Job ID = 9027405 sra ファイルのダウンロード中... Completed: 728535K bytes transferred in 8 seconds (677533K 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 20110 0 20110 0 0 2480 0 --:--:-- 0:00:08 --:--:-- 11956 100 47678 0 47678 0 0 5238 0 --:--:-- 0:00:09 --:--:-- 17803 100 49549 0 49549 0 0 5443 0 --:--:-- 0:00:09 --:--:-- 18495 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 35457974 spots for /home/okishinya/chipatlas/results/ce10/SRX466579/SRR1163645.sra Written 35457974 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: 00:07:21 35457974 reads; of these: 35457974 (100.00%) were unpaired; of these: 4203775 (11.86%) aligned 0 times 23722147 (66.90%) aligned exactly 1 time 7532052 (21.24%) aligned >1 times 88.14% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 7646766 / 31254199 = 0.2447 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 08:41:59: # Command line: callpeak -t SRX466579.bam -f BAM -g ce -n SRX466579.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX466579.20 # format = BAM # ChIP-seq file = ['SRX466579.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 08:41:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:41:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:41:59: # Command line: callpeak -t SRX466579.bam -f BAM -g ce -n SRX466579.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX466579.05 # format = BAM # ChIP-seq file = ['SRX466579.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 08:41:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:41:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:41:59: # Command line: callpeak -t SRX466579.bam -f BAM -g ce -n SRX466579.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX466579.10 # format = BAM # ChIP-seq file = ['SRX466579.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 08:41:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:41:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:42:06: 1000000 INFO @ Sat, 03 Jun 2017 08:42:06: 1000000 INFO @ Sat, 03 Jun 2017 08:42:06: 1000000 INFO @ Sat, 03 Jun 2017 08:42:13: 2000000 INFO @ Sat, 03 Jun 2017 08:42:13: 2000000 INFO @ Sat, 03 Jun 2017 08:42:13: 2000000 INFO @ Sat, 03 Jun 2017 08:42:18: 3000000 INFO @ Sat, 03 Jun 2017 08:42:20: 3000000 INFO @ Sat, 03 Jun 2017 08:42:20: 3000000 INFO @ Sat, 03 Jun 2017 08:42:24: 4000000 INFO @ Sat, 03 Jun 2017 08:42:26: 4000000 INFO @ Sat, 03 Jun 2017 08:42:26: 4000000 INFO @ Sat, 03 Jun 2017 08:42:29: 5000000 INFO @ Sat, 03 Jun 2017 08:42:32: 5000000 INFO @ Sat, 03 Jun 2017 08:42:32: 5000000 INFO @ Sat, 03 Jun 2017 08:42:35: 6000000 INFO @ Sat, 03 Jun 2017 08:42:39: 6000000 INFO @ Sat, 03 Jun 2017 08:42:39: 6000000 INFO @ Sat, 03 Jun 2017 08:42:41: 7000000 INFO @ Sat, 03 Jun 2017 08:42:45: 7000000 INFO @ Sat, 03 Jun 2017 08:42:45: 7000000 INFO @ Sat, 03 Jun 2017 08:42:46: 8000000 INFO @ Sat, 03 Jun 2017 08:42:51: 8000000 INFO @ Sat, 03 Jun 2017 08:42:51: 8000000 INFO @ Sat, 03 Jun 2017 08:42:52: 9000000 INFO @ Sat, 03 Jun 2017 08:42:57: 9000000 INFO @ Sat, 03 Jun 2017 08:42:57: 9000000 INFO @ Sat, 03 Jun 2017 08:42:57: 10000000 INFO @ Sat, 03 Jun 2017 08:43:03: 11000000 INFO @ Sat, 03 Jun 2017 08:43:04: 10000000 INFO @ Sat, 03 Jun 2017 08:43:04: 10000000 INFO @ Sat, 03 Jun 2017 08:43:09: 12000000 INFO @ Sat, 03 Jun 2017 08:43:10: 11000000 INFO @ Sat, 03 Jun 2017 08:43:10: 11000000 INFO @ Sat, 03 Jun 2017 08:43:14: 13000000 INFO @ Sat, 03 Jun 2017 08:43:16: 12000000 INFO @ Sat, 03 Jun 2017 08:43:16: 12000000 INFO @ Sat, 03 Jun 2017 08:43:20: 14000000 INFO @ Sat, 03 