Job ID = 11388796 sra ファイルのダウンロード中... Completed: 241194K bytes transferred in 7 seconds (255774K bits/sec), in 1 file. Completed: 251927K bytes transferred in 8 seconds (233250K 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 11049206 spots for /home/okishinya/chipatlas/results/rn6/SRX3657368/SRR6681053.sra Written 11049206 spots for /home/okishinya/chipatlas/results/rn6/SRX3657368/SRR6681053.sra Read 11408108 spots for /home/okishinya/chipatlas/results/rn6/SRX3657368/SRR6681054.sra Written 11408108 spots for /home/okishinya/chipatlas/results/rn6/SRX3657368/SRR6681054.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: 00:40:35 22457314 reads; of these: 22457314 (100.00%) were unpaired; of these: 2124796 (9.46%) aligned 0 times 14973113 (66.67%) aligned exactly 1 time 5359405 (23.86%) aligned >1 times 90.54% overall alignment rate Time searching: 00:40:39 Overall time: 00:40:39 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] 5949632 / 20332518 = 0.2926 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 23:34:58: # Command line: callpeak -t SRX3657368.bam -f BAM -g 2.15e9 -n SRX3657368.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3657368.05 # format = BAM # ChIP-seq file = ['SRX3657368.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 23:34:58: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:34:58: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:34:59: # Command line: callpeak -t SRX3657368.bam -f BAM -g 2.15e9 -n SRX3657368.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3657368.20 # format = BAM # ChIP-seq file = ['SRX3657368.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 23:34:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:34:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:34:59: # Command line: callpeak -t SRX3657368.bam -f BAM -g 2.15e9 -n SRX3657368.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3657368.10 # format = BAM # ChIP-seq file = ['SRX3657368.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 23:34:59: #1 read tag files... INFO @ Wed, 12 Dec 2018 23:34:59: #1 read treatment tags... INFO @ Wed, 12 Dec 2018 23:35:14: 1000000 INFO @ Wed, 12 Dec 2018 23:35:15: 1000000 INFO @ Wed, 12 Dec 2018 23:35:18: 1000000 INFO @ Wed, 12 Dec 2018 23:35:26: 2000000 INFO @ Wed, 12 Dec 2018 23:35:35: 2000000 INFO @ Wed, 12 Dec 2018 23:35:37: 2000000 INFO @ Wed, 12 Dec 2018 23:35:38: 3000000 INFO @ Wed, 12 Dec 2018 23:35:51: 4000000 INFO @ Wed, 12 Dec 2018 23:35:55: 3000000 INFO @ Wed, 12 Dec 2018 23:35:55: 3000000 INFO @ Wed, 12 Dec 2018 23:36:03: 5000000 INFO @ Wed, 12 Dec 2018 23:36:12: 4000000 INFO @ Wed, 12 Dec 2018 23:36:12: 4000000 INFO @ Wed, 12 Dec 2018 23:36:16: 6000000 INFO @ Wed, 12 Dec 2018 23:36:28: 7000000 INFO @ Wed, 12 Dec 2018 23:36:29: 5000000 INFO @ Wed, 12 Dec 2018 23:36:31: 5000000 INFO @ Wed, 12 Dec 2018 23:36:40: 8000000 INFO @ Wed, 12 Dec 2018 23:36:47: 6000000 INFO @ Wed, 12 Dec 2018 23:36:49: 6000000 INFO @ Wed, 12 Dec 2018 23:36:53: 9000000 INFO @ Wed, 12 Dec 2018 23:37:05: 10000000 INFO @ Wed, 12 Dec 2018 23:37:06: 7000000 INFO @ Wed, 12 Dec 2018 23:37:09: 7000000 INFO @ Wed, 12 Dec 2018 23:37:18: 11000000 INFO @ Wed, 12 Dec 2018 23:37:25: 8000000 INFO @ Wed, 12 Dec 2018 23:37:29: 8000000 INFO @ Wed, 12 Dec 2018 23:37:32: 12000000 INFO @ Wed, 12 Dec 2018 23:37:44: 9000000 INFO @ Wed, 12 Dec 2018 23:37:44: 13000000 INFO @ Wed, 12 Dec 2018 23:37:48: 9000000 INFO @ Wed, 12 Dec 2018 23:37:57: 14000000 INFO @ Wed, 12 Dec 2018 23:38:01: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:38:01: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:38:01: #1 total tags in treatment: 14382886 INFO @ Wed, 12 Dec 2018 23:38:01: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:38:01: #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 23:38:02: #1 tags after filtering in treatment: 14382735 INFO @ Wed, 12 Dec 2018 23:38:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:38:02: #1 finished! INFO @ Wed, 12 Dec 2018 23:38:02: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:38:03: 10000000 INFO @ Wed, 12 Dec 2018 23:38:04: #2 number of paired peaks: 10559 INFO @ Wed, 12 Dec 2018 23:38:04: start model_add_line... INFO @ Wed, 12 Dec 2018 23:38:04: start X-correlation... INFO @ Wed, 12 Dec 2018 23:38:05: end of X-cor INFO @ Wed, 12 Dec 2018 23:38:05: #2 finished! INFO @ Wed, 12 Dec 2018 23:38:05: #2 predicted fragment length is 61 bps INFO @ Wed, 12 Dec 2018 23:38:05: #2 alternative fragment length(s) may be 61 bps INFO @ Wed, 12 Dec 2018 23:38:05: #2.2 Generate R script for model : SRX3657368.10_model.r WARNING @ Wed, 12 Dec 2018 23:38:05: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:38:05: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Wed, 12 Dec 2018 23:38:05: #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 23:38:05: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:38:05: 