Job ID = 11170871 sra ファイルのダウンロード中... Completed: 456626K bytes transferred in 24 seconds (154035K 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 16348560 spots for /home/okishinya/chipatlas/results/ce10/SRX3942553/SRR7010074.sra Written 16348560 spots for /home/okishinya/chipatlas/results/ce10/SRX3942553/SRR7010074.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: 00:06:25 16348560 reads; of these: 16348560 (100.00%) were unpaired; of these: 2869431 (17.55%) aligned 0 times 10224282 (62.54%) aligned exactly 1 time 3254847 (19.91%) aligned >1 times 82.45% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 6377122 / 13479129 = 0.4731 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 11:36:27: # Command line: callpeak -t SRX3942553.bam -f BAM -g ce -n SRX3942553.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3942553.20 # format = BAM # ChIP-seq file = ['SRX3942553.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 11:36:27: # Command line: callpeak -t SRX3942553.bam -f BAM -g ce -n SRX3942553.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3942553.10 # format = BAM # ChIP-seq file = ['SRX3942553.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 11:36:27: # Command line: callpeak -t SRX3942553.bam -f BAM -g ce -n SRX3942553.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3942553.05 # format = BAM # ChIP-seq file = ['SRX3942553.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 11:36:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:36:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:36:34: 1000000 INFO @ Sat, 08 Sep 2018 11:36:34: 1000000 INFO @ Sat, 08 Sep 2018 11:36:35: 1000000 INFO @ Sat, 08 Sep 2018 11:36:41: 2000000 INFO @ Sat, 08 Sep 2018 11:36:41: 2000000 INFO @ Sat, 08 Sep 2018 11:36:42: 2000000 INFO @ Sat, 08 Sep 2018 11:36:49: 3000000 INFO @ Sat, 08 Sep 2018 11:36:49: 3000000 INFO @ Sat, 08 Sep 2018 11:36:50: 3000000 INFO @ Sat, 08 Sep 2018 11:36:56: 4000000 INFO @ Sat, 08 Sep 2018 11:36:56: 4000000 INFO @ Sat, 08 Sep 2018 11:36:58: 4000000 INFO @ Sat, 08 Sep 2018 11:37:03: 5000000 INFO @ Sat, 08 Sep 2018 11:37:04: 5000000 INFO @ Sat, 08 Sep 2018 11:37:06: 5000000 INFO @ Sat, 08 Sep 2018 11:37:10: 6000000 INFO @ Sat, 08 Sep 2018 11:37:11: 6000000 INFO @ Sat, 08 Sep 2018 11:37:14: 6000000 INFO @ Sat, 08 Sep 2018 11:37:18: 7000000 INFO @ Sat, 08 Sep 2018 11:37:19: 7000000 INFO @ Sat, 08 Sep 2018 11:37:19: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:19: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:19: #1 total tags in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:19: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:19: #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 11:37:19: #1 tags after filtering in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:19: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:19: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:19: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:19: #1 total tags in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:19: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:19: #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 11:37:20: #1 tags after filtering in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:20: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:20: #2 number of paired peaks: 1593 INFO @ Sat, 08 Sep 2018 11:37:20: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:20: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:20: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:20: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:20: #2 predicted fragment length is 83 bps INFO @ Sat, 08 Sep 2018 11:37:20: #2 alternative fragment length(s) may be 2,83 bps INFO @ Sat, 08 Sep 2018 11:37:20: #2.2 Generate R script for model : SRX3942553.10_model.r WARNING @ Sat, 08 Sep 2018 11:37:20: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:20: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Sat, 08 Sep 2018 11:37:20: #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 11:37:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:20: #2 number of paired peaks: 1593 INFO @ Sat, 08 Sep 2018 11:37:20: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:20: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:20: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:20: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:20: #2 predicted fragment length is 83 bps INFO @ Sat, 08 Sep 2018 11:37:20: #2 alternative fragment length(s) may be 2,83 bps INFO @ Sat, 08 Sep 2018 11:37:20: #2.2 Generate R script for model : SRX3942553.05_model.r WARNING @ Sat, 08 Sep 2018 11:37:20: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:20: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Sat, 08 Sep 2018 11:37:20: #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 11:37:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:22: 7000000 INFO @ Sat, 08 Sep 2018 11:37:23: #1 tag size is determined as 75 bps INFO @ Sat, 08 Sep 2018 11:37:23: #1 tag size = 75 INFO @ Sat, 08 Sep 2018 11:37:23: #1 total tags in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:37:23: #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 11:37:23: #1 tags after filtering in treatment: 7102007 INFO @ Sat, 08 Sep 2018 11:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:37:23: #1 finished! INFO @ Sat, 08 Sep 2018 11:37:23: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:37:23: #2 number of paired peaks: 1593 INFO @ Sat, 08 Sep 2018 11:37:23: start model_add_line... INFO @ Sat, 08 Sep 2018 11:37:24: start X-correlation... INFO @ Sat, 08 Sep 2018 11:37:24: end of X-cor INFO @ Sat, 08 Sep 2018 11:37:24: #2 finished! INFO @ Sat, 08 Sep 2018 11:37:24: #2 predicted fragment length is 83 bps INFO @ Sat, 08 Sep 2018 11:37:24: #2 alternative fragment length(s) may be 2,83 bps INFO @ Sat, 08 Sep 2018 11:37:24: #2.2 Generate R script for model : SRX3942553.20_model.r WARNING @ Sat, 08 Sep 2018 11:37:24: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:37:24: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Sat, 08 Sep 2018 11:37:24: #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 11:37:24: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:37:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:37:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write output xls file... SRX3942553.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write peak in narrowPeak format file... SRX3942553.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:47: #4 Write summits bed file... SRX3942553.05_summits.bed INFO @ Sat, 08 Sep 2018 11:37:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:37:48: #4 Write output xls file... SRX3942553.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:48: #4 Write peak in narrowPeak format file... SRX3942553.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:48: #4 Write summits bed file... SRX3942553.10_summits.bed INFO @ Sat, 08 Sep 2018 11:37:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write output xls file... SRX3942553.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write peak in narrowPeak format file... SRX3942553.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:37:50: #4 Write summits bed file... SRX3942553.20_summits.bed INFO @ Sat, 08 Sep 2018 11:37:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (244 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。