Jun 2017 08:43:23: 13000000 INFO @ Sat, 03 Jun 2017 08:43:23: 13000000 INFO @ Sat, 03 Jun 2017 08:43:26: 15000000 INFO @ Sat, 03 Jun 2017 08:43:29: 14000000 INFO @ Sat, 03 Jun 2017 08:43:29: 14000000 INFO @ Sat, 03 Jun 2017 08:43:32: 16000000 INFO @ Sat, 03 Jun 2017 08:43:35: 15000000 INFO @ Sat, 03 Jun 2017 08:43:35: 15000000 INFO @ Sat, 03 Jun 2017 08:43:37: 17000000 INFO @ Sat, 03 Jun 2017 08:43:42: 16000000 INFO @ Sat, 03 Jun 2017 08:43:42: 16000000 INFO @ Sat, 03 Jun 2017 08:43:43: 18000000 INFO @ Sat, 03 Jun 2017 08:43:48: 17000000 INFO @ Sat, 03 Jun 2017 08:43:48: 17000000 INFO @ Sat, 03 Jun 2017 08:43:49: 19000000 INFO @ Sat, 03 Jun 2017 08:43:54: 20000000 INFO @ Sat, 03 Jun 2017 08:43:54: 18000000 INFO @ Sat, 03 Jun 2017 08:43:54: 18000000 INFO @ Sat, 03 Jun 2017 08:44:00: 21000000 INFO @ Sat, 03 Jun 2017 08:44:01: 19000000 INFO @ Sat, 03 Jun 2017 08:44:01: 19000000 INFO @ Sat, 03 Jun 2017 08:44:05: 22000000 INFO @ Sat, 03 Jun 2017 08:44:07: 20000000 INFO @ Sat, 03 Jun 2017 08:44:07: 20000000 INFO @ Sat, 03 Jun 2017 08:44:10: 23000000 INFO @ Sat, 03 Jun 2017 08:44:14: 21000000 INFO @ Sat, 03 Jun 2017 08:44:14: 21000000 INFO @ Sat, 03 Jun 2017 08:44:14: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 08:44:14: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 08:44:14: #1 total tags in treatment: 23607433 INFO @ Sat, 03 Jun 2017 08:44:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:44:14: #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 08:44:19: #1 tags after filtering in treatment: 23603589 INFO @ Sat, 03 Jun 2017 08:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:44:19: #1 finished! INFO @ Sat, 03 Jun 2017 08:44:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:44:20: 22000000 INFO @ Sat, 03 Jun 2017 08:44:20: 22000000 INFO @ Sat, 03 Jun 2017 08:44:22: #2 number of paired peaks: 536 WARNING @ Sat, 03 Jun 2017 08:44:22: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 03 Jun 2017 08:44:22: start model_add_line... INFO @ Sat, 03 Jun 2017 08:44:27: 23000000 INFO @ Sat, 03 Jun 2017 08:44:27: 23000000 INFO @ Sat, 03 Jun 2017 08:44:31: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 08:44:31: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 08:44:31: #1 total tags in treatment: 23607433 INFO @ Sat, 03 Jun 2017 08:44:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:44:31: #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 08:44:31: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 08:44:31: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 08:44:31: #1 total tags in treatment: 23607433 INFO @ Sat, 03 Jun 2017 08:44:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:44:31: #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 08:44:34: start X-correlation... INFO @ Sat, 03 Jun 2017 08:44:34: end of X-cor INFO @ Sat, 03 Jun 2017 08:44:34: #2 finished! INFO @ Sat, 03 Jun 2017 08:44:34: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 08:44:34: #2 alternative fragment length(s) may be 2,40,59 bps INFO @ Sat, 03 Jun 2017 08:44:34: #2.2 Generate R script for model : SRX466579.10_model.r WARNING @ Sat, 03 Jun 2017 08:44:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:44:34: #2 You may need to consider one of the other alternative d(s): 2,40,59 WARNING @ Sat, 03 Jun 2017 08:44:34: #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 08:44:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:44:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:44:35: #1 tags after filtering in treatment: 23603589 