Job ID = 2590074 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,877,758 reads read : 26,877,758 reads written : 26,877,758 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: 00:06:40 26877758 reads; of these: 26877758 (100.00%) were unpaired; of these: 1663141 (6.19%) aligned 0 times 20502568 (76.28%) aligned exactly 1 time 4712049 (17.53%) aligned >1 times 93.81% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 7478353 / 25214617 = 0.2966 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 19:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.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 19:48:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.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 19:48:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.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 19:48:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:53: 1000000 INFO @ Mon, 12 Aug 2019 19:48:54: 1000000 INFO @ Mon, 12 Aug 2019 19:48:55: 1000000 INFO @ Mon, 12 Aug 2019 19:49:01: 2000000 INFO @ Mon, 12 Aug 2019 19:49:04: 2000000 INFO @ Mon, 12 Aug 2019 19:49:05: 2000000 INFO @ Mon, 12 Aug 2019 19:49:09: 3000000 INFO @ Mon, 12 Aug 2019 19:49:15: 3000000 INFO @ Mon, 12 Aug 2019 19:49:16: 3000000 INFO @ Mon, 12 Aug 2019 19:49:16: 4000000 INFO @ Mon, 12 Aug 2019 19:49:24: 5000000 INFO @ Mon, 12 Aug 2019 19:49:25: 4000000 INFO @ Mon, 12 Aug 2019 19:49:26: 4000000 INFO @ Mon, 12 Aug 2019 19:49:31: 6000000 INFO @ Mon, 12 Aug 2019 19:49:35: 5000000 INFO @ Mon, 12 Aug 2019 19:49:36: 5000000 INFO @ Mon, 12 Aug 2019 19:49:39: 7000000 INFO @ Mon, 12 Aug 2019 19:49:45: 6000000 INFO @ Mon, 12 Aug 2019 19:49:46: 6000000 INFO @ Mon, 12 Aug 2019 19:49:47: 8000000 INFO @ Mon, 12 Aug 2019 19:49:54: 9000000 INFO @ Mon, 12 Aug 2019 19:49:55: 7000000 INFO @ Mon, 12 Aug 2019 19:49:57: 7000000 INFO @ Mon, 12 Aug 2019 19:50:02: 10000000 INFO @ Mon, 12 Aug 2019 19:50:06: 8000000 INFO @ Mon, 12 Aug 2019 19:50:07: 8000000 INFO @ Mon, 12 Aug 2019 19:50:09: 11000000 INFO @ Mon, 12 Aug 2019 19:50:16: 9000000 INFO @ Mon, 12 Aug 2019 19:50:17: 9000000 INFO @ Mon, 12 Aug 2019 19:50:17: 12000000 INFO @ Mon, 12 Aug 2019 19:50:25: 13000000 INFO @ Mon, 12 Aug 2019 19:50:26: 10000000 INFO @ Mon, 12 Aug 2019 19:50:27: 10000000 INFO @ Mon, 12 Aug 2019 19:50:32: 14000000 INFO @ Mon, 12 Aug 2019 19:50:36: 11000000 INFO @ Mon, 12 Aug 2019 19:50:37: 11000000 INFO @ Mon, 12 Aug 2019 19:50:40: 15000000 INFO @ Mon, 12 Aug 2019 19:50:46: 12000000 INFO @ Mon, 12 Aug 2019 19:50:47: 16000000 INFO @ Mon, 12 Aug 2019 19:50:47: 12000000 INFO @ Mon, 12 Aug 2019 19:50:55: 17000000 INFO @ Mon, 12 Aug 2019 19:50:56: 13000000 INFO @ Mon, 12 Aug 2019 19:50:57: 13000000 INFO @ Mon, 12 Aug 2019 19:51:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:51:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:51:01: #1 total tags in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:51:01: #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 19:51:01: #1 tags after filtering in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:51:01: #1 finished! INFO @ Mon, 12 Aug 2019 19:51:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:51:03: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 19:51:03: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 19:51:03: start model_add_line... INFO @ Mon, 12 Aug 2019 19:51:03: start X-correlation... INFO @ Mon, 12 Aug 2019 19:51:03: end of X-cor INFO @ Mon, 12 Aug 2019 19:51:03: #2 finished! INFO @ Mon, 12 Aug 2019 19:51:03: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:51:03: #2 alternative fragment length(s) may be 1,18,46,552,554,559,597 bps INFO @ Mon, 12 Aug 2019 19:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20_model.r WARNING @ Mon, 12 Aug 2019 19:51:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:51:03: #2 You may need to consider one of the other alternative d(s): 1,18,46,552,554,559,597 WARNING @ Mon, 12 Aug 2019 19:51:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:51:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:51:05: 14000000 INFO @ Mon, 12 Aug 2019 19:51:06: 14000000 INFO @ Mon, 12 Aug 2019 19:51:15: 15000000 INFO @ Mon, 12 Aug 2019 19:51:15: 15000000 INFO @ Mon, 12 Aug 2019 19:51:24: 16000000 INFO @ Mon, 12 Aug 2019 19:51:25: 16000000 INFO @ Mon, 12 Aug 2019 19:51:33: 17000000 INFO @ Mon, 12 Aug 2019 19:51:34: 17000000 INFO @ Mon, 12 Aug 2019 19:51:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:51:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:51:40: #1 total tags in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:51:40: #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 19:51:40: #1 tags after filtering in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:51:40: #1 finished! INFO @ Mon, 12 Aug 2019 19:51:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:51:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:51:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:51:40: #1 total tags in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:51:40: #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 19:51:41: #1 tags after filtering in treatment: 17736264 INFO @ Mon, 12 Aug 2019 19:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:51:41: #1 finished! INFO @ Mon, 12 Aug 2019 19:51:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:51:42: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 19:51:42: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 19:51:42: start model_add_line... INFO @ Mon, 12 Aug 2019 19:51:42: start X-correlation... INFO @ Mon, 12 Aug 2019 19:51:42: end of X-cor INFO @ Mon, 12 Aug 2019 19:51:42: #2 finished! INFO @ Mon, 12 Aug 2019 19:51:42: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:51:42: #2 alternative fragment length(s) may be 1,18,46,552,554,559,597 bps INFO @ Mon, 12 Aug 2019 19:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05_model.r WARNING @ Mon, 12 Aug 2019 19:51:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:51:42: #2 You may need to consider one of the other alternative d(s): 1,18,46,552,554,559,597 WARNING @ Mon, 12 Aug 2019 19:51:42: #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 19:51:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:51:42: #2 number of paired peaks: 367 WARNING @ Mon, 12 Aug 2019 19:51:42: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 12 Aug 2019 19:51:42: start model_add_line... INFO @ Mon, 12 Aug 2019 19:51:43: start X-correlation... INFO @ Mon, 12 Aug 2019 19:51:43: end of X-cor INFO @ Mon, 12 Aug 2019 19:51:43: #2 finished! INFO @ Mon, 12 Aug 2019 19:51:43: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:51:43: #2 alternative fragment length(s) may be 1,18,46,552,554,559,597 bps INFO @ Mon, 12 Aug 2019 19:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10_model.r WARNING @ Mon, 12 Aug 2019 19:51:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:51:43: #2 You may need to consider one of the other alternative d(s): 1,18,46,552,554,559,597 WARNING @ Mon, 12 Aug 2019 19:51:43: #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 19:51:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:51:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.20_summits.bed INFO @ Mon, 12 Aug 2019 19:52:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:52:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:52:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.05_summits.bed INFO @ Mon, 12 Aug 2019 19:52:40: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494916/SRX494916.10_summits.bed INFO @ Mon, 12 Aug 2019 19:52:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。