Job ID = 1290625 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,041,038 reads read : 11,041,038 reads written : 11,041,038 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: 00:02:41 11041038 reads; of these: 11041038 (100.00%) were unpaired; of these: 1167873 (10.58%) aligned 0 times 8131759 (73.65%) aligned exactly 1 time 1741406 (15.77%) aligned >1 times 89.42% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 913467 / 9873165 = 0.0925 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 @ Sat, 01 Jun 2019 21:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.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 @ Sat, 01 Jun 2019 21:49:55: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:49:55: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.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 @ Sat, 01 Jun 2019 21:49:55: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:49:55: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.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 @ Sat, 01 Jun 2019 21:49:56: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:49:56: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:03: 1000000 INFO @ Sat, 01 Jun 2019 21:50:03: 1000000 INFO @ Sat, 01 Jun 2019 21:50:03: 1000000 INFO @ Sat, 01 Jun 2019 21:50:09: 2000000 INFO @ Sat, 01 Jun 2019 21:50:10: 2000000 INFO @ Sat, 01 Jun 2019 21:50:11: 2000000 INFO @ Sat, 01 Jun 2019 21:50:16: 3000000 INFO @ Sat, 01 Jun 2019 21:50:18: 3000000 INFO @ Sat, 01 Jun 2019 21:50:18: 3000000 INFO @ Sat, 01 Jun 2019 21:50:22: 4000000 INFO @ Sat, 01 Jun 2019 21:50:24: 4000000 INFO @ Sat, 01 Jun 2019 21:50:25: 4000000 INFO @ Sat, 01 Jun 2019 21:50:29: 5000000 INFO @ Sat, 01 Jun 2019 21:50:31: 5000000 INFO @ Sat, 01 Jun 2019 21:50:32: 5000000 INFO @ Sat, 01 Jun 2019 21:50:36: 6000000 INFO @ Sat, 01 Jun 2019 21:50:39: 6000000 INFO @ Sat, 01 Jun 2019 21:50:39: 6000000 INFO @ Sat, 01 Jun 2019 21:50:43: 7000000 INFO @ Sat, 01 Jun 2019 21:50:46: 7000000 INFO @ Sat, 01 Jun 2019 21:50:47: 7000000 INFO @ Sat, 01 Jun 2019 21:50:50: 8000000 INFO @ Sat, 01 Jun 2019 21:50:54: 8000000 INFO @ Sat, 01 Jun 2019 21:50:55: 8000000 INFO @ Sat, 01 Jun 2019 21:50:57: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:50:57: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:50:57: #1 total tags in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:50:57: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:50:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:50:58: #1 tags after filtering in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:50:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:50:58: #1 finished! INFO @ Sat, 01 Jun 2019 21:50:58: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:50:58: #2 number of paired peaks: 377 WARNING @ Sat, 01 Jun 2019 21:50:58: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 01 Jun 2019 21:50:58: start model_add_line... INFO @ Sat, 01 Jun 2019 21:50:59: start X-correlation... INFO @ Sat, 01 Jun 2019 21:50:59: end of X-cor INFO @ Sat, 01 Jun 2019 21:50:59: #2 finished! INFO @ Sat, 01 Jun 2019 21:50:59: #2 predicted fragment length is 58 bps INFO @ Sat, 01 Jun 2019 21:50:59: #2 alternative fragment length(s) may be 4,58,568 bps INFO @ Sat, 01 Jun 2019 21:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20_model.r WARNING @ Sat, 01 Jun 2019 21:50:59: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:50:59: #2 You may need to consider one of the other alternative d(s): 4,58,568 WARNING @ Sat, 01 Jun 2019 21:50:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:50:59: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:01: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:01: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:01: #1 total tags in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:51:01: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:01: #1 tags after filtering in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:01: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:01: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:02: #2 number of paired peaks: 377 WARNING @ Sat, 01 Jun 2019 21:51:02: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:02: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:02: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:02: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:02: #1 total tags in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:51:02: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:02: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:02: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:02: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:02: #2 predicted fragment length is 58 bps INFO @ Sat, 01 Jun 2019 21:51:02: #2 alternative fragment length(s) may be 4,58,568 bps INFO @ Sat, 01 Jun 2019 21:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05_model.r WARNING @ Sat, 01 Jun 2019 21:51:02: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:02: #2 You may need to consider one of the other alternative d(s): 4,58,568 WARNING @ Sat, 01 Jun 2019 21:51:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:02: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:02: #1 tags after filtering in treatment: 8959698 INFO @ Sat, 01 Jun 2019 21:51:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:02: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:02: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:03: #2 number of paired peaks: 377 WARNING @ Sat, 01 Jun 2019 21:51:03: Fewer paired peaks (377) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 377 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:03: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:03: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:03: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:03: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:03: #2 predicted fragment length is 58 bps INFO @ Sat, 01 Jun 2019 21:51:03: #2 alternative fragment length(s) may be 4,58,568 bps INFO @ Sat, 01 Jun 2019 21:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10_model.r WARNING @ Sat, 01 Jun 2019 21:51:03: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:03: #2 You may need to consider one of the other alternative d(s): 4,58,568 WARNING @ Sat, 01 Jun 2019 21:51:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:03: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:25: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:51:27: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:51:29: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.20_summits.bed INFO @ Sat, 01 Jun 2019 21:51:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.05_summits.bed INFO @ Sat, 01 Jun 2019 21:51:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (683 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982084/SRX982084.10_summits.bed INFO @ Sat, 01 Jun 2019 21:51:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (348 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。