INFO @ Sat, 03 Jun 2017 08:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:44:35: #1 finished! INFO @ Sat, 03 Jun 2017 08:44:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:44:35: #1 tags after filtering in treatment: 23603589 INFO @ Sat, 03 Jun 2017 08:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:44:35: #1 finished! INFO @ Sat, 03 Jun 2017 08:44:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:44:39: #2 number of paired peaks: 536 WARNING @ Sat, 03 Jun 2017 08:44:39: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 03 Jun 2017 08:44:39: start model_add_line... INFO @ Sat, 03 Jun 2017 08:44:40: #2 number of paired peaks: 536 WARNING @ Sat, 03 Jun 2017 08:44:40: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 03 Jun 2017 08:44:40: start model_add_line... INFO @ Sat, 03 Jun 2017 08:44:51: start X-correlation... INFO @ Sat, 03 Jun 2017 08:44:51: end of X-cor INFO @ Sat, 03 Jun 2017 08:44:51: #2 finished! INFO @ Sat, 03 Jun 2017 08:44:51: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 08:44:51: #2 alternative fragment length(s) may be 2,40,59 bps INFO @ Sat, 03 Jun 2017 08:44:51: #2.2 Generate R script for model : SRX466579.20_model.r WARNING @ Sat, 03 Jun 2017 08:44:51: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:44:51: #2 You may need to consider one of the other alternative d(s): 2,40,59 WARNING @ Sat, 03 Jun 2017 08:44:51: #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 08:44:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:44:52: start X-correlation... INFO @ Sat, 03 Jun 2017 08:44:52: end of X-cor INFO @ Sat, 03 Jun 2017 08:44:52: #2 finished! INFO @ Sat, 03 Jun 2017 08:44:52: #2 predicted fragment length is 59 bps INFO @ Sat, 03 Jun 2017 08:44:52: #2 alternative fragment length(s) may be 2,40,59 bps INFO @ Sat, 03 Jun 2017 08:44:52: #2.2 Generate R script for model : SRX466579.05_model.r WARNING @ Sat, 03 Jun 2017 08:44:52: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:44:52: #2 You may need to consider one of the other alternative d(s): 2,40,59 WARNING @ Sat, 03 Jun 2017 08:44:52: #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 08:44:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:46:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:46:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:46:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:47:43: #4 Write output xls file... SRX466579.10_peaks.xls INFO @ Sat, 03 Jun 2017 08:47:43: #4 Write peak in narrowPeak format file... SRX466579.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:47:43: #4 Write summits bed file... SRX466579.10_summits.bed INFO @ Sat, 03 Jun 2017 08:47:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7335 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 08:47:58: #4 Write output xls file... SRX466579.05_peaks.xls INFO @ Sat, 03 Jun 2017 08:47:58: #4 Write peak in narrowPeak format file... SRX466579.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:47:58: #4 Write summits bed file... SRX466579.05_summits.bed INFO @ Sat, 03 Jun 2017 08:47:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14557 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 08:48:05: #4 Write output xls file... SRX466579.20_peaks.xls INFO @ Sat, 03 Jun 2017 08:48:05: #4 Write peak in narrowPeak format file... SRX466579.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:48:05: #4 Write summits bed file... SRX466579.20_summits.bed INFO @ Sat, 03 Jun 2017 08:48:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。