Job ID = 9025670 sra ファイルのダウンロード中... Completed: 2973648K bytes transferred in 44 seconds (547110K 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 9111 0 9111 0 0 1065 0 --:--:-- 0:00:08 --:--:-- 4281 100 31171 0 31171 0 0 3322 0 --:--:-- 0:00:09 --:--:-- 10534 100 31171 0 31171 0 0 3322 0 --:--:-- 0:00:09 --:--:-- 10530 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 50549812 spots for /home/okishinya/chipatlas/results/ce10/SRX2163950/SRR4242865.sra Written 50549812 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: 00:20:35 50549812 reads; of these: 50549812 (100.00%) were unpaired; of these: 9218870 (18.24%) aligned 0 times 36282528 (71.78%) aligned exactly 1 time 5048414 (9.99%) aligned >1 times 81.76% overall alignment rate Time searching: 00:20:35 Overall time: 00:20:35 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 20 files... [bam_rmdupse_core] 18170379 / 41330942 = 0.4396 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 05:28:23: # Command line: callpeak -t SRX2163950.bam -f BAM -g ce -n SRX2163950.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2163950.20 # format = BAM # ChIP-seq file = ['SRX2163950.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 05:28:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:28:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:28:23: # Command line: callpeak -t SRX2163950.bam -f BAM -g ce -n SRX2163950.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2163950.05 # format = BAM # ChIP-seq file = ['SRX2163950.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 05:28:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:28:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:28:23: # Command line: callpeak -t SRX2163950.bam -f BAM -g ce -n SRX2163950.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2163950.10 # format = BAM # ChIP-seq file = ['SRX2163950.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 05:28:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 05:28:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 05:28:32: 1000000 INFO @ Sat, 03 Jun 2017 05:28:32: 1000000 INFO @ Sat, 03 Jun 2017 05:28:32: 1000000 INFO @ Sat, 03 Jun 2017 05:28:40: 2000000 INFO @ Sat, 03 Jun 2017 05:28:40: 2000000 INFO @ Sat, 03 Jun 2017 05:28:41: 2000000 INFO @ Sat, 03 Jun 2017 05:28:49: 3000000 INFO @ Sat, 03 Jun 2017 05:28:49: 3000000 INFO @ Sat, 03 Jun 2017 05:28:49: 3000000 INFO @ Sat, 03 Jun 2017 05:28:58: 4000000 INFO @ Sat, 03 Jun 2017 05:28:58: 4000000 INFO @ Sat, 03 Jun 2017 05:28:58: 4000000 INFO @ Sat, 03 Jun 2017 05:29:07: 5000000 INFO @ Sat, 03 Jun 2017 05:29:07: 5000000 INFO @ Sat, 03 Jun 2017 05:29:07: 5000000 INFO @ Sat, 03 Jun 2017 05:29:16: 6000000 INFO @ Sat, 03 Jun 2017 05:29:16: 6000000 INFO @ Sat, 03 Jun 2017 05:29:16: 6000000 INFO @ Sat, 03 Jun 2017 05:29:25: 7000000 INFO @ Sat, 03 Jun 2017 05:29:25: 7000000 INFO @ Sat, 03 Jun 2017 05:29:25: 7000000 INFO @ Sat, 03 Jun 2017 05:29:33: 8000000 INFO @ Sat, 03 Jun 2017 05:29:33: 8000000 INFO @ Sat, 03 Jun 2017 05:29:34: 8000000 INFO @ Sat, 03 Jun 2017 05:29:42: 9000000 INFO @ Sat, 03 Jun 2017 05:29:42: 9000000 INFO @ Sat, 03 Jun 2017 05:29:43: 9000000 INFO @ Sat, 03 Jun 2017 05:29:51: 10000000 INFO @ Sat, 03 Jun 2017 05:29:51: 10000000 INFO @ Sat, 03 Jun 2017 05:29:52: 10000000 INFO @ Sat, 03 Jun 2017 05:30:00: 11000000 INFO @ Sat, 03 Jun 2017 05:30:00: 11000000 INFO @ Sat, 03 Jun 2017 05:30:01: 11000000 INFO @ Sat, 03 Jun 2017 05:30:09: 12000000 INFO @ Sat, 03 Jun 2017 05:30:09: 12000000 INFO @ Sat, 03 Jun 2017 05:30:10: 12000000 INFO @ Sat, 03 Jun 2017 05:30:18: 13000000 INFO @ Sat, 03 Jun 2017 05:30:19: 13000000 INFO @ Sat, 03 Jun 2017 05:30:20: 13000000 INFO @ Sat, 03 Jun 2017 05:30:28: 14000000 INFO @ Sat, 03 Jun 2017 05:30:28: 14000000 INFO @ Sat, 03 Jun 2017 05:30:29: 14000000 INFO @ Sat, 03 Jun 2017 05:30:37: 15000000 INFO @ Sat, 03 Jun 2017 05:30:38: 15000000 INFO @ Sat, 03 Jun 2017 05:30:39: 15000000 INFO @ Sat, 03 Jun 2017 05:30:46: 16000000 INFO @ Sat, 03 Jun 2017 05:30:47: 16000000 INFO @ Sat, 03 Jun 2017 05:30:49: 16000000 INFO @ Sat, 03 Jun 2017 05:30:56: 17000000 INFO @ Sat, 03 Jun 2017 05:30:56: 17000000 INFO @ Sat, 03 Jun 2017 05:30:59: 17000000 INFO @ Sat, 03 Jun 2017 05:31:05: 18000000 INFO @ Sat, 03 Jun 2017 05:31:06: 18000000 INFO @ Sat, 03 Jun 2017 05:31:08: 18000000 INFO @ Sat, 03 Jun 2017 05:31:14: 19000000 INFO @ Sat, 03 Jun 2017 05:31:15: 19000000 INFO @ Sat, 03 Jun 2017 05:31:17: 19000000 INFO @ Sat, 03 Jun 2017 05:31:23: 20000000 INFO @ Sat, 03 Jun 2017 05:31:24: 20000000 INFO @ Sat, 03 Jun 2017 05:31:26: 20000000 INFO @ Sat, 03 Jun 2017 05:31:32: 21000000 INFO @ Sat, 03 Jun 2017 05:31:33: 21000000 INFO @ Sat, 03 Jun 2017 05:31:35: 21000000 INFO @ Sat, 03 Jun 2017 05:31:42: 22000000 INFO @ Sat, 03 Jun 2017 05:31:42: 22000000 INFO @ Sat, 03 Jun 2017 05:31:46: 22000000 INFO @ Sat, 03 Jun 2017 05:31:52: 23000000 INFO @ Sat, 03 Jun 2017 05:31:53: 23000000 INFO @ Sat, 03 Jun 2017 05:31:54: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:31:54: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:31:54: #1 total tags in treatment: 23160563 INFO @ Sat, 03 Jun 2017 05:31:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:31:54: #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 05:31:54: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:31:54: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:31:54: #1 