Job ID = 4178403 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,029,672 reads read : 24,059,344 reads written : 12,029,672 reads 0-length : 12,029,672 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:52 12029672 reads; of these: 12029672 (100.00%) were unpaired; of these: 399008 (3.32%) aligned 0 times 9610063 (79.89%) aligned exactly 1 time 2020601 (16.80%) aligned >1 times 96.68% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1044440 / 11630664 = 0.0898 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.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 @ Thu, 05 Dec 2019 12:30:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:08: 1000000 INFO @ Thu, 05 Dec 2019 12:30:13: 2000000 INFO @ Thu, 05 Dec 2019 12:30:18: 3000000 INFO @ Thu, 05 Dec 2019 12:30:23: 4000000 INFO @ Thu, 05 Dec 2019 12:30:27: 5000000 INFO @ Thu, 05 Dec 2019 12:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.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 @ Thu, 05 Dec 2019 12:30:32: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:32: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:32: 6000000 INFO @ Thu, 05 Dec 2019 12:30:37: 1000000 INFO @ Thu, 05 Dec 2019 12:30:37: 7000000 INFO @ Thu, 05 Dec 2019 12:30:42: 2000000 INFO @ Thu, 05 Dec 2019 12:30:43: 8000000 INFO @ Thu, 05 Dec 2019 12:30:48: 3000000 INFO @ Thu, 05 Dec 2019 12:30:48: 9000000 INFO @ Thu, 05 Dec 2019 12:30:53: 4000000 INFO @ Thu, 05 Dec 2019 12:30:53: 10000000 INFO @ Thu, 05 Dec 2019 12:30:56: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:30:56: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:30:56: #1 total tags in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:30:56: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:56: #1 tags after filtering in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:56: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:56: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:57: #2 number of paired peaks: 325 WARNING @ Thu, 05 Dec 2019 12:30:57: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 05 Dec 2019 12:30:57: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:57: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:57: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:57: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:57: #2 predicted fragment length is 71 bps INFO @ Thu, 05 Dec 2019 12:30:57: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 05 Dec 2019 12:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05_model.r WARNING @ Thu, 05 Dec 2019 12:30:57: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:30:57: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 05 Dec 2019 12:30:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:30:57: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:58: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.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 @ Thu, 05 Dec 2019 12:31:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:31:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:31:03: 6000000 INFO @ Thu, 05 Dec 2019 12:31:07: 1000000 INFO @ Thu, 05 Dec 2019 12:31:09: 7000000 INFO @ Thu, 05 Dec 2019 12:31:13: 2000000 INFO @ Thu, 05 Dec 2019 12:31:14: 8000000 INFO @ Thu, 05 Dec 2019 12:31:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:18: 3000000 INFO @ Thu, 05 Dec 2019 12:31:20: 9000000 INFO @ Thu, 05 Dec 2019 12:31:24: 4000000 INFO @ Thu, 05 Dec 2019 12:31:25: 10000000 INFO @ Thu, 05 Dec 2019 12:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.05_summits.bed INFO @ Thu, 05 Dec 2019 12:31:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1076 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:31:29: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:31:29: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:31:29: #1 total tags in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:31:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:29: #1 tags after filtering in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:31:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:29: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:29: 5000000 INFO @ Thu, 05 Dec 2019 12:31:30: #2 number of paired peaks: 325 WARNING @ Thu, 05 Dec 2019 12:31:30: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 05 Dec 2019 12:31:30: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:30: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:30: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:30: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:30: #2 predicted fragment length is 71 bps INFO @ Thu, 05 Dec 2019 12:31:30: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 05 Dec 2019 12:31:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10_model.r WARNING @ Thu, 05 Dec 2019 12:31:30: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:31:30: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 05 Dec 2019 12:31:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:31:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:34: 6000000 INFO @ Thu, 05 Dec 2019 12:31:39: 7000000 INFO @ Thu, 05 Dec 2019 12:31:44: 8000000 INFO @ Thu, 05 Dec 2019 12:31:49: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:49: 9000000 INFO @ Thu, 05 Dec 2019 12:31:54: 10000000 INFO @ Thu, 05 Dec 2019 12:31:57: #1 tag size is determined as 76 bps INFO @ Thu, 05 Dec 2019 12:31:57: #1 tag size = 76 INFO @ Thu, 05 Dec 2019 12:31:57: #1 total tags in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:31:57: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:57: #1 tags after filtering in treatment: 10586224 INFO @ Thu, 05 Dec 2019 12:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:57: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:57: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:58: #2 number of paired peaks: 325 WARNING @ Thu, 05 Dec 2019 12:31:58: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Thu, 05 Dec 2019 12:31:58: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:58: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:58: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:58: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:58: #2 predicted fragment length is 71 bps INFO @ Thu, 05 Dec 2019 12:31:58: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 05 Dec 2019 12:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20_model.r WARNING @ Thu, 05 Dec 2019 12:31:58: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:31:58: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 05 Dec 2019 12:31:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:31:58: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.10_summits.bed INFO @ Thu, 05 Dec 2019 12:32:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5729150/SRX5729150.20_summits.bed INFO @ Thu, 05 Dec 2019 12:32:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。