Job ID = 2589948 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,748,232 reads read : 21,748,232 reads written : 21,748,232 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163523.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: 00:05:55 21748232 reads; of these: 21748232 (100.00%) were unpaired; of these: 258561 (1.19%) aligned 0 times 19257399 (88.55%) aligned exactly 1 time 2232272 (10.26%) aligned >1 times 98.81% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 5213872 / 21489671 = 0.2426 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 19:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.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 19:03:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.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 19:03:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.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 19:03:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:21: 1000000 INFO @ Mon, 12 Aug 2019 19:03:22: 1000000 INFO @ Mon, 12 Aug 2019 19:03:23: 1000000 INFO @ Mon, 12 Aug 2019 19:03:28: 2000000 INFO @ Mon, 12 Aug 2019 19:03:29: 2000000 INFO @ Mon, 12 Aug 2019 19:03:32: 2000000 INFO @ Mon, 12 Aug 2019 19:03:35: 3000000 INFO @ Mon, 12 Aug 2019 19:03:36: 3000000 INFO @ Mon, 12 Aug 2019 19:03:42: 3000000 INFO @ Mon, 12 Aug 2019 19:03:42: 4000000 INFO @ Mon, 12 Aug 2019 19:03:43: 4000000 INFO @ Mon, 12 Aug 2019 19:03:49: 5000000 INFO @ Mon, 12 Aug 2019 19:03:50: 5000000 INFO @ Mon, 12 Aug 2019 19:03:51: 4000000 INFO @ Mon, 12 Aug 2019 19:03:57: 6000000 INFO @ Mon, 12 Aug 2019 19:03:58: 6000000 INFO @ Mon, 12 Aug 2019 19:04:00: 5000000 INFO @ Mon, 12 Aug 2019 19:04:04: 7000000 INFO @ Mon, 12 Aug 2019 19:04:05: 7000000 INFO @ Mon, 12 Aug 2019 19:04:10: 6000000 INFO @ Mon, 12 Aug 2019 19:04:11: 8000000 INFO @ Mon, 12 Aug 2019 19:04:12: 8000000 INFO @ Mon, 12 Aug 2019 19:04:18: 9000000 INFO @ Mon, 12 Aug 2019 19:04:19: 7000000 INFO @ Mon, 12 Aug 2019 19:04:19: 9000000 INFO @ Mon, 12 Aug 2019 19:04:25: 10000000 INFO @ Mon, 12 Aug 2019 19:04:26: 10000000 INFO @ Mon, 12 Aug 2019 19:04:28: 8000000 INFO @ Mon, 12 Aug 2019 19:04:32: 11000000 INFO @ Mon, 12 Aug 2019 19:04:34: 11000000 INFO @ Mon, 12 Aug 2019 19:04:37: 9000000 INFO @ Mon, 12 Aug 2019 19:04:40: 12000000 INFO @ Mon, 12 Aug 2019 19:04:41: 12000000 INFO @ Mon, 12 Aug 2019 19:04:47: 10000000 INFO @ Mon, 12 Aug 2019 19:04:47: 13000000 INFO @ Mon, 12 Aug 2019 19:04:48: 13000000 INFO @ Mon, 12 Aug 2019 19:04:54: 14000000 INFO @ Mon, 12 Aug 2019 19:04:55: 14000000 INFO @ Mon, 12 Aug 2019 19:04:56: 11000000 INFO @ Mon, 12 Aug 2019 19:05:01: 15000000 INFO @ Mon, 12 Aug 2019 19:05:02: 15000000 INFO @ Mon, 12 Aug 2019 19:05:05: 12000000 INFO @ Mon, 12 Aug 2019 19:05:08: 16000000 INFO @ Mon, 12 Aug 2019 19:05:09: 16000000 INFO @ Mon, 12 Aug 2019 19:05:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:05:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:05:10: #1 total tags in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:10: #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 19:05:11: #1 tags after filtering in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:11: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:05:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:05:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:05:12: #1 total tags in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:12: #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 19:05:12: #1 tags after filtering in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:12: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:05:12: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 19:05:12: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:12: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:12: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:12: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:12: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:12: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:05:12: #2 alternative fragment length(s) may be 1,45,107,174,351,474,499,534,565,597 bps INFO @ Mon, 12 Aug 2019 19:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10_model.r WARNING @ Mon, 12 Aug 2019 19:05:12: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:12: #2 You may need to consider one of the other alternative d(s): 1,45,107,174,351,474,499,534,565,597 WARNING @ Mon, 12 Aug 2019 19:05:12: #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 19:05:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:05:13: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 19:05:13: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:13: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:13: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:13: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:13: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:13: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:05:13: #2 alternative fragment length(s) may be 1,45,107,174,351,474,499,534,565,597 bps INFO @ Mon, 12 Aug 2019 19:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20_model.r WARNING @ Mon, 12 Aug 2019 19:05:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:13: #2 You may need to consider one of the other alternative d(s): 1,45,107,174,351,474,499,534,565,597 WARNING @ Mon, 12 Aug 2019 19:05:13: #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 19:05:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:05:14: 13000000 INFO @ Mon, 12 Aug 2019 19:05:23: 14000000 INFO @ Mon, 12 Aug 2019 19:05:32: 15000000 INFO @ Mon, 12 Aug 2019 19:05:41: 16000000 INFO @ Mon, 12 Aug 2019 19:05:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:05:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:05:44: #1 total tags in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:05:44: #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 19:05:44: #1 tags after filtering in treatment: 16275799 INFO @ Mon, 12 Aug 2019 19:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:05:44: #1 finished! INFO @ Mon, 12 Aug 2019 19:05:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:05:45: #2 number of paired peaks: 120 WARNING @ Mon, 12 Aug 2019 19:05:45: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 12 Aug 2019 19:05:45: start model_add_line... INFO @ Mon, 12 Aug 2019 19:05:45: start X-correlation... INFO @ Mon, 12 Aug 2019 19:05:45: end of X-cor INFO @ Mon, 12 Aug 2019 19:05:45: #2 finished! INFO @ Mon, 12 Aug 2019 19:05:45: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:05:45: #2 alternative fragment length(s) may be 1,45,107,174,351,474,499,534,565,597 bps INFO @ Mon, 12 Aug 2019 19:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05_model.r WARNING @ Mon, 12 Aug 2019 19:05:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:05:45: #2 You may need to consider one of the other alternative d(s): 1,45,107,174,351,474,499,534,565,597 WARNING @ Mon, 12 Aug 2019 19:05:45: #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 19:05:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:05:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:05:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.10_summits.bed INFO @ Mon, 12 Aug 2019 19:06:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.20_summits.bed INFO @ Mon, 12 Aug 2019 19:06:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:06:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:06:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466457/SRX466457.05_summits.bed INFO @ Mon, 12 Aug 2019 19:06:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2102 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。