Job ID = 1295211 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:29 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1124966 (6.08%) aligned 0 times 13120988 (70.95%) aligned exactly 1 time 4247174 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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 8 files... [bam_rmdupse_core] 1482275 / 17368162 = 0.0853 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, 03 Jun 2019 13:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.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, 03 Jun 2019 13:01:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:01:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.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, 03 Jun 2019 13:01:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:01:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.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, 03 Jun 2019 13:01:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:01:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:01:55: 1000000 INFO @ Mon, 03 Jun 2019 13:01:55: 1000000 INFO @ Mon, 03 Jun 2019 13:01:57: 1000000 INFO @ Mon, 03 Jun 2019 13:02:03: 2000000 INFO @ Mon, 03 Jun 2019 13:02:03: 2000000 INFO @ Mon, 03 Jun 2019 13:02:07: 2000000 INFO @ Mon, 03 Jun 2019 13:02:11: 3000000 INFO @ Mon, 03 Jun 2019 13:02:11: 3000000 INFO @ Mon, 03 Jun 2019 13:02:18: 3000000 INFO @ Mon, 03 Jun 2019 13:02:19: 4000000 INFO @ Mon, 03 Jun 2019 13:02:19: 4000000 INFO @ Mon, 03 Jun 2019 13:02:28: 5000000 INFO @ Mon, 03 Jun 2019 13:02:28: 5000000 INFO @ Mon, 03 Jun 2019 13:02:28: 4000000 INFO @ Mon, 03 Jun 2019 13:02:36: 6000000 INFO @ Mon, 03 Jun 2019 13:02:36: 6000000 INFO @ Mon, 03 Jun 2019 13:02:39: 5000000 INFO @ Mon, 03 Jun 2019 13:02:44: 7000000 INFO @ Mon, 03 Jun 2019 13:02:44: 7000000 INFO @ Mon, 03 Jun 2019 13:02:50: 6000000 INFO @ Mon, 03 Jun 2019 13:02:52: 8000000 INFO @ Mon, 03 Jun 2019 13:02:52: 8000000 INFO @ Mon, 03 Jun 2019 13:03:00: 7000000 INFO @ Mon, 03 Jun 2019 13:03:00: 9000000 INFO @ Mon, 03 Jun 2019 13:03:00: 9000000 INFO @ Mon, 03 Jun 2019 13:03:08: 10000000 INFO @ Mon, 03 Jun 2019 13:03:08: 10000000 INFO @ Mon, 03 Jun 2019 13:03:10: 8000000 INFO @ Mon, 03 Jun 2019 13:03:16: 11000000 INFO @ Mon, 03 Jun 2019 13:03:16: 11000000 INFO @ Mon, 03 Jun 2019 13:03:21: 9000000 INFO @ Mon, 03 Jun 2019 13:03:24: 12000000 INFO @ Mon, 03 Jun 2019 13:03:24: 12000000 INFO @ Mon, 03 Jun 2019 13:03:31: 10000000 INFO @ Mon, 03 Jun 2019 13:03:32: 13000000 INFO @ Mon, 03 Jun 2019 13:03:33: 13000000 INFO @ Mon, 03 Jun 2019 13:03:40: 14000000 INFO @ Mon, 03 Jun 2019 13:03:41: 14000000 INFO @ Mon, 03 Jun 2019 13:03:42: 11000000 INFO @ Mon, 03 Jun 2019 13:03:48: 15000000 INFO @ Mon, 03 Jun 2019 13:03:48: 15000000 INFO @ Mon, 03 Jun 2019 13:03:52: 12000000 INFO @ Mon, 03 Jun 2019 13:03:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:03:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:03:56: #1 total tags in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:03:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:03:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:03:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:03:56: #1 total tags in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:03:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:03:56: #1 tags after filtering in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:56: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:56: #1 tags after filtering in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:03:56: #1 finished! INFO @ Mon, 03 Jun 2019 13:03:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:03:57: #2 number of paired peaks: 170 WARNING @ Mon, 03 Jun 2019 13:03:57: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 03 Jun 2019 13:03:57: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:57: #2 number of paired peaks: 170 WARNING @ Mon, 03 Jun 2019 13:03:57: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 03 Jun 2019 13:03:57: start model_add_line... INFO @ Mon, 03 Jun 2019 13:03:57: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:57: start X-correlation... INFO @ Mon, 03 Jun 2019 13:03:57: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:57: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:57: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 13:03:57: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 13:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10_model.r WARNING @ Mon, 03 Jun 2019 13:03:57: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:03:57: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 13:03:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:03:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:03:57: end of X-cor INFO @ Mon, 03 Jun 2019 13:03:57: #2 finished! INFO @ Mon, 03 Jun 2019 13:03:57: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 13:03:57: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 13:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20_model.r WARNING @ Mon, 03 Jun 2019 13:03:57: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:03:57: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 13:03:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:03:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:04:02: 13000000 INFO @ Mon, 03 Jun 2019 13:04:12: 14000000 INFO @ Mon, 03 Jun 2019 13:04:22: 15000000 INFO @ Mon, 03 Jun 2019 13:04:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:04:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:04:30: #1 total tags in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:04:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:04:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:04:31: #1 tags after filtering in treatment: 15885887 INFO @ Mon, 03 Jun 2019 13:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:04:31: #1 finished! INFO @ Mon, 03 Jun 2019 13:04:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:04:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:04:32: #2 number of paired peaks: 170 WARNING @ Mon, 03 Jun 2019 13:04:32: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 03 Jun 2019 13:04:32: start model_add_line... INFO @ Mon, 03 Jun 2019 13:04:32: start X-correlation... INFO @ Mon, 03 Jun 2019 13:04:32: end of X-cor INFO @ Mon, 03 Jun 2019 13:04:32: #2 finished! INFO @ Mon, 03 Jun 2019 13:04:32: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 13:04:32: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 13:04:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05_model.r WARNING @ Mon, 03 Jun 2019 13:04:32: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:04:32: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 13:04:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 13:04:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:04:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:04:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.10_summits.bed INFO @ Mon, 03 Jun 2019 13:04:59: Done! INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.20_summits.bed INFO @ Mon, 03 Jun 2019 13:04:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1600 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:05:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331389/SRX331389.05_summits.bed INFO @ Mon, 03 Jun 2019 13:05:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1968 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。