Job ID = 10845156 sra ファイルのダウンロード中... Completed: 1267787K bytes transferred in 90 seconds (114902K 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 25229792 spots for /home/okishinya/chipatlas/results/ce10/SRX2973396/SRR5786973.sra Written 25229792 spots for /home/okishinya/chipatlas/results/ce10/SRX2973396/SRR5786973.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: 00:13:15 25229792 reads; of these: 25229792 (100.00%) were unpaired; of these: 2189594 (8.68%) aligned 0 times 19319153 (76.57%) aligned exactly 1 time 3721045 (14.75%) aligned >1 times 91.32% overall alignment rate Time searching: 00:13:15 Overall time: 00:13:15 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] 2626364 / 23040198 = 0.1140 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 09:49:45: # Command line: callpeak -t SRX2973396.bam -f BAM -g ce -n SRX2973396.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2973396.20 # format = BAM # ChIP-seq file = ['SRX2973396.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 09:49:45: # Command line: callpeak -t SRX2973396.bam -f BAM -g ce -n SRX2973396.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2973396.10 # format = BAM # ChIP-seq file = ['SRX2973396.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 09:49:45: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:49:45: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:49:45: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:49:45: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:49:45: # Command line: callpeak -t SRX2973396.bam -f BAM -g ce -n SRX2973396.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2973396.05 # format = BAM # ChIP-seq file = ['SRX2973396.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 09:49:45: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:49:45: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:49:52: 1000000 INFO @ Wed, 04 Jul 2018 09:49:52: 1000000 INFO @ Wed, 04 Jul 2018 09:49:53: 1000000 INFO @ Wed, 04 Jul 2018 09:50:00: 2000000 INFO @ Wed, 04 Jul 2018 09:50:00: 2000000 INFO @ Wed, 04 Jul 2018 09:50:00: 2000000 INFO @ Wed, 04 Jul 2018 09:50:07: 3000000 INFO @ Wed, 04 Jul 2018 09:50:07: 3000000 INFO @ Wed, 04 Jul 2018 09:50:07: 3000000 INFO @ Wed, 04 Jul 2018 09:50:14: 4000000 INFO @ Wed, 04 Jul 2018 09:50:14: 4000000 INFO @ Wed, 04 Jul 2018 09:50:15: 4000000 INFO @ Wed, 04 Jul 2018 09:50:21: 5000000 INFO @ Wed, 04 Jul 2018 09:50:22: 5000000 INFO @ Wed, 04 Jul 2018 09:50:22: 5000000 INFO @ Wed, 04 Jul 2018 09:50:28: 6000000 INFO @ Wed, 04 Jul 2018 09:50:29: 6000000 INFO @ Wed, 04 Jul 2018 09:50:30: 6000000 INFO @ Wed, 04 Jul 2018 09:50:35: 7000000 INFO @ Wed, 04 Jul 2018 09:50:37: 7000000 INFO @ Wed, 04 Jul 2018 09:50:37: 7000000 INFO @ Wed, 04 Jul 2018 09:50:42: 8000000 INFO @ Wed, 04 Jul 2018 09:50:44: 8000000 INFO @ Wed, 04 Jul 2018 09:50:45: 8000000 INFO @ Wed, 04 Jul 2018 09:50:49: 9000000 INFO @ Wed, 04 Jul 2018 09:50:52: 9000000 INFO @ Wed, 04 Jul 2018 09:50:53: 9000000 INFO @ Wed, 04 Jul 2018 09:50:57: 10000000 INFO @ Wed, 04 Jul 2018 09:50:59: 10000000 INFO @ Wed, 04 Jul 2018 09:51:00: 10000000 INFO @ Wed, 04 Jul 2018 09:51:04: 11000000 INFO @ Wed, 04 Jul 2018 09:51:07: 11000000 INFO @ Wed, 04 Jul 2018 09:51:07: 11000000 INFO @ Wed, 04 Jul 2018 09:51:12: 12000000 INFO @ Wed, 04 Jul 2018 09:51:14: 12000000 INFO @ Wed, 04 Jul 2018 09:51:15: 12000000 INFO @ Wed, 04 Jul 2018 09:51:19: 13000000 INFO @ Wed, 04 Jul 2018 09:51:22: 13000000 INFO @ Wed, 04 Jul 2018 09:51:22: 13000000 INFO @ Wed, 04 Jul 2018 09:51:26: 14000000 INFO @ Wed, 04 Jul 2018 09:51:29: 14000000 INFO @ Wed, 04 Jul 2018 09:51:30: 14000000 INFO @ Wed, 04 Jul 2018 09:51:33: 15000000 INFO @ Wed, 04 Jul 2018 09:51:37: 15000000 INFO @ Wed, 04 Jul 2018 09:51:38: 15000000 INFO @ Wed, 04 Jul 2018 09:51:40: 16000000 INFO @ Wed, 04 Jul 2018 09:51:44: 16000000 INFO @ Wed, 04 Jul 2018 09:51:46: 16000000 INFO @ Wed, 04 Jul 2018 09:51:47: 17000000 INFO @ Wed, 04 Jul 2018 09:51:52: 17000000 INFO @ Wed, 04 Jul 2018 09:51:54: 18000000 INFO @ Wed, 04 Jul 2018 09:51:55: 17000000 INFO @ Wed, 04 Jul 2018 09:51:59: 18000000 INFO @ Wed, 04 Jul 2018 09:52:01: 19000000 INFO @ Wed, 04 Jul 2018 09:52:03: 18000000 INFO @ Wed, 04 Jul 2018 09:52:06: 19000000 INFO @ Wed, 04 Jul 2018 09:52:08: 20000000 INFO @ Wed, 04 Jul 2018 09:52:10: 19000000 INFO @ Wed, 04 Jul 2018 09:52:11: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:52:11: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:52:11: #1 total tags in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:11: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:52:11: #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 09:52:11: #1 tags after filtering in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:52:11: #1 finished! INFO @ Wed, 04 Jul 2018 09:52:11: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:52:13: #2 number of paired peaks: 150 WARNING @ Wed, 04 Jul 2018 