Job ID = 9025453 sra ファイルのダウンロード中... Completed: 1184570K bytes transferred in 13 seconds (721582K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1698 0 --:--:-- 0:00:08 --:--:-- 7219 100 46318 0 46318 0 0 4911 0 --:--:-- 0:00:09 --:--:-- 15542 100 73224 0 73224 0 0 7499 0 --:--:-- 0:00:09 --:--:-- 22115 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 38254702 spots for /home/okishinya/chipatlas/results/ce10/SRX1007138/SRR1993098.sra Written 38254702 spots total 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: 00:07:56 38254702 reads; of these: 38254702 (100.00%) were unpaired; of these: 8896895 (23.26%) aligned 0 times 25015198 (65.39%) aligned exactly 1 time 4342609 (11.35%) aligned >1 times 76.74% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 6863665 / 29357807 = 0.2338 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, 03 Jun 2017 04:07:04: # Command line: callpeak -t SRX1007138.bam -f BAM -g ce -n SRX1007138.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007138.05 # format = BAM # ChIP-seq file = ['SRX1007138.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 INFO @ Sat, 03 Jun 2017 04:07:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:04: # Command line: callpeak -t SRX1007138.bam -f BAM -g ce -n SRX1007138.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007138.20 # format = BAM # ChIP-seq file = ['SRX1007138.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 INFO @ Sat, 03 Jun 2017 04:07:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:04: # Command line: callpeak -t SRX1007138.bam -f BAM -g ce -n SRX1007138.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007138.10 # format = BAM # ChIP-seq file = ['SRX1007138.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 INFO @ Sat, 03 Jun 2017 04:07:04: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:04: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:11: 1000000 INFO @ Sat, 03 Jun 2017 04:07:11: 1000000 INFO @ Sat, 03 Jun 2017 04:07:11: 1000000 INFO @ Sat, 03 Jun 2017 04:07:18: 2000000 INFO @ Sat, 03 Jun 2017 04:07:18: 2000000 INFO @ Sat, 03 Jun 2017 04:07:18: 2000000 INFO @ Sat, 03 Jun 2017 04:07:24: 3000000 INFO @ Sat, 03 Jun 2017 04:07:25: 3000000 INFO @ Sat, 03 Jun 2017 04:07:25: 3000000 INFO @ Sat, 03 Jun 2017 04:07:31: 4000000 INFO @ Sat, 03 Jun 2017 04:07:31: 4000000 INFO @ Sat, 03 Jun 2017 04:07:32: 4000000 INFO @ Sat, 03 Jun 2017 04:07:38: 5000000 INFO @ Sat, 03 Jun 2017 04:07:38: 5000000 INFO @ Sat, 03 Jun 2017 04:07:38: 5000000 INFO @ Sat, 03 Jun 2017 04:07:44: 6000000 INFO @ Sat, 03 Jun 2017 04:07:45: 6000000 INFO @ Sat, 03 Jun 2017 04:07:45: 6000000 INFO @ Sat, 03 Jun 2017 04:07:51: 7000000 INFO @ Sat, 03 Jun 2017 04:07:52: 7000000 INFO @ Sat, 03 Jun 2017 04:07:52: 7000000 INFO @ Sat, 03 Jun 2017 04:07:58: 8000000 INFO @ Sat, 03 Jun 2017 04:07:59: 8000000 INFO @ Sat, 03 Jun 2017 04:07:59: 8000000 INFO @ Sat, 03 Jun 2017 04:08:04: 9000000 INFO @ Sat, 03 Jun 2017 04:08:05: 9000000 INFO @ Sat, 03 Jun 2017 04:08:05: 9000000 INFO @ Sat, 03 Jun 2017 04:08:11: 10000000 INFO @ Sat, 03 Jun 2017 04:08:12: 10000000 INFO @ Sat, 03 Jun 2017 04:08:13: 10000000 INFO @ Sat, 03 Jun 2017 04:08:18: 11000000 INFO @ Sat, 03 Jun 2017 04:08:19: 11000000 INFO @ Sat, 03 Jun 2017 04:08:21: 11000000 INFO @ Sat, 03 Jun 2017 04:08:24: 12000000 INFO @ Sat, 03 Jun 2017 04:08:26: 12000000 INFO @ Sat, 03 Jun 2017 04:08:28: 12000000 INFO @ Sat, 03 Jun 2017 04:08:31: 13000000 INFO @ Sat, 03 Jun 2017 04:08:34: 13000000 INFO @ Sat, 03 Jun 2017 04:08:36: 13000000 INFO @ Sat, 03 Jun 2017 04:08:37: 14000000 INFO @ Sat, 03 Jun 2017 04:08:42: 14000000 INFO @ Sat, 03 Jun 2017 04:08:43: 14000000 INFO @ Sat, 03 Jun 2017 04:08:43: 15000000 INFO @ Sat, 03 Jun 2017 04:08:49: 15000000 INFO @ Sat, 03 Jun 2017 04:08:50: 15000000 INFO @ Sat, 03 Jun 2017 04:08:51: 16000000 INFO @ Sat, 03 Jun 2017 04:08:56: 16000000 INFO @ Sat, 03 Jun 2017 04:08:57: 16000000 INFO @ Sat, 03 Jun 2017 04:08:57: 17000000 INFO @ Sat, 03 Jun 2017 04:09:03: 17000000 INFO @ Sat, 03 Jun 2017 04:09:04: 18000000 INFO @ Sat, 03 Jun 2017 04:09:05: 17000000 INFO @ Sat, 03 Jun 2017 04:09:09: 18000000 INFO @ Sat, 03 Jun 2017 04:09:11: 19000000 INFO @ Sat, 03 Jun 2017 04:09:12: 18000000 INFO @ Sat, 03 Jun 2017 04:09:16: 19000000 INFO @ Sat, 03 Jun 2017 04:09:18: 20000000 INFO @ Sat, 03 Jun 2017 04:09:20: 19000000 INFO @ Sat, 03 Jun 2017 04:09:22: 20000000 INFO @ Sat, 03 Jun 2017 04:09:25: 21000000 INFO @ Sat, 03 Jun 2017 04:09:28: 20000000 INFO @ Sat, 03 Jun 2017 04:09:29: 21000000 INFO @ Sat, 03 Jun 2017 04:09:32: 22000000 INFO @ Sat, 03 Jun 2017 04:09:35: 22000000 INFO @ Sat, 03 Jun 2017 04:09:35: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:35: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:35: #1 total tags in treatment: 22494142 INFO @ Sat, 03 Jun 2017 04:09:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:09:35: 