Job ID = 10845153 sra ファイルのダウンロード中... Completed: 1173908K bytes transferred in 81 seconds (118641K 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 23051447 spots for /home/okishinya/chipatlas/results/ce10/SRX2973390/SRR5786979.sra Written 23051447 spots for /home/okishinya/chipatlas/results/ce10/SRX2973390/SRR5786979.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 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:13 23051447 reads; of these: 23051447 (100.00%) were unpaired; of these: 2727925 (11.83%) aligned 0 times 17725923 (76.90%) aligned exactly 1 time 2597599 (11.27%) aligned >1 times 88.17% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3154957 / 20323522 = 0.1552 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, 04 Jul 2018 09:46:24: # Command line: callpeak -t SRX2973390.bam -f BAM -g ce -n SRX2973390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2973390.10 # format = BAM # ChIP-seq file = ['SRX2973390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Jul 2018 09:46:24: # Command line: callpeak -t SRX2973390.bam -f BAM -g ce -n SRX2973390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2973390.20 # format = BAM # ChIP-seq file = ['SRX2973390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Jul 2018 09:46:24: # Command line: callpeak -t SRX2973390.bam -f BAM -g ce -n SRX2973390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2973390.05 # format = BAM # ChIP-seq file = ['SRX2973390.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 04 Jul 2018 09:46:24: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:24: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:24: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:46:24: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:24: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:24: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:46:33: 1000000 INFO @ Wed, 04 Jul 2018 09:46:33: 1000000 INFO @ Wed, 04 Jul 2018 09:46:33: 1000000 INFO @ Wed, 04 Jul 2018 09:46:41: 2000000 INFO @ Wed, 04 Jul 2018 09:46:42: 2000000 INFO @ Wed, 04 Jul 2018 09:46:42: 2000000 INFO @ Wed, 04 Jul 2018 09:46:50: 3000000 INFO @ Wed, 04 Jul 2018 09:46:50: 3000000 INFO @ Wed, 04 Jul 2018 09:46:51: 3000000 INFO @ Wed, 04 Jul 2018 09:46:59: 4000000 INFO @ Wed, 04 Jul 2018 09:46:59: 4000000 INFO @ Wed, 04 Jul 2018 09:47:00: 4000000 INFO @ Wed, 04 Jul 2018 09:47:07: 5000000 INFO @ Wed, 04 Jul 2018 09:47:09: 5000000 INFO @ Wed, 04 Jul 2018 09:47:10: 5000000 INFO @ Wed, 04 Jul 2018 09:47:16: 6000000 INFO @ Wed, 04 Jul 2018 09:47:18: 6000000 INFO @ Wed, 04 Jul 2018 09:47:19: 6000000 INFO @ Wed, 04 Jul 2018 09:47:24: 7000000 INFO @ Wed, 04 Jul 2018 09:47:27: 7000000 INFO @ Wed, 04 Jul 2018 09:47:29: 7000000 INFO @ Wed, 04 Jul 2018 09:47:33: 8000000 INFO @ Wed, 04 Jul 2018 09:47:36: 8000000 INFO @ Wed, 04 Jul 2018 09:47:38: 8000000 INFO @ Wed, 04 Jul 2018 09:47:41: 9000000 INFO @ Wed, 04 Jul 2018 09:47:45: 9000000 INFO @ Wed, 04 Jul 2018 09:47:48: 9000000 INFO @ Wed, 04 Jul 2018 09:47:50: 10000000 INFO @ Wed, 04 Jul 2018 09:47:54: 10000000 INFO @ Wed, 04 Jul 2018 09:47:57: 10000000 INFO @ Wed, 04 Jul 2018 09:47:58: 11000000 INFO @ Wed, 04 Jul 2018 09:48:03: 11000000 INFO @ Wed, 04 Jul 2018 09:48:06: 11000000 INFO @ Wed, 04 Jul 2018 09:48:07: 12000000 INFO @ Wed, 04 Jul 2018 09:48:13: 12000000 INFO @ Wed, 04 Jul 2018 09:48:16: 13000000 INFO @ Wed, 04 Jul 2018 09:48:16: 12000000 INFO @ Wed, 04 Jul 2018 09:48:22: 13000000 INFO @ Wed, 04 Jul 2018 09:48:24: 14000000 INFO @ Wed, 04 Jul 2018 09:48:25: 13000000 INFO @ Wed, 04 Jul 2018 09:48:31: 14000000 INFO @ Wed, 04 Jul 2018 09:48:33: 15000000 INFO @ Wed, 04 Jul 2018 09:48:35: 14000000 INFO @ Wed, 04 Jul 2018 09:48:40: 15000000 INFO @ Wed, 04 Jul 2018 09:48:42: 16000000 INFO @ Wed, 04 Jul 2018 09:48:44: 15000000 INFO @ Wed, 04 Jul 2018 09:48:49: 16000000 INFO @ Wed, 04 Jul 2018 09:48:50: 17000000 INFO @ Wed, 04 Jul 2018 09:48:51: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:48:51: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:48:51: #1 total tags in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:48:51: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:48:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:48:52: #1 tags after filtering in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:48:52: #1 finished! INFO @ Wed, 04 Jul 2018 09:48:52: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:48:53: #2 number of paired peaks: 1252 INFO @ Wed, 04 Jul 2018 09:48:53: start model_add_line... INFO @ Wed, 04 Jul 2018 09:48:53: start X-correlation... INFO @ Wed, 04 Jul 2018 09:48:53: end of X-cor INFO @ Wed, 04 Jul 2018 09:48:53: #2 finished! INFO @ Wed, 04 Jul 2018 09:48:53: #2 predicted fragment length is 147 bps INFO @ Wed, 04 Jul 2018 09:48:53: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 04 Jul 2018 09:48:53: #2.2 Generate R script for model : SRX2973390.10_model.r WARNING @ Wed, 04 Jul 2018 09:48:53: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:48:53: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 04 Jul 2018 09:48:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:48:53: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:48:54: 16000000 INFO @ Wed, 04 Jul 2018 09:48:58: 17000000 INFO @ Wed, 04 Jul 2018 09:49:00: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:49:00: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:49:00: #1 total tags in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:49:00: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:49:00: #1 tags after filtering in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:49:00: #1 finished! INFO @ Wed, 04 Jul 2018 09:49:00: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:49:02: #2 number of paired peaks: 1252 INFO @ Wed, 04 Jul 2018 09:49:02: start model_add_line... INFO @ Wed, 04 Jul 2018 09:49:02: start X-correlation... INFO @ Wed, 04 Jul 2018 09:49:02: end of X-cor INFO @ Wed, 04 Jul 2018 09:49:02: #2 finished! INFO @ Wed, 04 Jul 2018 09:49:02: #2 predicted fragment length is 147 bps INFO @ Wed, 04 Jul 2018 09:49:02: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 04 Jul 2018 09:49:02: #2.2 Generate R script for model : SRX2973390.20_model.r WARNING @ Wed, 04 Jul 2018 09:49:02: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:49:02: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 04 Jul 2018 09:49:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:49:02: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:49:03: 17000000 INFO @ Wed, 04 Jul 2018 09:49:04: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:49:04: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:49:04: #1 total tags in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:49:04: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:49:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:49:05: #1 tags after filtering in treatment: 17168565 INFO @ Wed, 04 Jul 2018 09:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:49:05: #1 finished! INFO @ Wed, 04 Jul 2018 09:49:05: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:49:06: #2 number of paired peaks: 1252 INFO @ Wed, 04 Jul 2018 09:49:06: start model_add_line... INFO @ Wed, 04 Jul 2018 09:49:06: start X-correlation... INFO @ Wed, 04 Jul 2018 09:49:06: end of X-cor INFO @ Wed, 04 Jul 2018 09:49:06: #2 finished! INFO @ Wed, 04 Jul 2018 09:49:06: #2 predicted fragment length is 147 bps INFO @ Wed, 04 Jul 2018 09:49:06: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 04 Jul 2018 09:49:06: #2.2 Generate R script for model : SRX2973390.05_model.r WARNING @ Wed, 04 Jul 2018 09:49:06: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:49:06: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 04 Jul 2018 09:49:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:49:06: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:49:32: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:49:41: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:49:49: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:49:53: #4 Write output xls file... SRX2973390.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:49:53: #4 Write peak in narrowPeak format file... SRX2973390.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:49:53: #4 Write summits bed file... SRX2973390.10_summits.bed INFO @ Wed, 04 Jul 2018 09:49:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3894 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:50:01: #4 Write output xls file... SRX2973390.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:50:01: #4 Write peak in narrowPeak format file... SRX2973390.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:50:01: #4 Write summits bed file... SRX2973390.20_summits.bed INFO @ Wed, 04 Jul 2018 09:50:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2696 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:50:09: #4 Write output xls file... SRX2973390.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:50:09: #4 Write peak in narrowPeak format file... SRX2973390.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:50:09: #4 Write summits bed file... SRX2973390.05_summits.bed INFO @ Wed, 04 Jul 2018 09:50:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5397 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。