Job ID = 10201995 sra ファイルのダウンロード中... Completed: 762784K bytes transferred in 13 seconds (457758K 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... Written 22624236 spots for /home/okishinya/chipatlas/results/ce10/SRX2576664/SRR5272621.sra Written 22624236 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:12:46 22624236 reads; of these: 22624236 (100.00%) were unpaired; of these: 895657 (3.96%) aligned 0 times 18042566 (79.75%) aligned exactly 1 time 3686013 (16.29%) aligned >1 times 96.04% overall alignment rate Time searching: 00:12:46 Overall time: 00:12:46 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] 2785736 / 21728579 = 0.1282 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, 13 Nov 2017 13:31:27: # Command line: callpeak -t SRX2576664.bam -f BAM -g ce -n SRX2576664.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576664.20 # format = BAM # ChIP-seq file = ['SRX2576664.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, 13 Nov 2017 13:31:27: # Command line: callpeak -t SRX2576664.bam -f BAM -g ce -n SRX2576664.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576664.05 # format = BAM # ChIP-seq file = ['SRX2576664.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, 13 Nov 2017 13:31:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:31:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:31:27: # Command line: callpeak -t SRX2576664.bam -f BAM -g ce -n SRX2576664.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576664.10 # format = BAM # ChIP-seq file = ['SRX2576664.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, 13 Nov 2017 13:31:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:31:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:31:27: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:31:27: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:31:36: 1000000 INFO @ Mon, 13 Nov 2017 13:31:44: 1000000 INFO @ Mon, 13 Nov 2017 13:31:44: 1000000 INFO @ Mon, 13 Nov 2017 13:31:45: 2000000 INFO @ Mon, 13 Nov 2017 13:31:54: 3000000 INFO @ Mon, 13 Nov 2017 13:32:00: 2000000 INFO @ Mon, 13 Nov 2017 13:32:00: 2000000 INFO @ Mon, 13 Nov 2017 13:32:02: 4000000 INFO @ Mon, 13 Nov 2017 13:32:10: 5000000 INFO @ Mon, 13 Nov 2017 13:32:16: 3000000 INFO @ Mon, 13 Nov 2017 13:32:19: 3000000 INFO @ Mon, 13 Nov 2017 13:32:19: 6000000 INFO @ Mon, 13 Nov 2017 13:32:28: 4000000 INFO @ Mon, 13 Nov 2017 13:32:29: 7000000 INFO @ Mon, 13 Nov 2017 13:32:37: 4000000 INFO @ Mon, 13 Nov 2017 13:32:39: 8000000 INFO @ Mon, 13 Nov 2017 13:32:40: 5000000 INFO @ Mon, 13 Nov 2017 13:32:48: 9000000 INFO @ Mon, 13 Nov 2017 13:32:51: 6000000 INFO @ Mon, 13 Nov 2017 13:32:55: 5000000 INFO @ Mon, 13 Nov 2017 13:32:57: 10000000 INFO @ Mon, 13 Nov 2017 13:33:03: 7000000 INFO @ Mon, 13 Nov 2017 13:33:06: 11000000 INFO @ Mon, 13 Nov 2017 13:33:14: 6000000 INFO @ Mon, 13 Nov 2017 13:33:14: 8000000 INFO @ Mon, 13 Nov 2017 13:33:16: 12000000 INFO @ Mon, 13 Nov 2017 13:33:25: 9000000 INFO @ Mon, 13 Nov 2017 13:33:26: 13000000 INFO @ Mon, 13 Nov 2017 13:33:34: 7000000 INFO @ Mon, 13 Nov 2017 13:33:36: 14000000 INFO @ Mon, 13 Nov 2017 13:33:36: 10000000 INFO @ Mon, 13 Nov 2017 13:33:45: 15000000 INFO @ Mon, 13 Nov 2017 13:33:47: 11000000 INFO @ Mon, 13 Nov 2017 13:33:53: 8000000 INFO @ Mon, 13 Nov 2017 13:33:55: 16000000 INFO @ Mon, 13 Nov 2017 13:33:58: 12000000 INFO @ Mon, 13 Nov 2017 13:34:04: 17000000 INFO @ Mon, 13 Nov 2017 13:34:10: 13000000 INFO @ Mon, 13 Nov 2017 13:34:13: 9000000 INFO @ Mon, 13 Nov 2017 13:34:13: 18000000 INFO @ Mon, 13 Nov 2017 13:34:21: 14000000 INFO @ Mon, 13 Nov 2017 13:34:22: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:34:22: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:34:22: #1 total tags in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:34:22: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:34:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:34:23: #1 tags after filtering in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:34:23: #1 finished! INFO @ Mon, 13 Nov 2017 13:34:23: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:34:24: #2 number of paired peaks: 226 WARNING @ Mon, 13 Nov 2017 13:34:24: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Mon, 13 Nov 2017 13:34:24: start model_add_line... INFO @ Mon, 13 Nov 2017 13:34:25: start X-correlation... INFO @ Mon, 13 Nov 2017 13:34:25: end of X-cor INFO @ Mon, 13 Nov 2017 13:34:25: #2 finished! INFO @ Mon, 13 Nov 2017 13:34:25: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:34:25: #2 alternative fragment length(s) may be 1,46,526,565 bps INFO @ Mon, 13 Nov 2017 13:34:25: #2.2 Generate R script for model : SRX2576664.05_model.r WARNING @ Mon, 13 Nov 2017 13:34:25: #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, 13 Nov 2017 13:34:25: #2 You may need to consider one of the other alternative d(s): 1,46,526,565 WARNING @ Mon, 13 Nov 2017 