Job ID = 2589972 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163569.sra.cache’: 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: 00:04:59 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256441 (1.19%) aligned 0 times 17820703 (82.85%) aligned exactly 1 time 3432465 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 3666786 / 21253168 = 0.1725 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, 12 Aug 2019 19:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.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 @ Mon, 12 Aug 2019 19:05:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.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 @ Mon, 12 Aug 2019 19:05:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.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 @ Mon, 12 Aug 2019 19:05:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:09: 1000000 INFO @ Mon, 12 Aug 2019 19:05:10: 1000000 INFO @ Mon, 12 Aug 2019 19:05:11: 1000000 INFO @ Mon, 12 Aug 2019 19:05:15: 2000000 INFO @ Mon, 12 Aug 2019 19:05:17: 2000000 INFO @ Mon, 12 Aug 2019 19:05:17: 2000000 INFO @ Mon, 12 Aug 2019 19:05:21: 3000000 INFO @ Mon, 12 Aug 2019 19:05:25: 3000000 INFO @ Mon, 12 Aug 2019 19:05:25: 3000000 INFO @ Mon, 12 Aug 2019 19:05:28: 4000000 INFO @ Mon, 12 Aug 2019 19:05:32: 4000000 INFO @ Mon, 12 Aug 2019 19:05:33: 4000000 INFO @ Mon, 12 Aug 2019 19:05:34: 5000000 INFO @ Mon, 12 Aug 2019 19:05:39: 5000000 INFO @ Mon, 12 Aug 2019 19:05:40: 5000000 INFO @ Mon, 12 Aug 2019 19:05:41: 6000000 INFO @ Mon, 12 Aug 2019 19:05:46: 6000000 INFO @ Mon, 12 Aug 2019 19:05:47: 7000000 INFO @ Mon, 12 Aug 2019 19:05:48: 6000000 INFO @ Mon, 12 Aug 2019 19:05:53: 7000000 INFO @ Mon, 12 Aug 2019 19:05:54: 8000000 INFO @ Mon, 12 Aug 2019 19:05:55: 7000000 INFO @ Mon, 12 Aug 2019 19:05:59: 8000000 INFO @ Mon, 12 Aug 2019 19:06:00: 9000000 INFO @ Mon, 12 Aug 2019 19:06:02: 8000000 INFO @ Mon, 12 Aug 2019 19:06:06: 9000000 INFO @ Mon, 12 Aug 2019 19:06:06: 10000000 INFO @ Mon, 12 Aug 2019 19:06:09: 9000000 INFO @ Mon, 12 Aug 2019 19:06:12: 10000000 INFO @ Mon, 12 Aug 2019 19:06:13: 11000000 INFO @ Mon, 12 Aug 2019 19:06:17: 10000000 INFO @ Mon, 12 Aug 2019 19:06:19: 12000000 INFO @ Mon, 12 Aug 2019 19:06:19: 11000000 INFO @ Mon, 12 Aug 2019 19:06:24: 11000000 INFO @ Mon, 12 Aug 2019 19:06:25: 13000000 INFO @ Mon, 12 Aug 2019 19:06:25: 12000000 INFO @ Mon, 12 Aug 2019 19:06:31: 12000000 INFO @ Mon, 12 Aug 2019 19:06:31: 14000000 INFO @ Mon, 12 Aug 2019 19:06:32: 13000000 INFO @ Mon, 12 Aug 2019 19:06:37: 15000000 INFO @ Mon, 12 Aug 2019 19:06:38: 13000000 INFO @ Mon, 12 Aug 2019 19:06:38: 14000000 INFO @ Mon, 12 Aug 2019 19:06:43: 16000000 INFO @ Mon, 12 Aug 2019 19:06:45: 15000000 INFO @ Mon, 12 Aug 2019 19:06:45: 14000000 INFO @ Mon, 12 Aug 2019 19:06:49: 17000000 INFO @ Mon, 12 Aug 2019 19:06:51: 16000000 INFO @ Mon, 12 Aug 2019 19:06:52: 15000000 INFO @ Mon, 12 Aug 2019 19:06:53: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:06:53: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:06:53: #1 total tags in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:06:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:06:54: #1 tags after filtering in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:54: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:55: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 19:06:55: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 19:06:55: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:55: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:55: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:55: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:55: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:06:55: #2 alternative fragment length(s) may be 1,38,543,576 bps INFO @ Mon, 12 Aug 2019 19:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05_model.r WARNING @ Mon, 12 Aug 2019 19:06:55: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:06:55: #2 You may need to consider one of the other alternative d(s): 1,38,543,576 WARNING @ Mon, 12 Aug 2019 19:06:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:06:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:57: 17000000 INFO @ Mon, 12 Aug 2019 19:06:59: 16000000 INFO @ Mon, 12 Aug 2019 19:07:01: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:07:01: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:07:01: #1 total tags in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:07:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:07:02: #1 tags after filtering in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:02: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:03: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 19:07:03: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 19:07:03: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:03: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:03: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:03: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:03: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:07:03: #2 alternative fragment length(s) may be 1,38,543,576 bps INFO @ Mon, 12 Aug 2019 19:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20_model.r WARNING @ Mon, 12 Aug 2019 19:07:04: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:04: #2 You may need to consider one of the other alternative d(s): 1,38,543,576 WARNING @ Mon, 12 Aug 2019 19:07:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:07:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:06: 17000000 INFO @ Mon, 12 Aug 2019 19:07:10: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:07:10: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:07:10: #1 total tags in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:07:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:07:10: #1 tags after filtering in treatment: 17586382 INFO @ Mon, 12 Aug 2019 19:07:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:10: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:12: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 19:07:12: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 19:07:12: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:12: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:12: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:12: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:12: #2 predicted fragment length is 38 bps INFO @ Mon, 12 Aug 2019 19:07:12: #2 alternative fragment length(s) may be 1,38,543,576 bps INFO @ Mon, 12 Aug 2019 19:07:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10_model.r WARNING @ Mon, 12 Aug 2019 19:07:12: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:12: #2 You may need to consider one of the other alternative d(s): 1,38,543,576 WARNING @ Mon, 12 Aug 2019 19:07:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:07:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.05_summits.bed INFO @ Mon, 12 Aug 2019 19:07:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.20_summits.bed INFO @ Mon, 12 Aug 2019 19:08:03: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (100 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466503/SRX466503.10_summits.bed INFO @ Mon, 12 Aug 2019 19:08:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (331 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。