Job ID = 1295021 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,020,623 reads read : 19,020,623 reads written : 19,020,623 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: 00:08:00 19020623 reads; of these: 19020623 (100.00%) were unpaired; of these: 861791 (4.53%) aligned 0 times 12494106 (65.69%) aligned exactly 1 time 5664726 (29.78%) aligned >1 times 95.47% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 1777959 / 18158832 = 0.0979 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 11:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.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 11:39:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.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 11:39:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.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 11:39:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:39:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:39:19: 1000000 INFO @ Mon, 03 Jun 2019 11:39:19: 1000000 INFO @ Mon, 03 Jun 2019 11:39:20: 1000000 INFO @ Mon, 03 Jun 2019 11:39:29: 2000000 INFO @ Mon, 03 Jun 2019 11:39:30: 2000000 INFO @ Mon, 03 Jun 2019 11:39:30: 2000000 INFO @ Mon, 03 Jun 2019 11:39:38: 3000000 INFO @ Mon, 03 Jun 2019 11:39:39: 3000000 INFO @ Mon, 03 Jun 2019 11:39:41: 3000000 INFO @ Mon, 03 Jun 2019 11:39:48: 4000000 INFO @ Mon, 03 Jun 2019 11:39:49: 4000000 INFO @ Mon, 03 Jun 2019 11:39:52: 4000000 INFO @ Mon, 03 Jun 2019 11:39:57: 5000000 INFO @ Mon, 03 Jun 2019 11:39:59: 5000000 INFO @ Mon, 03 Jun 2019 11:40:03: 5000000 INFO @ Mon, 03 Jun 2019 11:40:07: 6000000 INFO @ Mon, 03 Jun 2019 11:40:10: 6000000 INFO @ Mon, 03 Jun 2019 11:40:14: 6000000 INFO @ Mon, 03 Jun 2019 11:40:17: 7000000 INFO @ Mon, 03 Jun 2019 11:40:19: 7000000 INFO @ Mon, 03 Jun 2019 11:40:24: 7000000 INFO @ Mon, 03 Jun 2019 11:40:26: 8000000 INFO @ Mon, 03 Jun 2019 11:40:29: 8000000 INFO @ Mon, 03 Jun 2019 11:40:35: 8000000 INFO @ Mon, 03 Jun 2019 11:40:37: 9000000 INFO @ Mon, 03 Jun 2019 11:40:41: 9000000 INFO @ Mon, 03 Jun 2019 11:40:47: 9000000 INFO @ Mon, 03 Jun 2019 11:40:49: 10000000 INFO @ Mon, 03 Jun 2019 11:40:53: 10000000 INFO @ Mon, 03 Jun 2019 11:40:59: 10000000 INFO @ Mon, 03 Jun 2019 11:41:00: 11000000 INFO @ Mon, 03 Jun 2019 11:41:04: 11000000 INFO @ Mon, 03 Jun 2019 11:41:10: 12000000 INFO @ Mon, 03 Jun 2019 11:41:11: 11000000 INFO @ Mon, 03 Jun 2019 11:41:14: 12000000 INFO @ Mon, 03 Jun 2019 11:41:20: 13000000 INFO @ Mon, 03 Jun 2019 11:41:22: 12000000 INFO @ Mon, 03 Jun 2019 11:41:25: 13000000 INFO @ Mon, 03 Jun 2019 11:41:30: 14000000 INFO @ Mon, 03 Jun 2019 11:41:33: 13000000 INFO @ Mon, 03 Jun 2019 11:41:35: 14000000 INFO @ Mon, 03 Jun 2019 11:41:41: 15000000 INFO @ Mon, 03 Jun 2019 11:41:45: 14000000 INFO @ Mon, 03 Jun 2019 11:41:46: 15000000 INFO @ Mon, 03 Jun 2019 11:41:52: 16000000 INFO @ Mon, 03 Jun 2019 11:41:56: 15000000 INFO @ Mon, 03 Jun 2019 11:41:56: 16000000 INFO @ Mon, 03 Jun 2019 11:41:56: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:41:56: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:41:56: #1 total tags in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:41:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:41:56: #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 11:41:57: #1 tags after filtering in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:41:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:41:57: #1 finished! INFO @ Mon, 03 Jun 2019 11:41:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:41:58: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 11:41:58: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 11:41:58: start model_add_line... INFO @ Mon, 03 Jun 2019 11:41:58: start X-correlation... INFO @ Mon, 03 Jun 2019 11:41:58: end of X-cor INFO @ Mon, 03 Jun 2019 11:41:58: #2 finished! INFO @ Mon, 03 Jun 2019 11:41:58: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 11:41:58: #2 alternative fragment length(s) may be 3,51,563,571 bps INFO @ Mon, 03 Jun 2019 11:41:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20_model.r WARNING @ Mon, 03 Jun 2019 11:41:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:41:59: #2 You may need to consider one of the other alternative d(s): 3,51,563,571 WARNING @ Mon, 03 Jun 2019 11:41:59: #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 11:41:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:00: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:42:00: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:42:00: #1 total tags in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:42:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:42:00: #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 11:42:00: #1 tags after filtering in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:42:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:42:00: #1 finished! INFO @ Mon, 03 Jun 2019 11:42:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:42:02: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 11:42:02: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 11:42:02: start model_add_line... INFO @ Mon, 03 Jun 2019 11:42:02: start X-correlation... INFO @ Mon, 03 Jun 2019 11:42:02: end of X-cor INFO @ Mon, 03 Jun 2019 11:42:02: #2 finished! INFO @ Mon, 03 Jun 2019 11:42:02: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 11:42:02: #2 alternative fragment length(s) may be 3,51,563,571 bps INFO @ Mon, 03 Jun 2019 11:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10_model.r WARNING @ Mon, 03 Jun 2019 11:42:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:42:02: #2 You may need to consider one of the other alternative d(s): 3,51,563,571 WARNING @ Mon, 03 Jun 2019 11:42:02: #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 11:42:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:07: 16000000 INFO @ Mon, 03 Jun 2019 11:42:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:42:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:42:11: #1 total tags in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:42:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:42:11: #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 11:42:11: #1 tags after filtering in treatment: 16380873 INFO @ Mon, 03 Jun 2019 11:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:42:11: #1 finished! INFO @ Mon, 03 Jun 2019 11:42:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:42:13: #2 number of paired peaks: 409 WARNING @ Mon, 03 Jun 2019 11:42:13: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Mon, 03 Jun 2019 11:42:13: start model_add_line... INFO @ Mon, 03 Jun 2019 11:42:13: start X-correlation... INFO @ Mon, 03 Jun 2019 11:42:13: end of X-cor INFO @ Mon, 03 Jun 2019 11:42:13: #2 finished! INFO @ Mon, 03 Jun 2019 11:42:13: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 11:42:13: #2 alternative fragment length(s) may be 3,51,563,571 bps INFO @ Mon, 03 Jun 2019 11:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05_model.r WARNING @ Mon, 03 Jun 2019 11:42:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:42:13: #2 You may need to consider one of the other alternative d(s): 3,51,563,571 WARNING @ Mon, 03 Jun 2019 11:42:13: #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 11:42:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:42:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:42:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:43:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.20_summits.bed INFO @ Mon, 03 Jun 2019 11:43:10: Done! INFO @ Mon, 03 Jun 2019 11:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.10_summits.bed INFO @ Mon, 03 Jun 2019 11:43:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2065 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (948 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306192/SRX306192.05_summits.bed INFO @ Mon, 03 Jun 2019 11:43:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3133 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。