Job ID = 11170846 sra ファイルのダウンロード中... Completed: 1016384K bytes transferred in 100 seconds (82660K 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 37460851 spots for /home/okishinya/chipatlas/results/ce10/SRX3583346/SRR6494002.sra Written 37460851 spots for /home/okishinya/chipatlas/results/ce10/SRX3583346/SRR6494002.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: 00:14:05 37460851 reads; of these: 37460851 (100.00%) were unpaired; of these: 3719376 (9.93%) aligned 0 times 28246818 (75.40%) aligned exactly 1 time 5494657 (14.67%) aligned >1 times 90.07% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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 16 files... [bam_rmdupse_core] 8520554 / 33741475 = 0.2525 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 11:51:12: # Command line: callpeak -t SRX3583346.bam -f BAM -g ce -n SRX3583346.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583346.20 # format = BAM # ChIP-seq file = ['SRX3583346.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 11:51:12: # Command line: callpeak -t SRX3583346.bam -f BAM -g ce -n SRX3583346.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583346.05 # format = BAM # ChIP-seq file = ['SRX3583346.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 11:51:12: # Command line: callpeak -t SRX3583346.bam -f BAM -g ce -n SRX3583346.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583346.10 # format = BAM # ChIP-seq file = ['SRX3583346.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 11:51:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:51:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:51:12: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:51:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:51:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:51:12: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:51:19: 1000000 INFO @ Sat, 08 Sep 2018 11:51:20: 1000000 INFO @ Sat, 08 Sep 2018 11:51:20: 1000000 INFO @ Sat, 08 Sep 2018 11:51:27: 2000000 INFO @ Sat, 08 Sep 2018 11:51:27: 2000000 INFO @ Sat, 08 Sep 2018 11:51:27: 2000000 INFO @ Sat, 08 Sep 2018 11:51:35: 3000000 INFO @ Sat, 08 Sep 2018 11:51:35: 3000000 INFO @ Sat, 08 Sep 2018 11:51:35: 3000000 INFO @ Sat, 08 Sep 2018 11:51:42: 4000000 INFO @ Sat, 08 Sep 2018 11:51:43: 4000000 INFO @ Sat, 08 Sep 2018 11:51:43: 4000000 INFO @ Sat, 08 Sep 2018 11:51:50: 5000000 INFO @ Sat, 08 Sep 2018 11:51:51: 5000000 INFO @ Sat, 08 Sep 2018 11:51:51: 5000000 INFO @ Sat, 08 Sep 2018 11:51:58: 6000000 INFO @ Sat, 08 Sep 2018 11:51:58: 6000000 INFO @ Sat, 08 Sep 2018 11:51:58: 6000000 INFO @ Sat, 08 Sep 2018 11:52:05: 7000000 INFO @ Sat, 08 Sep 2018 11:52:06: 7000000 INFO @ Sat, 08 Sep 2018 11:52:06: 7000000 INFO @ Sat, 08 Sep 2018 11:52:12: 8000000 INFO @ Sat, 08 Sep 2018 11:52:14: 8000000 INFO @ Sat, 08 Sep 2018 11:52:14: 8000000 INFO @ Sat, 08 Sep 2018 11:52:20: 9000000 INFO @ Sat, 08 Sep 2018 11:52:21: 9000000 INFO @ Sat, 08 Sep 2018 11:52:22: 9000000 INFO @ Sat, 08 Sep 2018 11:52:27: 10000000 INFO @ Sat, 08 Sep 2018 11:52:29: 10000000 INFO @ Sat, 08 Sep 2018 11:52:29: 10000000 INFO @ Sat, 08 Sep 2018 11:52:34: 11000000 INFO @ Sat, 08 Sep 2018 11:52:37: 11000000 INFO @ Sat, 08 Sep 2018 11:52:37: 11000000 INFO @ Sat, 08 Sep 2018 11:52:42: 12000000 INFO @ Sat, 08 Sep 2018 11:52:45: 12000000 INFO @ Sat, 08 Sep 2018 11:52:45: 12000000 INFO @ Sat, 08 Sep 2018 11:52:49: 13000000 INFO @ Sat, 08 Sep 2018 11:52:52: 13000000 INFO @ Sat, 08 Sep 2018 11:52:53: 13000000 INFO @ Sat, 08 Sep 2018 11:52:56: 14000000 INFO @ Sat, 08 Sep 2018 11:53:00: 14000000 INFO @ Sat, 08 Sep 2018 11:53:00: 14000000 INFO @ Sat, 08 Sep 2018 11:53:04: 15000000 INFO @ Sat, 08 Sep 2018 11:53:08: 15000000 INFO @ Sat, 08 Sep 2018 11:53:08: 15000000 INFO @ Sat, 08 Sep 2018 11:53:11: 16000000 INFO @ Sat, 08 Sep 2018 11:53:16: 16000000 INFO @ Sat, 08 Sep 2018 11:53:16: 16000000 INFO @ Sat, 08 Sep 2018 11:53:18: 17000000 INFO @ Sat, 08 Sep 2018 11:53:23: 17000000 INFO @ Sat, 08 Sep 2018 11:53:24: 17000000 INFO @ Sat, 08 Sep 2018 11:53:25: 18000000 INFO @ Sat, 08 Sep 2018 11:53:31: 18000000 INFO @ Sat, 08 Sep 2018 11:53:32: 18000000 INFO @ Sat, 08 Sep 2018 11:53:33: 19000000 INFO @ Sat, 08 Sep 2018 11:53:39: 19000000 INFO @ Sat, 08 Sep 2018 11:53:39: 19000000 INFO @ Sat, 08 Sep 2018 11:53:40: 20000000 INFO @ Sat, 08 Sep 2018 11:53:47: 20000000 INFO @ Sat, 08 Sep 2018 11:53:47: 21000000 INFO @ Sat, 08 Sep 2018 11:53:47: 20000000 INFO @ Sat, 08 Sep 2018 11:53:54: 22000000 INFO @ Sat, 08 Sep 2018 11:53:55: 21000000 INFO @ Sat, 08 Sep 2018 11:53:55: 21000000 INFO @ Sat, 08 Sep 2018 11:54:02: 23000000 INFO @ Sat, 08 Sep 2018 11:54:02: 22000000 INFO @ Sat, 08 Sep 2018 11:54:03: 22000000 INFO @ Sat, 08 Sep 2018 11:54:09: 24000000 INFO @ Sat, 08 Sep 2018 11:54:10: 23000000 INFO @ Sat, 08 Sep 2018 11:54:11: 23000000 INFO @ Sat, 08 Sep 2018 11:54:16: 25000000 INFO @ Sat, 08 Sep 2018 11:54:18: 24000000 INFO @ Sat, 08 Sep 2018 11:54:18: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:54:18: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:54:18: #1 total tags in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:18: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:54:18: #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 11:54:19: 24000000 INFO @ Sat, 08 Sep 2018 11:54:19: #1 tags after filtering in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:54:19: #1 finished! INFO @ Sat, 08 Sep 2018 11:54:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:54:21: #2 number of paired peaks: 132 WARNING @ Sat, 08 Sep 2018 11:54:21: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 08 Sep 2018 11:54:21: start model_add_line... INFO @ Sat, 08 Sep 2018 11:54:21: start X-correlation... INFO @ Sat, 08 Sep 2018 11:54:21: end of X-cor INFO @ Sat, 08 Sep 2018 11:54:21: #2 finished! INFO @ Sat, 08 Sep 2018 11:54:21: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:54:21: #2 alternative fragment length(s) may be 1,12,33,587 bps INFO @ Sat, 08 Sep 2018 11:54:21: #2.2 Generate R script for model : SRX3583346.10_model.r WARNING @ Sat, 08 Sep 2018 11:54:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:54:21: #2 You may need to consider one of the other alternative d(s): 1,12,33,587 WARNING @ Sat, 08 Sep 2018 11:54:21: #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 11:54:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:54:26: 25000000 INFO @ Sat, 08 Sep 2018 11:54:26: 25000000 INFO @ Sat, 08 Sep 2018 11:54:27: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:54:27: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:54:27: #1 total tags in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:54:27: #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 11:54:28: #1 tags after filtering in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:54:28: #1 finished! INFO @ Sat, 08 Sep 2018 11:54:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:54:28: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:54:28: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:54:28: #1 total tags in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:54:28: #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 11:54:28: #1 tags after filtering in treatment: 25220921 INFO @ Sat, 08 Sep 2018 11:54:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:54:28: #1 finished! INFO @ Sat, 08 Sep 2018 11:54:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:54:30: #2 number of paired peaks: 132 WARNING @ Sat, 08 Sep 2018 11:54:30: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 08 Sep 2018 11:54:30: start model_add_line... INFO @ Sat, 08 Sep 2018 11:54:30: #2 number of paired peaks: 132 WARNING @ Sat, 08 Sep 2018 11:54:30: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 08 Sep 2018 11:54:30: start model_add_line... INFO @ Sat, 08 Sep 2018 11:54:30: start X-correlation... INFO @ Sat, 08 Sep 2018 11:54:30: end of X-cor INFO @ Sat, 08 Sep 2018 11:54:30: #2 finished! INFO @ Sat, 08 Sep 2018 11:54:30: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:54:30: #2 alternative fragment length(s) may be 1,12,33,587 bps INFO @ Sat, 08 Sep 2018 11:54:30: #2.2 Generate R script for model : SRX3583346.05_model.r WARNING @ Sat, 08 Sep 2018 11:54:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:54:30: #2 You may need to consider one of the other alternative d(s): 1,12,33,587 WARNING @ Sat, 08 Sep 2018 11:54:30: #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 11:54:30: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:54:30: start X-correlation... INFO @ Sat, 08 Sep 2018 11:54:30: end of X-cor INFO @ Sat, 08 Sep 2018 11:54:30: #2 finished! INFO @ Sat, 08 Sep 2018 11:54:30: #2 predicted fragment length is 1 bps INFO @ Sat, 08 Sep 2018 11:54:30: #2 alternative fragment length(s) may be 1,12,33,587 bps INFO @ Sat, 08 Sep 2018 11:54:30: #2.2 Generate R script for model : SRX3583346.20_model.r WARNING @ Sat, 08 Sep 2018 11:54:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:54:30: #2 You may need to consider one of the other alternative d(s): 1,12,33,587 WARNING @ Sat, 08 Sep 2018 11:54:30: #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 11:54:30: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:55:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:55:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:55:10: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:55:18: #4 Write output xls file... SRX3583346.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:55:18: #4 Write peak in narrowPeak format file... SRX3583346.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:55:18: #4 Write summits bed file... SRX3583346.10_summits.bed INFO @ Sat, 08 Sep 2018 11:55:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write output xls file... SRX3583346.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write output xls file... SRX3583346.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write peak in narrowPeak format file... SRX3583346.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write peak in narrowPeak format file... SRX3583346.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write summits bed file... SRX3583346.20_summits.bed INFO @ Sat, 08 Sep 2018 11:55:28: #4 Write summits bed file... SRX3583346.05_summits.bed INFO @ Sat, 08 Sep 2018 11:55:28: Done! INFO @ Sat, 08 Sep 2018 11:55:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。