Job ID = 1292330 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 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: 00:04:16 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289121 (1.53%) aligned 0 times 14953785 (79.31%) aligned exactly 1 time 3611908 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 3522201 / 18565693 = 0.1897 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 18:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.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 18:01:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.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 18:01:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.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 18:01:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:02:00: 1000000 INFO @ Sun, 02 Jun 2019 18:02:00: 1000000 INFO @ Sun, 02 Jun 2019 18:02:00: 1000000 INFO @ Sun, 02 Jun 2019 18:02:07: 2000000 INFO @ Sun, 02 Jun 2019 18:02:07: 2000000 INFO @ Sun, 02 Jun 2019 18:02:07: 2000000 INFO @ Sun, 02 Jun 2019 18:02:14: 3000000 INFO @ Sun, 02 Jun 2019 18:02:14: 3000000 INFO @ Sun, 02 Jun 2019 18:02:14: 3000000 INFO @ Sun, 02 Jun 2019 18:02:21: 4000000 INFO @ Sun, 02 Jun 2019 18:02:21: 4000000 INFO @ Sun, 02 Jun 2019 18:02:21: 4000000 INFO @ Sun, 02 Jun 2019 18:02:27: 5000000 INFO @ Sun, 02 Jun 2019 18:02:28: 5000000 INFO @ Sun, 02 Jun 2019 18:02:28: 5000000 INFO @ Sun, 02 Jun 2019 18:02:34: 6000000 INFO @ Sun, 02 Jun 2019 18:02:35: 6000000 INFO @ Sun, 02 Jun 2019 18:02:35: 6000000 INFO @ Sun, 02 Jun 2019 18:02:41: 7000000 INFO @ Sun, 02 Jun 2019 18:02:41: 7000000 INFO @ Sun, 02 Jun 2019 18:02:41: 7000000 INFO @ Sun, 02 Jun 2019 18:02:47: 8000000 INFO @ Sun, 02 Jun 2019 18:02:48: 8000000 INFO @ Sun, 02 Jun 2019 18:02:48: 8000000 INFO @ Sun, 02 Jun 2019 18:02:54: 9000000 INFO @ Sun, 02 Jun 2019 18:02:55: 9000000 INFO @ Sun, 02 Jun 2019 18:02:55: 9000000 INFO @ Sun, 02 Jun 2019 18:03:01: 10000000 INFO @ Sun, 02 Jun 2019 18:03:02: 10000000 INFO @ Sun, 02 Jun 2019 18:03:02: 10000000 INFO @ Sun, 02 Jun 2019 18:03:07: 11000000 INFO @ Sun, 02 Jun 2019 18:03:09: 11000000 INFO @ Sun, 02 Jun 2019 18:03:09: 11000000 INFO @ Sun, 02 Jun 2019 18:03:14: 12000000 INFO @ Sun, 02 Jun 2019 18:03:16: 12000000 INFO @ Sun, 02 Jun 2019 18:03:16: 12000000 INFO @ Sun, 02 Jun 2019 18:03:21: 13000000 INFO @ Sun, 02 Jun 2019 18:03:22: 13000000 INFO @ Sun, 02 Jun 2019 18:03:23: 13000000 INFO @ Sun, 02 Jun 2019 18:03:27: 14000000 INFO @ Sun, 02 Jun 2019 18:03:29: 14000000 INFO @ Sun, 02 Jun 2019 18:03:30: 14000000 INFO @ Sun, 02 Jun 2019 18:03:34: 15000000 INFO @ Sun, 02 Jun 2019 18:03:34: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:34: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:34: #1 total tags in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:34: #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 18:03:34: #1 tags after filtering in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:34: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:36: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 18:03:36: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:36: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:36: 15000000 INFO @ Sun, 02 Jun 2019 18:03:36: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:36: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:36: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:36: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:03:36: #2 alternative fragment length(s) may be 2,61,598 bps INFO @ Sun, 02 Jun 2019 18:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10_model.r WARNING @ Sun, 02 Jun 2019 18:03:36: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:36: #2 You may need to consider one of the other alternative d(s): 2,61,598 WARNING @ Sun, 02 Jun 2019 18:03:36: #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 18:03:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:36: 15000000 INFO @ Sun, 02 Jun 2019 18:03:36: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:36: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:36: #1 total tags in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:36: #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 18:03:37: #1 tags after filtering in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:37: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:37: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:03:37: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:03:37: #1 total tags in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:37: #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 18:03:37: #1 tags after filtering in treatment: 15043492 INFO @ Sun, 02 Jun 2019 18:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:03:37: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:38: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 18:03:38: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:38: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:38: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:38: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:38: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:38: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:03:38: #2 alternative fragment length(s) may be 2,61,598 bps INFO @ Sun, 02 Jun 2019 18:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05_model.r WARNING @ Sun, 02 Jun 2019 18:03:38: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:38: #2 You may need to consider one of the other alternative d(s): 2,61,598 WARNING @ Sun, 02 Jun 2019 18:03:38: #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 18:03:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:38: #2 number of paired peaks: 429 WARNING @ Sun, 02 Jun 2019 18:03:38: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:38: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:38: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:39: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:39: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:39: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:03:39: #2 alternative fragment length(s) may be 2,61,598 bps INFO @ Sun, 02 Jun 2019 18:03:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20_model.r WARNING @ Sun, 02 Jun 2019 18:03:39: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:03:39: #2 You may need to consider one of the other alternative d(s): 2,61,598 WARNING @ Sun, 02 Jun 2019 18:03:39: #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 18:03:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:04:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.10_summits.bed INFO @ Sun, 02 Jun 2019 18:04:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1443 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.20_summits.bed INFO @ Sun, 02 Jun 2019 18:04:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331354/SRX331354.05_summits.bed INFO @ Sun, 02 Jun 2019 18:04:37: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5822 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。