Job ID = 2589974 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,287,635 reads read : 16,287,635 reads written : 16,287,635 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163571.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: 00:03:44 16287635 reads; of these: 16287635 (100.00%) were unpaired; of these: 230276 (1.41%) aligned 0 times 13725558 (84.27%) aligned exactly 1 time 2331801 (14.32%) aligned >1 times 98.59% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 3074659 / 16057359 = 0.1915 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 19:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.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 19:02:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.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 19:02:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.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 19:02:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:37: 1000000 INFO @ Mon, 12 Aug 2019 19:02:37: 1000000 INFO @ Mon, 12 Aug 2019 19:02:39: 1000000 INFO @ Mon, 12 Aug 2019 19:02:44: 2000000 INFO @ Mon, 12 Aug 2019 19:02:44: 2000000 INFO @ Mon, 12 Aug 2019 19:02:46: 2000000 INFO @ Mon, 12 Aug 2019 19:02:50: 3000000 INFO @ Mon, 12 Aug 2019 19:02:50: 3000000 INFO @ Mon, 12 Aug 2019 19:02:52: 3000000 INFO @ Mon, 12 Aug 2019 19:02:56: 4000000 INFO @ Mon, 12 Aug 2019 19:02:57: 4000000 INFO @ Mon, 12 Aug 2019 19:02:59: 4000000 INFO @ Mon, 12 Aug 2019 19:03:03: 5000000 INFO @ Mon, 12 Aug 2019 19:03:04: 5000000 INFO @ Mon, 12 Aug 2019 19:03:05: 5000000 INFO @ Mon, 12 Aug 2019 19:03:09: 6000000 INFO @ Mon, 12 Aug 2019 19:03:10: 6000000 INFO @ Mon, 12 Aug 2019 19:03:12: 6000000 INFO @ Mon, 12 Aug 2019 19:03:15: 7000000 INFO @ Mon, 12 Aug 2019 19:03:17: 7000000 INFO @ Mon, 12 Aug 2019 19:03:18: 7000000 INFO @ Mon, 12 Aug 2019 19:03:21: 8000000 INFO @ Mon, 12 Aug 2019 19:03:23: 8000000 INFO @ Mon, 12 Aug 2019 19:03:26: 8000000 INFO @ Mon, 12 Aug 2019 19:03:27: 9000000 INFO @ Mon, 12 Aug 2019 19:03:30: 9000000 INFO @ Mon, 12 Aug 2019 19:03:34: 10000000 INFO @ Mon, 12 Aug 2019 19:03:34: 9000000 INFO @ Mon, 12 Aug 2019 19:03:37: 10000000 INFO @ Mon, 12 Aug 2019 19:03:40: 11000000 INFO @ Mon, 12 Aug 2019 19:03:41: 10000000 INFO @ Mon, 12 Aug 2019 19:03:43: 11000000 INFO @ Mon, 12 Aug 2019 19:03:46: 12000000 INFO @ Mon, 12 Aug 2019 19:03:49: 11000000 INFO @ Mon, 12 Aug 2019 19:03:50: 12000000 INFO @ Mon, 12 Aug 2019 19:03:52: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:03:52: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:03:52: #1 total tags in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:03:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:52: #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 19:03:52: #1 tags after filtering in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:52: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:53: #2 number of paired peaks: 207 WARNING @ Mon, 12 Aug 2019 19:03:53: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:53: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:54: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:54: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:54: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:54: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 19:03:54: #2 alternative fragment length(s) may be 2,47,262,537,598 bps INFO @ Mon, 12 Aug 2019 19:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10_model.r WARNING @ Mon, 12 Aug 2019 19:03:54: #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 19:03:54: #2 You may need to consider one of the other alternative d(s): 2,47,262,537,598 WARNING @ Mon, 12 Aug 2019 19:03:54: #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 19:03:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:55: 12000000 INFO @ Mon, 12 Aug 2019 19:03:56: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:03:56: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:03:56: #1 total tags in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:03:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:56: #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 19:03:56: #1 tags after filtering in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:56: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:58: #2 number of paired peaks: 207 WARNING @ Mon, 12 Aug 2019 19:03:58: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:58: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:58: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:58: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:58: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:58: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 19:03:58: #2 alternative fragment length(s) may be 2,47,262,537,598 bps INFO @ Mon, 12 Aug 2019 19:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05_model.r WARNING @ Mon, 12 Aug 2019 19:03:58: #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 19:03:58: #2 You may need to consider one of the other alternative d(s): 2,47,262,537,598 WARNING @ Mon, 12 Aug 2019 19:03:58: #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 19:03:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:04:02: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:04:02: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:04:02: #1 total tags in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:04:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:04:02: #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 19:04:02: #1 tags after filtering in treatment: 12982700 INFO @ Mon, 12 Aug 2019 19:04:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:04:02: #1 finished! INFO @ Mon, 12 Aug 2019 19:04:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:04:03: #2 number of paired peaks: 207 WARNING @ Mon, 12 Aug 2019 19:04:03: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Mon, 12 Aug 2019 19:04:03: start model_add_line... INFO @ Mon, 12 Aug 2019 19:04:03: start X-correlation... INFO @ Mon, 12 Aug 2019 19:04:03: end of X-cor INFO @ Mon, 12 Aug 2019 19:04:03: #2 finished! INFO @ Mon, 12 Aug 2019 19:04:03: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 19:04:03: #2 alternative fragment length(s) may be 2,47,262,537,598 bps INFO @ Mon, 12 Aug 2019 19:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20_model.r WARNING @ Mon, 12 Aug 2019 19:04:03: #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 19:04:03: #2 You may need to consider one of the other alternative d(s): 2,47,262,537,598 WARNING @ Mon, 12 Aug 2019 19:04:03: #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 19:04:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:04:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.10_summits.bed INFO @ Mon, 12 Aug 2019 19:04:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.05_summits.bed INFO @ Mon, 12 Aug 2019 19:04:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:04:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:04:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:04:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466505/SRX466505.20_summits.bed INFO @ Mon, 12 Aug 2019 19:04:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 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。