Job ID = 2590158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,906,742 reads read : 22,906,742 reads written : 22,906,742 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: 00:05:17 22906742 reads; of these: 22906742 (100.00%) were unpaired; of these: 3076032 (13.43%) aligned 0 times 16016161 (69.92%) aligned exactly 1 time 3814549 (16.65%) aligned >1 times 86.57% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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 12 files... [bam_rmdupse_core] 2899937 / 19830710 = 0.1462 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 20:08:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.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 20:08:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.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 20:08:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.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 20:08:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:38: 1000000 INFO @ Mon, 12 Aug 2019 20:08:39: 1000000 INFO @ Mon, 12 Aug 2019 20:08:41: 1000000 INFO @ Mon, 12 Aug 2019 20:08:47: 2000000 INFO @ Mon, 12 Aug 2019 20:08:47: 2000000 INFO @ Mon, 12 Aug 2019 20:08:49: 2000000 INFO @ Mon, 12 Aug 2019 20:08:56: 3000000 INFO @ Mon, 12 Aug 2019 20:08:56: 3000000 INFO @ Mon, 12 Aug 2019 20:08:58: 3000000 INFO @ Mon, 12 Aug 2019 20:09:05: 4000000 INFO @ Mon, 12 Aug 2019 20:09:05: 4000000 INFO @ Mon, 12 Aug 2019 20:09:07: 4000000 INFO @ Mon, 12 Aug 2019 20:09:13: 5000000 INFO @ Mon, 12 Aug 2019 20:09:14: 5000000 INFO @ Mon, 12 Aug 2019 20:09:16: 5000000 INFO @ Mon, 12 Aug 2019 20:09:22: 6000000 INFO @ Mon, 12 Aug 2019 20:09:23: 6000000 INFO @ Mon, 12 Aug 2019 20:09:25: 6000000 INFO @ Mon, 12 Aug 2019 20:09:30: 7000000 INFO @ Mon, 12 Aug 2019 20:09:32: 7000000 INFO @ Mon, 12 Aug 2019 20:09:34: 7000000 INFO @ Mon, 12 Aug 2019 20:09:39: 8000000 INFO @ Mon, 12 Aug 2019 20:09:41: 8000000 INFO @ Mon, 12 Aug 2019 20:09:43: 8000000 INFO @ Mon, 12 Aug 2019 20:09:47: 9000000 INFO @ Mon, 12 Aug 2019 20:09:50: 9000000 INFO @ Mon, 12 Aug 2019 20:09:52: 9000000 INFO @ Mon, 12 Aug 2019 20:09:56: 10000000 INFO @ Mon, 12 Aug 2019 20:09:59: 10000000 INFO @ Mon, 12 Aug 2019 20:10:01: 10000000 INFO @ Mon, 12 Aug 2019 20:10:04: 11000000 INFO @ Mon, 12 Aug 2019 20:10:08: 11000000 INFO @ Mon, 12 Aug 2019 20:10:10: 11000000 INFO @ Mon, 12 Aug 2019 20:10:13: 12000000 INFO @ Mon, 12 Aug 2019 20:10:17: 12000000 INFO @ Mon, 12 Aug 2019 20:10:19: 12000000 INFO @ Mon, 12 Aug 2019 20:10:21: 13000000 INFO @ Mon, 12 Aug 2019 20:10:26: 13000000 INFO @ Mon, 12 Aug 2019 20:10:27: 13000000 INFO @ Mon, 12 Aug 2019 20:10:29: 14000000 INFO @ Mon, 12 Aug 2019 20:10:35: 14000000 INFO @ Mon, 12 Aug 2019 20:10:36: 14000000 INFO @ Mon, 12 Aug 2019 20:10:37: 15000000 INFO @ Mon, 12 Aug 2019 20:10:43: 15000000 INFO @ Mon, 12 Aug 2019 20:10:45: 15000000 INFO @ Mon, 12 Aug 2019 20:10:45: 16000000 INFO @ Mon, 12 Aug 2019 20:10:52: 16000000 INFO @ Mon, 12 Aug 2019 20:10:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:10:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:10:53: #1 total tags in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:10:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:53: #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 20:10:53: #1 tags after filtering in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:10:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:53: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:54: 16000000 INFO @ Mon, 12 Aug 2019 20:10:55: #2 number of paired peaks: 218 WARNING @ Mon, 12 Aug 2019 20:10:55: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:55: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:55: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:55: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:55: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:55: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:10:55: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Mon, 12 Aug 2019 20:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10_model.r WARNING @ Mon, 12 Aug 2019 20:10:55: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:55: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Mon, 12 Aug 2019 20:10:55: #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 20:10:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:01: #1 total tags in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:11:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:01: #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 20:11:01: #1 tags after filtering in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:11:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:01: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:02: #1 total tags in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:11:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:02: #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 20:11:02: #2 number of paired peaks: 218 WARNING @ Mon, 12 Aug 2019 20:11:02: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 12 Aug 2019 20:11:02: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:02: #1 tags after filtering in treatment: 16930773 INFO @ Mon, 12 Aug 2019 20:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:02: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:03: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:03: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:03: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:03: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:11:03: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Mon, 12 Aug 2019 20:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05_model.r WARNING @ Mon, 12 Aug 2019 20:11:03: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:11:03: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Mon, 12 Aug 2019 20:11:03: #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 20:11:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:04: #2 number of paired peaks: 218 WARNING @ Mon, 12 Aug 2019 20:11:04: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 12 Aug 2019 20:11:04: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:04: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:04: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:04: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:04: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 20:11:04: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Mon, 12 Aug 2019 20:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20_model.r WARNING @ Mon, 12 Aug 2019 20:11:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:11:04: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Mon, 12 Aug 2019 20:11:04: #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 20:11:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.10_summits.bed INFO @ Mon, 12 Aug 2019 20:11:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (708 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.05_summits.bed INFO @ Mon, 12 Aug 2019 20:12:03: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2583 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495028/SRX495028.20_summits.bed INFO @ Mon, 12 Aug 2019 20:12:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。