Job ID = 10924594 sra ファイルのダウンロード中... Completed: 1078777K bytes transferred in 41 seconds (214960K 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 21509609 spots for /home/okishinya/chipatlas/results/ce10/SRX4200541/SRR7298007.sra Written 21509609 spots for /home/okishinya/chipatlas/results/ce10/SRX4200541/SRR7298007.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: 00:04:32 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256466 (1.19%) aligned 0 times 17820550 (82.85%) aligned exactly 1 time 3432593 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 3667387 / 21253143 = 0.1726 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 @ Mon, 06 Aug 2018 10:36:30: # Command line: callpeak -t SRX4200541.bam -f BAM -g ce -n SRX4200541.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4200541.05 # format = BAM # ChIP-seq file = ['SRX4200541.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 @ Mon, 06 Aug 2018 10:36:30: # Command line: callpeak -t SRX4200541.bam -f BAM -g ce -n SRX4200541.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4200541.10 # format = BAM # ChIP-seq file = ['SRX4200541.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 @ Mon, 06 Aug 2018 10:36:30: # Command line: callpeak -t SRX4200541.bam -f BAM -g ce -n SRX4200541.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4200541.20 # format = BAM # ChIP-seq file = ['SRX4200541.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 @ Mon, 06 Aug 2018 10:36:30: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:30: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:30: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:36:30: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:30: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:30: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:36:36: 1000000 INFO @ Mon, 06 Aug 2018 10:36:36: 1000000 INFO @ Mon, 06 Aug 2018 10:36:36: 1000000 INFO @ Mon, 06 Aug 2018 10:36:42: 2000000 INFO @ Mon, 06 Aug 2018 10:36:42: 2000000 INFO @ Mon, 06 Aug 2018 10:36:42: 2000000 INFO @ Mon, 06 Aug 2018 10:36:47: 3000000 INFO @ Mon, 06 Aug 2018 10:36:48: 3000000 INFO @ Mon, 06 Aug 2018 10:36:48: 3000000 INFO @ Mon, 06 Aug 2018 10:36:53: 4000000 INFO @ Mon, 06 Aug 2018 10:36:53: 4000000 INFO @ Mon, 06 Aug 2018 10:36:54: 4000000 INFO @ Mon, 06 Aug 2018 10:36:58: 5000000 INFO @ Mon, 06 Aug 2018 10:36:59: 5000000 INFO @ Mon, 06 Aug 2018 10:36:59: 5000000 INFO @ Mon, 06 Aug 2018 10:37:04: 6000000 INFO @ Mon, 06 Aug 2018 10:37:05: 6000000 INFO @ Mon, 06 Aug 2018 10:37:05: 6000000 INFO @ Mon, 06 Aug 2018 10:37:10: 7000000 INFO @ Mon, 06 Aug 2018 10:37:11: 7000000 INFO @ Mon, 06 Aug 2018 10:37:11: 7000000 INFO @ Mon, 06 Aug 2018 10:37:15: 8000000 INFO @ Mon, 06 Aug 2018 10:37:17: 8000000 INFO @ Mon, 06 Aug 2018 10:37:17: 8000000 INFO @ Mon, 06 Aug 2018 10:37:21: 9000000 INFO @ Mon, 06 Aug 2018 10:37:23: 9000000 INFO @ Mon, 06 Aug 2018 10:37:23: 9000000 INFO @ Mon, 06 Aug 2018 10:37:27: 10000000 INFO @ Mon, 06 Aug 2018 10:37:28: 10000000 INFO @ Mon, 06 Aug 2018 10:37:29: 10000000 INFO @ Mon, 06 Aug 2018 10:37:32: 11000000 INFO @ Mon, 06 Aug 2018 10:37:34: 11000000 INFO @ Mon, 06 Aug 2018 10:37:35: 11000000 INFO @ Mon, 06 Aug 2018 10:37:38: 12000000 INFO @ Mon, 06 Aug 2018 10:37:40: 12000000 INFO @ Mon, 06 Aug 2018 10:37:40: 12000000 INFO @ Mon, 06 Aug 2018 10:37:44: 13000000 INFO @ Mon, 06 Aug 2018 10:37:46: 13000000 INFO @ Mon, 06 Aug 2018 10:37:46: 13000000 INFO @ Mon, 06 Aug 2018 10:37:49: 14000000 INFO @ Mon, 06 Aug 2018 10:37:52: 14000000 INFO @ Mon, 06 Aug 2018 10:37:52: 14000000 INFO @ Mon, 06 Aug 2018 10:37:55: 15000000 INFO @ Mon, 06 Aug 2018 10:37:58: 15000000 INFO @ Mon, 06 Aug 2018 10:37:58: 15000000 INFO @ Mon, 06 Aug 2018 10:38:01: 16000000 INFO @ Mon, 06 Aug 2018 10:38:04: 16000000 INFO @ Mon, 06 Aug 2018 10:38:04: 16000000 INFO @ Mon, 06 Aug 2018 10:38:06: 17000000 INFO @ Mon, 06 Aug 2018 10:38:10: #1 tag size is determined as 42 bps INFO @ Mon, 06 Aug 2018 10:38:10: #1 tag size = 42 INFO @ Mon, 06 Aug 2018 10:38:10: #1 total tags in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:10: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:38:10: 17000000 INFO @ Mon, 06 Aug 2018 10:38:10: #1 tags after filtering in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:10: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:10: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:10: 17000000 INFO @ Mon, 06 Aug 2018 10:38:11: #2 number of paired peaks: 213 WARNING @ Mon, 06 Aug 2018 