Job ID = 11388814 sra ファイルのダウンロード中... Completed: 235670K bytes transferred in 8 seconds (216828K bits/sec), in 1 file. Completed: 234124K bytes transferred in 9 seconds (195045K 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... Read 10414953 spots for /home/okishinya/chipatlas/results/rn6/SRX3657374/SRR6681066.sra Written 10414953 spots for /home/okishinya/chipatlas/results/rn6/SRX3657374/SRR6681066.sra Read 10435065 spots for /home/okishinya/chipatlas/results/rn6/SRX3657374/SRR6681065.sra Written 10435065 spots for /home/okishinya/chipatlas/results/rn6/SRX3657374/SRR6681065.sra 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 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: 00:33:58 20850018 reads; of these: 20850018 (100.00%) were unpaired; of these: 2164232 (10.38%) aligned 0 times 13493102 (64.72%) aligned exactly 1 time 5192684 (24.90%) aligned >1 times 89.62% overall alignment rate Time searching: 00:34:02 Overall time: 00:34:02 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] 5579270 / 18685786 = 0.2986 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 @ Wed, 12 Dec 2018 23:37:49: # Command line: callpeak -t SRX3657374.bam -f BAM -g 2.15e9 -n SRX3657374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657374.20 # format = BAM # ChIP-seq file = ['SRX3657374.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 @ Wed, 12 Dec 2018 23:37:49: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:37:49: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:37:49: # Command line: callpeak -t SRX3657374.bam -f BAM -g 2.15e9 -n SRX3657374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657374.10 # format = BAM # ChIP-seq file = ['SRX3657374.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 @ Wed, 12 Dec 2018 23:37:49: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:37:49: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:37:49: # Command line: callpeak -t SRX3657374.bam -f BAM -g 2.15e9 -n SRX3657374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657374.05 # format = BAM # ChIP-seq file = ['SRX3657374.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 @ Wed, 12 Dec 2018 23:37:49: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:37:49: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:37:59: 1000000 INFO @ Wed, 12 Dec 2018 23:38:02: 1000000 INFO @ Wed, 12 Dec 2018 23:38:02: 1000000 INFO @ Wed, 12 Dec 2018 23:38:08: 2000000 INFO @ Wed, 12 Dec 2018 23:38:16: 3000000 INFO @ Wed, 12 Dec 2018 23:38:19: 2000000 INFO @ Wed, 12 Dec 2018 23:38:19: 2000000 INFO @ Wed, 12 Dec 2018 23:38:25: 4000000 INFO @ Wed, 12 Dec 2018 23:38:38: 3000000 INFO @ Wed, 12 Dec 2018 23:38:38: 3000000 INFO @ Wed, 12 Dec 2018 23:38:39: 5000000 INFO @ Wed, 12 Dec 2018 23:38:48: 6000000 INFO @ Wed, 12 Dec 2018 23:38:56: 4000000 INFO @ Wed, 12 Dec 2018 23:38:56: 4000000 INFO @ Wed, 12 Dec 2018 23:39:00: 7000000 INFO @ Wed, 12 Dec 2018 23:39:09: 5000000 INFO @ Wed, 12 Dec 2018 23:39:09: 5000000 INFO @ Wed, 12 Dec 2018 23:39:09: 8000000 INFO @ Wed, 12 Dec 2018 23:39:21: 9000000 INFO @ Wed, 12 Dec 2018 23:39:23: 6000000 INFO @ Wed, 12 Dec 2018 23:39:23: 6000000 INFO @ Wed, 12 Dec 2018 23:39:31: 10000000 INFO @ Wed, 12 Dec 2018 23:39:36: 7000000 INFO @ Wed, 12 Dec 2018 23:39:36: 7000000 INFO @ Wed, 12 Dec 2018 23:39:41: 11000000 INFO @ Wed, 12 Dec 2018 23:39:45: 8000000 INFO @ Wed, 12 Dec 2018 23:39:46: 8000000 INFO @ Wed, 12 Dec 2018 23:39:51: 12000000 INFO @ Wed, 12 Dec 2018 23:39:57: 9000000 INFO @ Wed, 12 Dec 2018 23:39:57: 9000000 INFO @ Wed, 12 Dec 2018 23:40:01: 13000000 INFO @ Wed, 12 Dec 2018 23:40:03: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:40:03: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:40:03: #1 total tags in treatment: 13106516 INFO @ Wed, 12 Dec 2018 23:40:03: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:40:03: #1 tags after filtering in treatment: 13106360 INFO @ Wed, 12 Dec 2018 23:40:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:40:03: #1 finished! INFO @ Wed, 12 Dec 2018 23:40:03: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:40:05: #2 number of paired peaks: 6002 INFO @ Wed, 12 Dec 2018 23:40:05: start model_add_line... INFO @ Wed, 12 Dec 2018 23:40:05: start X-correlation... INFO @ Wed, 12 Dec 2018 23:40:05: end of X-cor INFO @ Wed, 12 Dec 2018 23:40:05: #2 finished! INFO @ Wed, 12 Dec 2018 23:40:05: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:40:05: #2 alternative fragment length(s) may be 49,150,224,387,417,510 bps INFO @ Wed, 12 Dec 2018 23:40:05: #2.2 Generate R script for model : SRX3657374.20_model.r WARNING @ Wed, 12 Dec 2018 23:40:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:40:05: #2 You may need to consider one of the other alternative d(s): 49,150,224,387,417,510 WARNING @ Wed, 12 Dec 2018 23:40:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:40:05: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:40:10: 10000000 INFO @ Wed, 12 Dec 2018 23:40:10: 10000000 INFO @ Wed, 12 Dec 2018 23:40:20: 11000000 INFO @ Wed, 12 Dec 2018 23:40:22: 11000000 INFO @ Wed, 12 Dec 2018 23:40:31: 12000000 INFO @ Wed, 12 Dec 2018 23:40:32: 12000000 INFO @ Wed, 12 Dec 2018 23:40:40: 13000000 INFO @ Wed, 12 Dec 2018 23:40:41: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:40:41: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:40:41: #1 total tags in treatment: 13106516 INFO @ Wed, 12 Dec 2018 23:40:41: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:40:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:40:42: #1 tags after filtering in treatment: 13106360 INFO @ Wed, 12 Dec 2018 23:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:40:42: #1 finished! INFO @ Wed, 12 Dec 2018 23:40:42: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:40:42: 13000000 INFO @ Wed, 12 Dec 2018 23:40:44: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:40:44: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:40:44: #1 total tags in treatment: 13106516 INFO @ Wed, 12 Dec 2018 23:40:44: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:40:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 12 Dec 2018 23:40:44: #2 number of paired peaks: 6002 INFO @ Wed, 12 Dec 2018 23:40:44: start model_add_line... INFO @ Wed, 12 Dec 2018 23:40:44: #1 tags after filtering in treatment: 13106360 INFO @ Wed, 12 Dec 2018 23:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:40:44: #1 finished! INFO @ Wed, 12 Dec 2018 23:40:44: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:40:44: start X-correlation... INFO @ Wed, 12 Dec 2018 23:40:44: end of X-cor INFO @ Wed, 12 Dec 2018 23:40:44: #2 finished! INFO @ Wed, 12 Dec 2018 23:40:44: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:40:44: #2 alternative fragment length(s) may be 49,150,224,387,417,510 bps INFO @ Wed, 12 Dec 2018 23:40:44: #2.2 Generate R script for model : SRX3657374.05_model.r WARNING @ Wed, 12 Dec 2018 23:40:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:40:44: #2 You may need to consider one of the other alternative d(s): 49,150,224,387,417,510 WARNING @ Wed, 12 Dec 2018 23:40:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:40:44: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:40:45: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:40:46: #2 number of paired peaks: 6002 INFO @ Wed, 12 Dec 2018 23:40:46: start model_add_line... INFO @ Wed, 12 Dec 2018 23:40:46: start X-correlation... INFO @ Wed, 12 Dec 2018 23:40:46: end of X-cor INFO @ Wed, 12 Dec 2018 23:40:46: #2 finished! INFO @ Wed, 12 Dec 2018 23:40:46: #2 predicted fragment length is 49 bps INFO @ Wed, 12 Dec 2018 23:40:46: #2 alternative fragment length(s) may be 49,150,224,387,417,510 bps INFO @ Wed, 12 Dec 2018 23:40:46: #2.2 Generate R script for model : SRX3657374.10_model.r WARNING @ Wed, 12 Dec 2018 23:40:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:40:46: #2 You may need to consider one of the other alternative d(s): 49,150,224,387,417,510 WARNING @ Wed, 12 Dec 2018 23:40:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 12 Dec 2018 23:40:46: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:41:07: #4 Write output xls file... SRX3657374.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:41:07: #4 Write peak in narrowPeak format file... SRX3657374.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:41:07: #4 Write summits bed file... SRX3657374.20_summits.bed INFO @ Wed, 12 Dec 2018 23:41:07: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (391 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:41:23: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:41:24: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write output xls file... SRX3657374.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write peak in narrowPeak format file... SRX3657374.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write summits bed file... SRX3657374.10_summits.bed INFO @ Wed, 12 Dec 2018 23:41:45: Done! INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write output xls file... SRX3657374.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write peak in narrowPeak format file... SRX3657374.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:41:45: #4 Write summits bed file... SRX3657374.05_summits.bed INFO @ Wed, 12 Dec 2018 23:41:45: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (812 records, 4 fields): 10 millis CompletedMACS2peakCalling pass1 - making usageList (62 chroms): 3 millis pass2 - checking and writing primary data (1313 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。