Job ID = 2589885 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,852,696 reads read : 6,852,696 reads written : 6,852,696 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947520.sra.cache’: 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: 00:01:11 6852696 reads; of these: 6852696 (100.00%) were unpaired; of these: 115517 (1.69%) aligned 0 times 5674077 (82.80%) aligned exactly 1 time 1063102 (15.51%) aligned >1 times 98.31% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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_rmdupse_core] 1657411 / 6737179 = 0.2460 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 18:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.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 18:43:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.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 18:43:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.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 18:43:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:29: 1000000 INFO @ Mon, 12 Aug 2019 18:43:32: 1000000 INFO @ Mon, 12 Aug 2019 18:43:32: 1000000 INFO @ Mon, 12 Aug 2019 18:43:36: 2000000 INFO @ Mon, 12 Aug 2019 18:43:39: 2000000 INFO @ Mon, 12 Aug 2019 18:43:40: 2000000 INFO @ Mon, 12 Aug 2019 18:43:43: 3000000 INFO @ Mon, 12 Aug 2019 18:43:46: 3000000 INFO @ Mon, 12 Aug 2019 18:43:48: 3000000 INFO @ Mon, 12 Aug 2019 18:43:50: 4000000 INFO @ Mon, 12 Aug 2019 18:43:54: 4000000 INFO @ Mon, 12 Aug 2019 18:43:57: 4000000 INFO @ Mon, 12 Aug 2019 18:43:57: 5000000 INFO @ Mon, 12 Aug 2019 18:43:58: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:58: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:58: #1 total tags in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:43:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:58: #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 18:43:58: #1 tags after filtering in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:58: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:59: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 18:43:59: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:59: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:59: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:59: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:59: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:59: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:43:59: #2 alternative fragment length(s) may be 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 bps INFO @ Mon, 12 Aug 2019 18:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05_model.r WARNING @ Mon, 12 Aug 2019 18:43:59: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:43:59: #2 You may need to consider one of the other alternative d(s): 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 WARNING @ Mon, 12 Aug 2019 18:43:59: #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 18:43:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:01: 5000000 INFO @ Mon, 12 Aug 2019 18:44:02: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:44:02: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:44:02: #1 total tags in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:44:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:44:02: #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 18:44:02: #1 tags after filtering in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:44:02: #1 finished! INFO @ Mon, 12 Aug 2019 18:44:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:44:02: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 18:44:02: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 18:44:02: start model_add_line... INFO @ Mon, 12 Aug 2019 18:44:02: start X-correlation... INFO @ Mon, 12 Aug 2019 18:44:02: end of X-cor INFO @ Mon, 12 Aug 2019 18:44:02: #2 finished! INFO @ Mon, 12 Aug 2019 18:44:02: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:44:02: #2 alternative fragment length(s) may be 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 bps INFO @ Mon, 12 Aug 2019 18:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20_model.r WARNING @ Mon, 12 Aug 2019 18:44:02: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:44:02: #2 You may need to consider one of the other alternative d(s): 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 WARNING @ Mon, 12 Aug 2019 18:44:02: #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 18:44:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:05: 5000000 INFO @ Mon, 12 Aug 2019 18:44:05: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:44:05: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:44:05: #1 total tags in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:44:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:44:05: #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 18:44:05: #1 tags after filtering in treatment: 5079768 INFO @ Mon, 12 Aug 2019 18:44:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:44:05: #1 finished! INFO @ Mon, 12 Aug 2019 18:44:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:44:06: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 18:44:06: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 18:44:06: start model_add_line... INFO @ Mon, 12 Aug 2019 18:44:06: start X-correlation... INFO @ Mon, 12 Aug 2019 18:44:06: end of X-cor INFO @ Mon, 12 Aug 2019 18:44:06: #2 finished! INFO @ Mon, 12 Aug 2019 18:44:06: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:44:06: #2 alternative fragment length(s) may be 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 bps INFO @ Mon, 12 Aug 2019 18:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10_model.r WARNING @ Mon, 12 Aug 2019 18:44:06: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:44:06: #2 You may need to consider one of the other alternative d(s): 2,34,60,87,105,124,130,143,168,195,221,252,273,301,330,351,382,410,435,469,494,519,545,574 WARNING @ Mon, 12 Aug 2019 18:44:06: #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 18:44:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:44:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.05_summits.bed INFO @ Mon, 12 Aug 2019 18:44:20: Done! INFO @ Mon, 12 Aug 2019 18:44:20: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.20_summits.bed INFO @ Mon, 12 Aug 2019 18:44:24: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331285/SRX331285.10_summits.bed INFO @ Mon, 12 Aug 2019 18:44:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 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。