Job ID = 1292336 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,754,124 reads read : 16,754,124 reads written : 16,754,124 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 16754124 reads; of these: 16754124 (100.00%) were unpaired; of these: 2019887 (12.06%) aligned 0 times 12116565 (72.32%) aligned exactly 1 time 2617672 (15.62%) aligned >1 times 87.94% 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] 8307418 / 14734237 = 0.5638 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 18:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.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 18:07:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.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 18:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.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 18:07:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:07:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:07:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:08:00: 1000000 INFO @ Sun, 02 Jun 2019 18:08:01: 1000000 INFO @ Sun, 02 Jun 2019 18:08:01: 1000000 INFO @ Sun, 02 Jun 2019 18:08:06: 2000000 INFO @ Sun, 02 Jun 2019 18:08:08: 2000000 INFO @ Sun, 02 Jun 2019 18:08:08: 2000000 INFO @ Sun, 02 Jun 2019 18:08:13: 3000000 INFO @ Sun, 02 Jun 2019 18:08:15: 3000000 INFO @ Sun, 02 Jun 2019 18:08:15: 3000000 INFO @ Sun, 02 Jun 2019 18:08:19: 4000000 INFO @ Sun, 02 Jun 2019 18:08:22: 4000000 INFO @ Sun, 02 Jun 2019 18:08:22: 4000000 INFO @ Sun, 02 Jun 2019 18:08:25: 5000000 INFO @ Sun, 02 Jun 2019 18:08:30: 5000000 INFO @ Sun, 02 Jun 2019 18:08:30: 5000000 INFO @ Sun, 02 Jun 2019 18:08:32: 6000000 INFO @ Sun, 02 Jun 2019 18:08:35: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:08:35: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:08:35: #1 total tags in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:35: #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 18:08:35: #1 tags after filtering in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:35: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:35: #2 number of paired peaks: 573 WARNING @ Sun, 02 Jun 2019 18:08:35: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:35: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:35: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:35: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:35: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:35: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:08:35: #2 alternative fragment length(s) may be 3,47,547 bps INFO @ Sun, 02 Jun 2019 18:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10_model.r WARNING @ Sun, 02 Jun 2019 18:08:35: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:35: #2 You may need to consider one of the other alternative d(s): 3,47,547 WARNING @ Sun, 02 Jun 2019 18:08:35: #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 18:08:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:37: 6000000 INFO @ Sun, 02 Jun 2019 18:08:37: 6000000 INFO @ Sun, 02 Jun 2019 18:08:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:08:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:08:40: #1 total tags in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:40: #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 18:08:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:08:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:08:40: #1 total tags in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:40: #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 18:08:40: #1 tags after filtering in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:40: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:40: #1 tags after filtering in treatment: 6426819 INFO @ Sun, 02 Jun 2019 18:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:40: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:41: #2 number of paired peaks: 573 WARNING @ Sun, 02 Jun 2019 18:08:41: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:41: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:41: #2 number of paired peaks: 573 WARNING @ Sun, 02 Jun 2019 18:08:41: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:41: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:41: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:41: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:41: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:41: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:41: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:08:41: #2 alternative fragment length(s) may be 3,47,547 bps INFO @ Sun, 02 Jun 2019 18:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20_model.r WARNING @ Sun, 02 Jun 2019 18:08:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:41: #2 You may need to consider one of the other alternative d(s): 3,47,547 WARNING @ Sun, 02 Jun 2019 18:08:41: #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 18:08:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:41: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:41: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:41: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 18:08:41: #2 alternative fragment length(s) may be 3,47,547 bps INFO @ Sun, 02 Jun 2019 18:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05_model.r WARNING @ Sun, 02 Jun 2019 18:08:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:08:41: #2 You may need to consider one of the other alternative d(s): 3,47,547 WARNING @ Sun, 02 Jun 2019 18:08:41: #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 18:08:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.10_summits.bed INFO @ Sun, 02 Jun 2019 18:09:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.20_summits.bed INFO @ Sun, 02 Jun 2019 18:09:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331360/SRX331360.05_summits.bed INFO @ Sun, 02 Jun 2019 18:09:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。