21000000 INFO @ Sat, 03 Jun 2017 04:09:39: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:39: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:39: #1 total tags in treatment: 22494142 INFO @ Sat, 03 Jun 2017 04:09:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:09:40: #1 tags after filtering in treatment: 22488271 INFO @ Sat, 03 Jun 2017 04:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:40: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:42: 22000000 INFO @ Sat, 03 Jun 2017 04:09:43: #1 tags after filtering in treatment: 22488271 INFO @ Sat, 03 Jun 2017 04:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:44: #2 number of paired peaks: 576 WARNING @ Sat, 03 Jun 2017 04:09:44: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:44: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:45: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:45: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:45: #1 total tags in treatment: 22494142 INFO @ Sat, 03 Jun 2017 04:09:45: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:09:46: #2 number of paired peaks: 576 WARNING @ Sat, 03 Jun 2017 04:09:46: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:46: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:50: #1 tags after filtering in treatment: 22488271 INFO @ Sat, 03 Jun 2017 04:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:50: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:54: #2 number of paired peaks: 576 WARNING @ Sat, 03 Jun 2017 04:09:54: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:54: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:55: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:55: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:55: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:55: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:09:55: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 04:09:55: #2.2 Generate R script for model : SRX1007138.20_model.r WARNING @ Sat, 03 Jun 2017 04:09:55: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:55: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 04:09:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:09:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:09:58: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:58: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:58: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:58: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:09:58: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 04:09:58: #2.2 Generate R script for model : SRX1007138.10_model.r WARNING @ Sat, 03 Jun 2017 04:09:58: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:58: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 04:09:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:09:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:10:05: start X-correlation... INFO @ Sat, 03 Jun 2017 04:10:05: end of X-cor INFO @ Sat, 03 Jun 2017 04:10:05: #2 finished! INFO @ Sat, 03 Jun 2017 04:10:05: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 04:10:05: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 04:10:05: #2.2 Generate R script for model : SRX1007138.05_model.r WARNING @ Sat, 03 Jun 2017 04:10:05: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:10:05: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 04:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:10:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:11:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:11:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:11:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:48: #4 Write output xls file... SRX1007138.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:48: #4 Write peak in narrowPeak format file... SRX1007138.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:48: #4 Write summits bed file... SRX1007138.20_summits.bed INFO @ Sat, 03 Jun 2017 04:12:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2129 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:12:58: #4 Write output xls file... SRX1007138.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:58: #4 Write peak in narrowPeak format file... SRX1007138.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:58: #4 Write summits bed file... SRX1007138.10_summits.bed INFO @ Sat, 03 Jun 2017 04:12:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5679 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:09: #4 Write output xls file... SRX1007138.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:09: #4 Write peak in narrowPeak format file... SRX1007138.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:09: #4 Write summits bed file... SRX1007138.05_summits.bed INFO @ Sat, 03 Jun 2017 04:13:10: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11416 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。