46: 11000000 INFO @ Fri, 10 Nov 2017 17:28:46: 11000000 INFO @ Fri, 10 Nov 2017 17:28:52: 15000000 INFO @ Fri, 10 Nov 2017 17:28:55: 12000000 INFO @ Fri, 10 Nov 2017 17:28:55: 12000000 INFO @ Fri, 10 Nov 2017 17:28:59: 16000000 INFO @ Fri, 10 Nov 2017 17:29:04: 13000000 INFO @ Fri, 10 Nov 2017 17:29:04: 13000000 INFO @ Fri, 10 Nov 2017 17:29:06: 17000000 INFO @ Fri, 10 Nov 2017 17:29:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:29:07: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:29:07: #1 total tags in treatment: 17157743 INFO @ Fri, 10 Nov 2017 17:29:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:29:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:29:08: #1 tags after filtering in treatment: 17157593 INFO @ Fri, 10 Nov 2017 17:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:29:08: #1 finished! INFO @ Fri, 10 Nov 2017 17:29:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:29:10: #2 number of paired peaks: 6588 INFO @ Fri, 10 Nov 2017 17:29:10: start model_add_line... INFO @ Fri, 10 Nov 2017 17:29:10: start X-correlation... INFO @ Fri, 10 Nov 2017 17:29:10: end of X-cor INFO @ Fri, 10 Nov 2017 17:29:10: #2 finished! INFO @ Fri, 10 Nov 2017 17:29:10: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Nov 2017 17:29:10: #2 alternative fragment length(s) may be 51,124,195,586 bps INFO @ Fri, 10 Nov 2017 17:29:10: #2.2 Generate R script for model : SRX1774920.05_model.r WARNING @ Fri, 10 Nov 2017 17:29:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:29:10: #2 You may need to consider one of the other alternative d(s): 51,124,195,586 WARNING @ Fri, 10 Nov 2017 17:29:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 17:29:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:29:11: 14000000 INFO @ Fri, 10 Nov 2017 17:29:13: 14000000 INFO @ Fri, 10 Nov 2017 17:29:18: 15000000 INFO @ Fri, 10 Nov 2017 17:29:22: 15000000 INFO @ Fri, 10 Nov 2017 17:29:25: 16000000 INFO @ Fri, 10 Nov 2017 17:29:30: 16000000 INFO @ Fri, 10 Nov 2017 17:29:31: 17000000 INFO @ Fri, 10 Nov 2017 17:29:33: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:29:33: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:29:33: #1 total tags in treatment: 17157743 INFO @ Fri, 10 Nov 2017 17:29:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:29:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:29:33: #1 tags after filtering in treatment: 17157593 INFO @ Fri, 10 Nov 2017 17:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:29:33: #1 finished! INFO @ Fri, 10 Nov 2017 17:29:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:29:35: #2 number of paired peaks: 6588 INFO @ Fri, 10 Nov 2017 17:29:35: start model_add_line... INFO @ Fri, 10 Nov 2017 17:29:35: start X-correlation... INFO @ Fri, 10 Nov 2017 17:29:35: end of X-cor INFO @ Fri, 10 Nov 2017 17:29:35: #2 finished! INFO @ Fri, 10 Nov 2017 17:29:35: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Nov 2017 17:29:35: #2 alternative fragment length(s) may be 51,124,195,586 bps INFO @ Fri, 10 Nov 2017 17:29:35: #2.2 Generate R script for model : SRX1774920.10_model.r WARNING @ Fri, 10 Nov 2017 17:29:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:29:35: #2 You may need to consider one of the other alternative d(s): 51,124,195,586 WARNING @ Fri, 10 Nov 2017 17:29:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 17:29:35: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:29:39: 17000000 INFO @ Fri, 10 Nov 2017 17:29:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:29:40: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:29:40: #1 total tags in treatment: 17157743 INFO @ Fri, 10 Nov 2017 17:29:40: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:29:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:29:41: #1 tags after filtering in treatment: 17157593 INFO @ Fri, 10 Nov 2017 17:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:29:41: #1 finished! INFO @ Fri, 10 Nov 2017 17:29:41: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:29:43: #2 number of paired peaks: 6588 INFO @ Fri, 10 Nov 2017 17:29:43: start model_add_line... INFO @ Fri, 10 Nov 2017 17:29:43: start X-correlation... INFO @ Fri, 10 Nov 2017 17:29:43: end of X-cor INFO @ Fri, 10 Nov 2017 17:29:43: #2 finished! INFO @ Fri, 10 Nov 2017 17:29:43: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Nov 2017 17:29:43: #2 alternative fragment length(s) may be 51,124,195,586 bps INFO @ Fri, 10 Nov 2017 17:29:43: #2.2 Generate R script for model : SRX1774920.20_model.r WARNING @ Fri, 10 Nov 2017 17:29:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 17:29:43: #2 You may need to consider one of the other alternative d(s): 51,124,195,586 WARNING @ Fri, 10 Nov 2017 17:29:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 17:29:43: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:29:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:30:17: #4 Write output xls file... SRX1774920.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:30:17: #4 Write peak in narrowPeak format file... SRX1774920.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:30:17: #4 Write summits bed file... SRX1774920.05_summits.bed INFO @ Fri, 10 Nov 2017 17:30:17: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (972 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:30:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:30:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:30:44: #4 Write output xls file... SRX1774920.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:30:44: #4 Write peak in narrowPeak format file... SRX1774920.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:30:44: #4 Write summits bed file... SRX1774920.10_summits.bed INFO @ Fri, 10 Nov 2017 17:30:44: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (571 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:30:49: #4 Write output xls file... SRX1774920.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:30:49: #4 Write peak in narrowPeak format file... SRX1774920.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:30:49: #4 Write summits bed file... SRX1774920.20_summits.bed INFO @ Fri, 10 Nov 2017 17:30:49: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。