10000000 INFO @ Wed, 12 Dec 2018 23:38:24: 11000000 INFO @ Wed, 12 Dec 2018 23:38:25: 11000000 INFO @ Wed, 12 Dec 2018 23:38:42: 12000000 INFO @ Wed, 12 Dec 2018 23:38:42: 12000000 INFO @ Wed, 12 Dec 2018 23:38:53: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:39:00: 13000000 INFO @ Wed, 12 Dec 2018 23:39:00: 13000000 INFO @ Wed, 12 Dec 2018 23:39:19: 14000000 INFO @ Wed, 12 Dec 2018 23:39:21: #4 Write output xls file... SRX3657368.10_peaks.xls INFO @ Wed, 12 Dec 2018 23:39:21: 14000000 INFO @ Wed, 12 Dec 2018 23:39:21: #4 Write peak in narrowPeak format file... SRX3657368.10_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:39:21: #4 Write summits bed file... SRX3657368.10_summits.bed INFO @ Wed, 12 Dec 2018 23:39:21: Done! pass1 - making usageList (54 chroms): 5 millis pass2 - checking and writing primary data (1048 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:39:25: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:39:25: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:39:25: #1 total tags in treatment: 14382886 INFO @ Wed, 12 Dec 2018 23:39:25: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:39:25: #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 23:39:26: #1 tags after filtering in treatment: 14382735 INFO @ Wed, 12 Dec 2018 23:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:39:26: #1 finished! INFO @ Wed, 12 Dec 2018 23:39:26: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:39:28: #1 tag size is determined as 50 bps INFO @ Wed, 12 Dec 2018 23:39:28: #1 tag size = 50 INFO @ Wed, 12 Dec 2018 23:39:28: #1 total tags in treatment: 14382886 INFO @ Wed, 12 Dec 2018 23:39:28: #1 user defined the maximum tags... INFO @ Wed, 12 Dec 2018 23:39:28: #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 23:39:28: #2 number of paired peaks: 10559 INFO @ Wed, 12 Dec 2018 23:39:28: start model_add_line... INFO @ Wed, 12 Dec 2018 23:39:29: start X-correlation... INFO @ Wed, 12 Dec 2018 23:39:29: end of X-cor INFO @ Wed, 12 Dec 2018 23:39:29: #2 finished! INFO @ Wed, 12 Dec 2018 23:39:29: #2 predicted fragment length is 61 bps INFO @ Wed, 12 Dec 2018 23:39:29: #2 alternative fragment length(s) may be 61 bps INFO @ Wed, 12 Dec 2018 23:39:29: #2.2 Generate R script for model : SRX3657368.20_model.r WARNING @ Wed, 12 Dec 2018 23:39:29: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:39:29: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Wed, 12 Dec 2018 23:39:29: #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 23:39:29: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:39:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:39:29: #1 tags after filtering in treatment: 14382735 INFO @ Wed, 12 Dec 2018 23:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 12 Dec 2018 23:39:29: #1 finished! INFO @ Wed, 12 Dec 2018 23:39:29: #2 Build Peak Model... INFO @ Wed, 12 Dec 2018 23:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 12 Dec 2018 23:39:31: #2 number of paired peaks: 10559 INFO @ Wed, 12 Dec 2018 23:39:31: start model_add_line... INFO @ Wed, 12 Dec 2018 23:39:31: start X-correlation... INFO @ Wed, 12 Dec 2018 23:39:31: end of X-cor INFO @ Wed, 12 Dec 2018 23:39:31: #2 finished! INFO @ Wed, 12 Dec 2018 23:39:31: #2 predicted fragment length is 61 bps INFO @ Wed, 12 Dec 2018 23:39:31: #2 alternative fragment length(s) may be 61 bps INFO @ Wed, 12 Dec 2018 23:39:31: #2.2 Generate R script for model : SRX3657368.05_model.r WARNING @ Wed, 12 Dec 2018 23:39:31: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 12 Dec 2018 23:39:31: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Wed, 12 Dec 2018 23:39:31: #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 23:39:31: #3 Call peaks... INFO @ Wed, 12 Dec 2018 23:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 12 Dec 2018 23:40:15: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:40:16: #3 Call peaks for each chromosome... INFO @ Wed, 12 Dec 2018 23:40:41: #4 Write output xls file... SRX3657368.20_peaks.xls INFO @ Wed, 12 Dec 2018 23:40:41: #4 Write peak in narrowPeak format file... SRX3657368.20_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:40:41: #4 Write summits bed file... SRX3657368.20_summits.bed INFO @ Wed, 12 Dec 2018 23:40:41: Done! pass1 - making usageList (44 chroms): 3 millis pass2 - checking and writing primary data (424 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 12 Dec 2018 23:40:41: #4 Write output xls file... SRX3657368.05_peaks.xls INFO @ Wed, 12 Dec 2018 23:40:41: #4 Write peak in narrowPeak format file... SRX3657368.05_peaks.narrowPeak INFO @ Wed, 12 Dec 2018 23:40:42: #4 Write summits bed file... SRX3657368.05_summits.bed INFO @ Wed, 12 Dec 2018 23:40:42: Done! pass1 - making usageList (61 chroms): 11 millis pass2 - checking and writing primary data (2443 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。