Job ID = 11170872 sra ファイルのダウンロード中... Completed: 414482K bytes transferred in 21 seconds (158209K 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 14716059 spots for /home/okishinya/chipatlas/results/ce10/SRX3942556/SRR7010077.sra Written 14716059 spots for /home/okishinya/chipatlas/results/ce10/SRX3942556/SRR7010077.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: 00:00:01 Multiseed full-index search: 00:05:51 14716059 reads; of these: 14716059 (100.00%) were unpaired; of these: 1293076 (8.79%) aligned 0 times 10731357 (72.92%) aligned exactly 1 time 2691626 (18.29%) aligned >1 times 91.21% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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 8 files... [bam_rmdupse_core] 2906080 / 13422983 = 0.2165 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 @ Sat, 08 Sep 2018 11:35:55: # Command line: callpeak -t SRX3942556.bam -f BAM -g ce -n SRX3942556.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942556.10 # format = BAM # ChIP-seq file = ['SRX3942556.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 @ Sat, 08 Sep 2018 11:35:55: # Command line: callpeak -t SRX3942556.bam -f BAM -g ce -n SRX3942556.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942556.05 # format = BAM # ChIP-seq file = ['SRX3942556.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 @ Sat, 08 Sep 2018 11:35:55: # Command line: callpeak -t SRX3942556.bam -f BAM -g ce -n SRX3942556.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942556.20 # format = BAM # ChIP-seq file = ['SRX3942556.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 @ Sat, 08 Sep 2018 11:35:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:35:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:35:55: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:35:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:35:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:35:55: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:01: 1000000 INFO @ Sat, 08 Sep 2018 11:36:01: 1000000 INFO @ Sat, 08 Sep 2018 11:36:02: 1000000 INFO @ Sat, 08 Sep 2018 11:36:08: 2000000 INFO @ Sat, 08 Sep 2018 11:36:08: 2000000 INFO @ Sat, 08 Sep 2018 11:36:09: 2000000 INFO @ Sat, 08 Sep 2018 11:36:15: 3000000 INFO @ Sat, 08 Sep 2018 11:36:15: 3000000 INFO @ Sat, 08 Sep 2018 11:36:16: 3000000 INFO @ Sat, 08 Sep 2018 11:36:22: 4000000 INFO @ Sat, 08 Sep 2018 11:36:23: 4000000 INFO @ Sat, 08 Sep 2018 11:36:24: 4000000 INFO @ Sat, 08 Sep 2018 11:36:29: 5000000 INFO @ Sat, 08 Sep 2018 11:36:30: 5000000 INFO @ Sat, 08 Sep 2018 11:36:32: 5000000 INFO @ Sat, 08 Sep 2018 11:36:37: 6000000 INFO @ Sat, 08 Sep 2018 11:36:38: 6000000 INFO @ Sat, 08 Sep 2018 11:36:40: 6000000 INFO @ Sat, 08 Sep 2018 11:36:44: 7000000 INFO @ Sat, 08 Sep 2018 11:36:45: 7000000 INFO @ Sat, 08 Sep 2018 11:36:48: 7000000 INFO @ Sat, 08 Sep 2018 11:36:51: 8000000 INFO @ Sat, 08 Sep 2018 11:36:52: 8000000 INFO @ Sat, 08 Sep 2018 11:36:56: 8000000 INFO @ Sat, 08 Sep 2018 11:36:58: 9000000 INFO @ Sat, 08 Sep 2018 11:37:00: 9000000 INFO @ Sat, 08 Sep 2018 11:37:04: 9000000 INFO @ Sat, 08 Sep 2018 11:37:06: 10000000 INFO @ Sat, 08 Sep 2018 11:37:07: 10000000 INFO @ Sat, 08 Sep 2018 11:37:09: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:09: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:09: #1 total tags in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:09: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:10: #1 tags after filtering in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:10: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:10: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:10: #2 number of paired peaks: 483 WARNING @ Sat, 08 Sep 2018 11:37:10: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:10: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:10: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:11: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:11: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:11: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:37:11: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sat, 08 Sep 2018 11:37:11: #2.2 Generate R script for model : SRX3942556.10_model.r WARNING @ Sat, 08 Sep 2018 11:37:11: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:11: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sat, 08 Sep 2018 11:37:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:11: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:11: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:11: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:11: #1 total tags in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:11: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:11: #1 tags after filtering in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:11: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:11: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:12: 10000000 INFO @ Sat, 08 Sep 2018 11:37:12: #2 number of paired peaks: 483 WARNING @ Sat, 08 Sep 2018 11:37:12: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:12: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:12: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:12: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:12: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:12: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:37:12: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sat, 08 Sep 2018 11:37:12: #2.2 Generate R script for model : SRX3942556.05_model.r WARNING @ Sat, 08 Sep 2018 11:37:12: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:12: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sat, 08 Sep 2018 11:37:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:12: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:15: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:15: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:15: #1 total tags in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:15: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:37:15: #1 tags after filtering in treatment: 10516903 INFO @ Sat, 08 Sep 2018 11:37:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:15: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:15: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:16: #2 number of paired peaks: 483 WARNING @ Sat, 08 Sep 2018 11:37:16: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Sat, 08 Sep 2018 11:37:16: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:16: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:16: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:16: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:16: #2 predicted fragment length is 66 bps INFO @ Sat, 08 Sep 2018 11:37:16: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sat, 08 Sep 2018 11:37:16: #2.2 Generate R script for model : SRX3942556.20_model.r WARNING @ Sat, 08 Sep 2018 11:37:16: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:16: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sat, 08 Sep 2018 11:37:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:37:16: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:41: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write output xls file... SRX3942556.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write peak in narrowPeak format file... SRX3942556.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write output xls file... SRX3942556.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write summits bed file... SRX3942556.05_summits.bed INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write peak in narrowPeak format file... SRX3942556.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:47: Done! INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write summits bed file... SRX3942556.10_summits.bed INFO @ Sat, 08 Sep 2018 11:37:47: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 3 millis pass2 - checking and writing primary data (2019 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:37:53: #4 Write output xls file... SRX3942556.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:53: #4 Write peak in narrowPeak format file... SRX3942556.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:53: #4 Write summits bed file... SRX3942556.20_summits.bed INFO @ Sat, 08 Sep 2018 11:37:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。