Job ID = 1292424 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,534,095 reads read : 13,068,190 reads written : 6,534,095 reads 0-length : 6,534,095 spots read : 6,386,147 reads read : 12,772,294 reads written : 6,386,147 reads 0-length : 6,386,147 spots read : 6,524,006 reads read : 13,048,012 reads written : 6,524,006 reads 0-length : 6,524,006 spots read : 6,315,285 reads read : 12,630,570 reads written : 6,315,285 reads 0-length : 6,315,285 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: 00:10:46 25759533 reads; of these: 25759533 (100.00%) were unpaired; of these: 334381 (1.30%) aligned 0 times 21480021 (83.39%) aligned exactly 1 time 3945131 (15.32%) aligned >1 times 98.70% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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 12 files... [bam_rmdupse_core] 4025642 / 25425152 = 0.1583 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 @ Sun, 02 Jun 2019 19:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:00:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:00:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:00:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:22: 1000000 INFO @ Sun, 02 Jun 2019 19:00:22: 1000000 INFO @ Sun, 02 Jun 2019 19:00:24: 1000000 INFO @ Sun, 02 Jun 2019 19:00:31: 2000000 INFO @ Sun, 02 Jun 2019 19:00:31: 2000000 INFO @ Sun, 02 Jun 2019 19:00:33: 2000000 INFO @ Sun, 02 Jun 2019 19:00:39: 3000000 INFO @ Sun, 02 Jun 2019 19:00:40: 3000000 INFO @ Sun, 02 Jun 2019 19:00:43: 3000000 INFO @ Sun, 02 Jun 2019 19:00:48: 4000000 INFO @ Sun, 02 Jun 2019 19:00:48: 4000000 INFO @ Sun, 02 Jun 2019 19:00:53: 4000000 INFO @ Sun, 02 Jun 2019 19:00:56: 5000000 INFO @ Sun, 02 Jun 2019 19:00:56: 5000000 INFO @ Sun, 02 Jun 2019 19:01:02: 5000000 INFO @ Sun, 02 Jun 2019 19:01:04: 6000000 INFO @ Sun, 02 Jun 2019 19:01:04: 6000000 INFO @ Sun, 02 Jun 2019 19:01:11: 7000000 INFO @ Sun, 02 Jun 2019 19:01:12: 6000000 INFO @ Sun, 02 Jun 2019 19:01:12: 7000000 INFO @ Sun, 02 Jun 2019 19:01:19: 8000000 INFO @ Sun, 02 Jun 2019 19:01:20: 8000000 INFO @ Sun, 02 Jun 2019 19:01:21: 7000000 INFO @ Sun, 02 Jun 2019 19:01:26: 9000000 INFO @ Sun, 02 Jun 2019 19:01:28: 9000000 INFO @ Sun, 02 Jun 2019 19:01:31: 8000000 INFO @ Sun, 02 Jun 2019 19:01:34: 10000000 INFO @ Sun, 02 Jun 2019 19:01:36: 10000000 INFO @ Sun, 02 Jun 2019 19:01:40: 9000000 INFO @ Sun, 02 Jun 2019 19:01:41: 11000000 INFO @ Sun, 02 Jun 2019 19:01:44: 11000000 INFO @ Sun, 02 Jun 2019 19:01:49: 12000000 INFO @ Sun, 02 Jun 2019 19:01:50: 10000000 INFO @ Sun, 02 Jun 2019 19:01:52: 12000000 INFO @ Sun, 02 Jun 2019 19:01:56: 13000000 INFO @ Sun, 02 Jun 2019 19:01:59: 11000000 INFO @ Sun, 02 Jun 2019 19:02:00: 13000000 INFO @ Sun, 02 Jun 2019 19:02:03: 14000000 INFO @ Sun, 02 Jun 2019 19:02:08: 14000000 INFO @ Sun, 02 Jun 2019 19:02:09: 12000000 INFO @ Sun, 02 Jun 2019 19:02:11: 15000000 INFO @ Sun, 02 Jun 2019 19:02:16: 15000000 INFO @ Sun, 02 Jun 2019 19:02:18: 13000000 INFO @ Sun, 02 Jun 2019 19:02:18: 16000000 INFO @ Sun, 02 Jun 2019 19:02:23: 16000000 INFO @ Sun, 02 Jun 2019 19:02:26: 17000000 INFO @ Sun, 02 Jun 2019 19:02:28: 14000000 INFO @ Sun, 02 Jun 2019 19:02:30: 17000000 INFO @ Sun, 02 Jun 2019 19:02:34: 18000000 INFO @ Sun, 02 Jun 2019 19:02:37: 15000000 INFO @ Sun, 02 Jun 2019 19:02:38: 18000000 INFO @ Sun, 02 Jun 2019 19:02:42: 19000000 INFO @ Sun, 02 Jun 2019 19:02:45: 19000000 INFO @ Sun, 02 Jun 2019 19:02:46: 16000000 INFO @ Sun, 02 Jun 2019 19:02:49: 20000000 INFO @ Sun, 02 Jun 2019 19:02:53: 20000000 INFO @ Sun, 02 Jun 2019 19:02:56: 17000000 INFO @ Sun, 02 Jun 2019 19:02:58: 21000000 INFO @ Sun, 02 Jun 2019 19:03:01: #1 tag size is determined as 72 bps INFO @ Sun, 02 Jun 2019 19:03:01: #1 tag size = 72 INFO @ Sun, 02 Jun 2019 19:03:01: #1 total tags in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:02: #1 tags after filtering in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:02: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:02: 21000000 INFO @ Sun, 02 Jun 2019 19:03:03: #2 number of paired peaks: 174 WARNING @ Sun, 02 Jun 2019 19:03:03: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:04: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:04: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:04: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:04: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:04: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 02 Jun 2019 19:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05_model.r WARNING @ Sun, 02 Jun 2019 19:03:04: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:04: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 02 Jun 2019 19:03:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:05: 18000000 INFO @ Sun, 02 Jun 2019 19:03:06: #1 tag size is determined as 72 bps INFO @ Sun, 02 Jun 2019 19:03:06: #1 tag size = 72 INFO @ Sun, 02 Jun 2019 19:03:06: #1 total tags in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:06: #1 tags after filtering in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:06: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:08: #2 number of paired peaks: 174 WARNING @ Sun, 02 Jun 2019 19:03:08: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:08: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:08: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:08: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:08: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:08: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:08: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 02 Jun 2019 19:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10_model.r WARNING @ Sun, 02 Jun 2019 19:03:08: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:08: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 02 Jun 2019 19:03:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:14: 19000000 INFO @ Sun, 02 Jun 2019 19:03:23: 20000000 INFO @ Sun, 02 Jun 2019 19:03:32: 21000000 INFO @ Sun, 02 Jun 2019 19:03:36: #1 tag size is determined as 72 bps INFO @ Sun, 02 Jun 2019 19:03:36: #1 tag size = 72 INFO @ Sun, 02 Jun 2019 19:03:36: #1 total tags in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:36: #1 tags after filtering in treatment: 21399510 INFO @ Sun, 02 Jun 2019 19:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:36: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:38: #2 number of paired peaks: 174 WARNING @ Sun, 02 Jun 2019 19:03:38: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:38: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:38: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:38: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:38: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:38: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:38: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sun, 02 Jun 2019 19:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20_model.r WARNING @ Sun, 02 Jun 2019 19:03:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:38: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sun, 02 Jun 2019 19:03:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:03:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.05_summits.bed INFO @ Sun, 02 Jun 2019 19:04:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.10_summits.bed INFO @ Sun, 02 Jun 2019 19:04:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194210/SRX4194210.20_summits.bed INFO @ Sun, 02 Jun 2019 19:04:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。