13:34:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:34:25: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:34:30: 10000000 INFO @ Mon, 13 Nov 2017 13:34:30: 15000000 INFO @ Mon, 13 Nov 2017 13:34:40: 16000000 INFO @ Mon, 13 Nov 2017 13:34:48: 11000000 INFO @ Mon, 13 Nov 2017 13:34:50: 17000000 INFO @ Mon, 13 Nov 2017 13:35:03: 18000000 INFO @ Mon, 13 Nov 2017 13:35:05: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:35:05: 12000000 INFO @ Mon, 13 Nov 2017 13:35:13: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:35:13: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:35:13: #1 total tags in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:35:13: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:35:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:35:14: #1 tags after filtering in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:35:14: #1 finished! INFO @ Mon, 13 Nov 2017 13:35:14: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:35:15: #2 number of paired peaks: 226 WARNING @ Mon, 13 Nov 2017 13:35:15: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Mon, 13 Nov 2017 13:35:15: start model_add_line... INFO @ Mon, 13 Nov 2017 13:35:16: start X-correlation... INFO @ Mon, 13 Nov 2017 13:35:16: end of X-cor INFO @ Mon, 13 Nov 2017 13:35:16: #2 finished! INFO @ Mon, 13 Nov 2017 13:35:16: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:35:16: #2 alternative fragment length(s) may be 1,46,526,565 bps INFO @ Mon, 13 Nov 2017 13:35:16: #2.2 Generate R script for model : SRX2576664.20_model.r WARNING @ Mon, 13 Nov 2017 13:35:16: #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, 13 Nov 2017 13:35:16: #2 You may need to consider one of the other alternative d(s): 1,46,526,565 WARNING @ Mon, 13 Nov 2017 13:35:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:35:16: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:35:22: 13000000 INFO @ Mon, 13 Nov 2017 13:35:25: #4 Write output xls file... SRX2576664.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:35:25: #4 Write peak in narrowPeak format file... SRX2576664.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:35:25: #4 Write summits bed file... SRX2576664.05_summits.bed INFO @ Mon, 13 Nov 2017 13:35:25: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:35:37: 14000000 INFO @ Mon, 13 Nov 2017 13:35:50: 15000000 INFO @ Mon, 13 Nov 2017 13:35:54: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:36:04: 16000000 INFO @ Mon, 13 Nov 2017 13:36:13: #4 Write output xls file... SRX2576664.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:36:13: #4 Write peak in narrowPeak format file... SRX2576664.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:36:13: #4 Write summits bed file... SRX2576664.20_summits.bed INFO @ Mon, 13 Nov 2017 13:36:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:36:18: 17000000 INFO @ Mon, 13 Nov 2017 13:36:32: 18000000 INFO @ Mon, 13 Nov 2017 13:36:45: #1 tag size is determined as 50 bps INFO @ Mon, 13 Nov 2017 13:36:45: #1 tag size = 50 INFO @ Mon, 13 Nov 2017 13:36:45: #1 total tags in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:36:45: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:36:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:36:46: #1 tags after filtering in treatment: 18942843 INFO @ Mon, 13 Nov 2017 13:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:36:46: #1 finished! INFO @ Mon, 13 Nov 2017 13:36:46: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:36:48: #2 number of paired peaks: 226 WARNING @ Mon, 13 Nov 2017 13:36:48: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Mon, 13 Nov 2017 13:36:48: start model_add_line... INFO @ Mon, 13 Nov 2017 13:36:48: start X-correlation... INFO @ Mon, 13 Nov 2017 13:36:48: end of X-cor INFO @ Mon, 13 Nov 2017 13:36:48: #2 finished! INFO @ Mon, 13 Nov 2017 13:36:48: #2 predicted fragment length is 1 bps INFO @ Mon, 13 Nov 2017 13:36:48: #2 alternative fragment length(s) may be 1,46,526,565 bps INFO @ Mon, 13 Nov 2017 13:36:48: #2.2 Generate R script for model : SRX2576664.10_model.r WARNING @ Mon, 13 Nov 2017 13:36:48: #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, 13 Nov 2017 13:36:48: #2 You may need to consider one of the other alternative d(s): 1,46,526,565 WARNING @ Mon, 13 Nov 2017 13:36:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:36:48: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:37:28: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:37:48: #4 Write output xls file... SRX2576664.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:37:48: #4 Write peak in narrowPeak format file... SRX2576664.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:37:48: #4 Write summits bed file... SRX2576664.10_summits.bed INFO @ Mon, 13 Nov 2017 13:37:48: Done! pass1 - making usageList (0 chroms): 2 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。