09:52:13: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Wed, 04 Jul 2018 09:52:13: start model_add_line... INFO @ Wed, 04 Jul 2018 09:52:13: start X-correlation... INFO @ Wed, 04 Jul 2018 09:52:13: end of X-cor INFO @ Wed, 04 Jul 2018 09:52:13: #2 finished! INFO @ Wed, 04 Jul 2018 09:52:13: #2 predicted fragment length is 98 bps INFO @ Wed, 04 Jul 2018 09:52:13: #2 alternative fragment length(s) may be 2,98 bps INFO @ Wed, 04 Jul 2018 09:52:13: #2.2 Generate R script for model : SRX2973396.20_model.r WARNING @ Wed, 04 Jul 2018 09:52:13: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:52:13: #2 You may need to consider one of the other alternative d(s): 2,98 WARNING @ Wed, 04 Jul 2018 09:52:13: #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 09:52:13: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:52:14: 20000000 INFO @ Wed, 04 Jul 2018 09:52:17: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:52:17: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:52:17: #1 total tags in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:17: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:52:17: #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 09:52:17: #1 tags after filtering in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:52:17: #1 finished! INFO @ Wed, 04 Jul 2018 09:52:17: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:52:18: 20000000 INFO @ Wed, 04 Jul 2018 09:52:19: #2 number of paired peaks: 150 WARNING @ Wed, 04 Jul 2018 09:52:19: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Wed, 04 Jul 2018 09:52:19: start model_add_line... INFO @ Wed, 04 Jul 2018 09:52:19: start X-correlation... INFO @ Wed, 04 Jul 2018 09:52:19: end of X-cor INFO @ Wed, 04 Jul 2018 09:52:19: #2 finished! INFO @ Wed, 04 Jul 2018 09:52:19: #2 predicted fragment length is 98 bps INFO @ Wed, 04 Jul 2018 09:52:19: #2 alternative fragment length(s) may be 2,98 bps INFO @ Wed, 04 Jul 2018 09:52:19: #2.2 Generate R script for model : SRX2973396.05_model.r WARNING @ Wed, 04 Jul 2018 09:52:19: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:52:19: #2 You may need to consider one of the other alternative d(s): 2,98 WARNING @ Wed, 04 Jul 2018 09:52:19: #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 09:52:19: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:52:21: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:52:21: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:52:21: #1 total tags in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:21: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:52:21: #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 09:52:22: #1 tags after filtering in treatment: 20413834 INFO @ Wed, 04 Jul 2018 09:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:52:22: #1 finished! INFO @ Wed, 04 Jul 2018 09:52:22: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:52:23: #2 number of paired peaks: 150 WARNING @ Wed, 04 Jul 2018 09:52:23: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Wed, 04 Jul 2018 09:52:23: start model_add_line... INFO @ Wed, 04 Jul 2018 09:52:23: start X-correlation... INFO @ Wed, 04 Jul 2018 09:52:23: end of X-cor INFO @ Wed, 04 Jul 2018 09:52:23: #2 finished! INFO @ Wed, 04 Jul 2018 09:52:23: #2 predicted fragment length is 98 bps INFO @ Wed, 04 Jul 2018 09:52:23: #2 alternative fragment length(s) may be 2,98 bps INFO @ Wed, 04 Jul 2018 09:52:23: #2.2 Generate R script for model : SRX2973396.10_model.r WARNING @ Wed, 04 Jul 2018 09:52:23: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:52:23: #2 You may need to consider one of the other alternative d(s): 2,98 WARNING @ Wed, 04 Jul 2018 09:52:23: #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 09:52:23: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:52:54: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:52:57: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:53:02: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write output xls file... SRX2973396.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write peak in narrowPeak format file... SRX2973396.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write summits bed file... SRX2973396.20_summits.bed INFO @ Wed, 04 Jul 2018 09:53:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write output xls file... SRX2973396.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write peak in narrowPeak format file... SRX2973396.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:14: #4 Write summits bed file... SRX2973396.05_summits.bed INFO @ Wed, 04 Jul 2018 09:53:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:53:19: #4 Write output xls file... SRX2973396.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:19: #4 Write peak in narrowPeak format file... SRX2973396.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:19: #4 Write summits bed file... SRX2973396.10_summits.bed INFO @ Wed, 04 Jul 2018 09:53:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。