Job ID = 10043482 sra ファイルのダウンロード中... Completed: 1115820K bytes transferred in 17 seconds (513371K bits/sec), in 2 files, 3 directories. 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 14488212 spots for /home/okishinya/chipatlas/results/dm3/SRX2165266/SRR4244762.sra Written 14488212 spots total Written 14835322 spots for /home/okishinya/chipatlas/results/dm3/SRX2165266/SRR4244761.sra Written 14835322 spots total 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: 00:13:42 29323534 reads; of these: 29323534 (100.00%) were unpaired; of these: 2678076 (9.13%) aligned 0 times 18605809 (63.45%) aligned exactly 1 time 8039649 (27.42%) aligned >1 times 90.87% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12439487 / 26645458 = 0.4669 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, 02 Oct 2017 03:49:25: # Command line: callpeak -t SRX2165266.bam -f BAM -g dm -n SRX2165266.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165266.05 # format = BAM # ChIP-seq file = ['SRX2165266.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:49:25: # Command line: callpeak -t SRX2165266.bam -f BAM -g dm -n SRX2165266.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165266.20 # format = BAM # ChIP-seq file = ['SRX2165266.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:49:25: # Command line: callpeak -t SRX2165266.bam -f BAM -g dm -n SRX2165266.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165266.10 # format = BAM # ChIP-seq file = ['SRX2165266.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 02 Oct 2017 03:49:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:25: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:49:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:49:25: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:49:32: 1000000 INFO @ Mon, 02 Oct 2017 03:49:32: 1000000 INFO @ Mon, 02 Oct 2017 03:49:32: 1000000 INFO @ Mon, 02 Oct 2017 03:49:39: 2000000 INFO @ Mon, 02 Oct 2017 03:49:40: 2000000 INFO @ Mon, 02 Oct 2017 03:49:40: 2000000 INFO @ Mon, 02 Oct 2017 03:49:47: 3000000 INFO @ Mon, 02 Oct 2017 03:49:48: 3000000 INFO @ Mon, 02 Oct 2017 03:49:48: 3000000 INFO @ Mon, 02 Oct 2017 03:49:54: 4000000 INFO @ Mon, 02 Oct 2017 03:49:55: 4000000 INFO @ Mon, 02 Oct 2017 03:49:55: 4000000 INFO @ Mon, 02 Oct 2017 03:50:01: 5000000 INFO @ Mon, 02 Oct 2017 03:50:03: 5000000 INFO @ Mon, 02 Oct 2017 03:50:03: 5000000 INFO @ Mon, 02 Oct 2017 03:50:08: 6000000 INFO @ Mon, 02 Oct 2017 03:50:11: 6000000 INFO @ Mon, 02 Oct 2017 03:50:11: 6000000 INFO @ Mon, 02 Oct 2017 03:50:15: 7000000 INFO @ Mon, 02 Oct 2017 03:50:18: 7000000 INFO @ Mon, 02 Oct 2017 03:50:18: 7000000 INFO @ Mon, 02 Oct 2017 03:50:23: 8000000 INFO @ Mon, 02 Oct 2017 03:50:26: 8000000 INFO @ Mon, 02 Oct 2017 03:50:26: 8000000 INFO @ Mon, 02 Oct 2017 03:50:30: 9000000 INFO @ Mon, 02 Oct 2017 03:50:34: 9000000 INFO @ Mon, 02 Oct 2017 03:50:34: 9000000 INFO @ Mon, 02 Oct 2017 03:50:37: 10000000 INFO @ Mon, 02 Oct 2017 03:50:41: 10000000 INFO @ Mon, 02 Oct 2017 03:50:41: 10000000 INFO @ Mon, 02 Oct 2017 03:50:44: 11000000 INFO @ Mon, 02 Oct 2017 03:50:49: 11000000 INFO @ Mon, 02 Oct 2017 03:50:49: 11000000 INFO @ Mon, 02 Oct 2017 03:50:51: 12000000 INFO @ Mon, 02 Oct 2017 03:50:57: 12000000 INFO @ Mon, 02 Oct 2017 03:50:57: 12000000 INFO @ Mon, 02 Oct 2017 03:50:59: 13000000 INFO @ Mon, 02 Oct 2017 03:51:04: 13000000 INFO @ Mon, 02 Oct 2017 03:51:04: 13000000 INFO @ Mon, 02 Oct 2017 03:51:06: 14000000 INFO @ Mon, 02 Oct 2017 03:51:07: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:07: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:07: #1 total tags in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:07: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:08: #1 tags after filtering in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:08: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:08: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:09: #2 number of paired peaks: 332 WARNING @ Mon, 02 Oct 2017 03:51:09: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:09: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:09: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:09: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:09: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:09: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:51:09: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:51:09: #2.2 Generate R script for model : SRX2165266.10_model.r WARNING @ Mon, 02 Oct 2017 03:51:09: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:51:09: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:51:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:51:09: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:51:12: 14000000 INFO @ Mon, 02 Oct 2017 03:51:12: 14000000 INFO @ Mon, 02 Oct 2017 03:51:13: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:13: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:13: #1 total tags in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:13: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:13: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:13: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:13: #1 total tags in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:13: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:14: #1 tags after filtering in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:14: #1 tags after filtering in treatment: 14205971 INFO @ Mon, 02 Oct 2017 03:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:14: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:14: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:14: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:14: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:15: #2 number of paired peaks: 332 WARNING @ Mon, 02 Oct 2017 03:51:15: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:15: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:15: #2 number of paired peaks: 332 WARNING @ Mon, 02 Oct 2017 03:51:15: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:15: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:15: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:15: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:15: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:15: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:51:15: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:51:15: #2.2 Generate R script for model : SRX2165266.05_model.r WARNING @ Mon, 02 Oct 2017 03:51:15: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:51:15: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:51:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:51:15: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:51:15: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:15: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:15: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:15: #2 predicted fragment length is 62 bps INFO @ Mon, 02 Oct 2017 03:51:15: #2 alternative fragment length(s) may be 62 bps INFO @ Mon, 02 Oct 2017 03:51:15: #2.2 Generate R script for model : SRX2165266.20_model.r WARNING @ Mon, 02 Oct 2017 03:51:15: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 02 Oct 2017 03:51:15: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Mon, 02 Oct 2017 03:51:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 02 Oct 2017 03:51:15: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:51:39: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:51:45: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:51:47: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:51:54: #4 Write output xls file... SRX2165266.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:51:54: #4 Write peak in narrowPeak format file... SRX2165266.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:51:55: #4 Write summits bed file... SRX2165266.10_summits.bed INFO @ Mon, 02 Oct 2017 03:51:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1729 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:52:03: #4 Write output xls file... SRX2165266.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:52:03: #4 Write peak in narrowPeak format file... SRX2165266.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:52:03: #4 Write summits bed file... SRX2165266.05_summits.bed INFO @ Mon, 02 Oct 2017 03:52:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2966 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:52:05: #4 Write output xls file... SRX2165266.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:52:05: #4 Write peak in narrowPeak format file... SRX2165266.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:52:05: #4 Write summits bed file... SRX2165266.20_summits.bed INFO @ Mon, 02 Oct 2017 03:52:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1061 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。