10:38:11: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:11: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:11: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:12: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:12: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:12: #2 predicted fragment length is 1 bps INFO @ Mon, 06 Aug 2018 10:38:12: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 06 Aug 2018 10:38:12: #2.2 Generate R script for model : SRX4200541.20_model.r WARNING @ Mon, 06 Aug 2018 10:38:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:38:12: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 06 Aug 2018 10:38:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:38:12: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:13: #1 tag size is determined as 42 bps INFO @ Mon, 06 Aug 2018 10:38:13: #1 tag size = 42 INFO @ Mon, 06 Aug 2018 10:38:13: #1 total tags in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:13: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:38:14: #1 tags after filtering in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:14: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:14: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:14: #1 tag size is determined as 42 bps INFO @ Mon, 06 Aug 2018 10:38:14: #1 tag size = 42 INFO @ Mon, 06 Aug 2018 10:38:14: #1 total tags in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:14: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:38:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:38:14: #1 tags after filtering in treatment: 17585756 INFO @ Mon, 06 Aug 2018 10:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:38:14: #1 finished! INFO @ Mon, 06 Aug 2018 10:38:14: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:38:15: #2 number of paired peaks: 213 WARNING @ Mon, 06 Aug 2018 10:38:15: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:15: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:15: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:15: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:15: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:15: #2 predicted fragment length is 1 bps INFO @ Mon, 06 Aug 2018 10:38:15: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 06 Aug 2018 10:38:15: #2.2 Generate R script for model : SRX4200541.05_model.r WARNING @ Mon, 06 Aug 2018 10:38:15: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:38:15: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 06 Aug 2018 10:38:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:38:15: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:15: #2 number of paired peaks: 213 WARNING @ Mon, 06 Aug 2018 10:38:15: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 06 Aug 2018 10:38:15: start model_add_line... INFO @ Mon, 06 Aug 2018 10:38:16: start X-correlation... INFO @ Mon, 06 Aug 2018 10:38:16: end of X-cor INFO @ Mon, 06 Aug 2018 10:38:16: #2 finished! INFO @ Mon, 06 Aug 2018 10:38:16: #2 predicted fragment length is 1 bps INFO @ Mon, 06 Aug 2018 10:38:16: #2 alternative fragment length(s) may be 1,38 bps INFO @ Mon, 06 Aug 2018 10:38:16: #2.2 Generate R script for model : SRX4200541.10_model.r WARNING @ Mon, 06 Aug 2018 10:38:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Aug 2018 10:38:16: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Mon, 06 Aug 2018 10:38:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Aug 2018 10:38:16: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:38:41: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:44: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:46: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:38:57: #4 Write output xls file... SRX4200541.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:38:57: #4 Write peak in narrowPeak format file... SRX4200541.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:38:57: #4 Write summits bed file... SRX4200541.20_summits.bed INFO @ Mon, 06 Aug 2018 10:38:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:39:00: #4 Write output xls file... SRX4200541.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:39:00: #4 Write peak in narrowPeak format file... SRX4200541.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:39:00: #4 Write summits bed file... SRX4200541.05_summits.bed INFO @ Mon, 06 Aug 2018 10:39:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 06 Aug 2018 10:39:03: #4 Write output xls file... SRX4200541.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:39:03: #4 Write peak in narrowPeak format file... SRX4200541.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:39:03: #4 Write summits bed file... SRX4200541.10_summits.bed INFO @ Mon, 06 Aug 2018 10:39:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。