total tags in treatment: 23160563 INFO @ Sat, 03 Jun 2017 05:31:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:31:54: #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 05:31:57: 23000000 INFO @ Sat, 03 Jun 2017 05:31:58: #1 tags after filtering in treatment: 23104285 INFO @ Sat, 03 Jun 2017 05:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:31:58: #1 finished! INFO @ Sat, 03 Jun 2017 05:31:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:31:59: #1 tag size is determined as 92 bps INFO @ Sat, 03 Jun 2017 05:31:59: #1 tag size = 92 INFO @ Sat, 03 Jun 2017 05:31:59: #1 total tags in treatment: 23160563 INFO @ Sat, 03 Jun 2017 05:31:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 05:31:59: #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 05:32:00: #1 tags after filtering in treatment: 23104285 INFO @ Sat, 03 Jun 2017 05:32:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:32:00: #1 finished! INFO @ Sat, 03 Jun 2017 05:32:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:32:02: #2 number of paired peaks: 331 WARNING @ Sat, 03 Jun 2017 05:32:02: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:02: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:03: #1 tags after filtering in treatment: 23104285 INFO @ Sat, 03 Jun 2017 05:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 05:32:03: #1 finished! INFO @ Sat, 03 Jun 2017 05:32:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 05:32:03: #2 number of paired peaks: 331 WARNING @ Sat, 03 Jun 2017 05:32:03: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:03: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:07: #2 number of paired peaks: 331 WARNING @ Sat, 03 Jun 2017 05:32:07: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sat, 03 Jun 2017 05:32:07: start model_add_line... INFO @ Sat, 03 Jun 2017 05:32:09: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:09: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:09: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:09: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Jun 2017 05:32:09: #2 alternative fragment length(s) may be 3,134 bps INFO @ Sat, 03 Jun 2017 05:32:09: #2.2 Generate R script for model : SRX2163950.05_model.r WARNING @ Sat, 03 Jun 2017 05:32:09: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:09: #2 You may need to consider one of the other alternative d(s): 3,134 WARNING @ Sat, 03 Jun 2017 05:32:09: #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 05:32:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:32:11: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:11: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:11: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:11: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Jun 2017 05:32:11: #2 alternative fragment length(s) may be 3,134 bps INFO @ Sat, 03 Jun 2017 05:32:11: #2.2 Generate R script for model : SRX2163950.20_model.r WARNING @ Sat, 03 Jun 2017 05:32:11: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:11: #2 You may need to consider one of the other alternative d(s): 3,134 WARNING @ Sat, 03 Jun 2017 05:32:11: #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 05:32:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:32:14: start X-correlation... INFO @ Sat, 03 Jun 2017 05:32:15: end of X-cor INFO @ Sat, 03 Jun 2017 05:32:15: #2 finished! INFO @ Sat, 03 Jun 2017 05:32:15: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Jun 2017 05:32:15: #2 alternative fragment length(s) may be 3,134 bps INFO @ Sat, 03 Jun 2017 05:32:15: #2.2 Generate R script for model : SRX2163950.10_model.r WARNING @ Sat, 03 Jun 2017 05:32:15: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 05:32:15: #2 You may need to consider one of the other alternative d(s): 3,134 WARNING @ Sat, 03 Jun 2017 05:32:15: #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 05:32:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 05:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 05:33:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:34:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:34:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 05:35:21: #4 Write output xls file... SRX2163950.20_peaks.xls INFO @ Sat, 03 Jun 2017 05:35:21: #4 Write peak in narrowPeak format file... SRX2163950.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:35:21: #4 Write summits bed file... SRX2163950.20_summits.bed INFO @ Sat, 03 Jun 2017 05:35:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2682 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:35:22: #4 Write output xls file... SRX2163950.05_peaks.xls INFO @ Sat, 03 Jun 2017 05:35:22: #4 Write peak in narrowPeak format file... SRX2163950.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:35:22: #4 Write summits bed file... SRX2163950.05_summits.bed INFO @ Sat, 03 Jun 2017 05:35:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6678 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 05:35:28: #4 Write output xls file... SRX2163950.10_peaks.xls INFO @ Sat, 03 Jun 2017 05:35:28: #4 Write peak in narrowPeak format file... SRX2163950.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 05:35:28: #4 Write summits bed file... SRX2163950.10_summits.bed INFO @ Sat, 03 Jun 2017 05:35:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4551 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。