Job ID = 1291671 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,975,281 reads read : 35,975,281 reads written : 35,975,281 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:29 35975281 reads; of these: 35975281 (100.00%) were unpaired; of these: 248538 (0.69%) aligned 0 times 29622277 (82.34%) aligned exactly 1 time 6104466 (16.97%) aligned >1 times 99.31% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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 16 files... [bam_rmdupse_core] 10389692 / 35726743 = 0.2908 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 @ Sun, 02 Jun 2019 16:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.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 @ Sun, 02 Jun 2019 16:34:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:34:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.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 @ Sun, 02 Jun 2019 16:34:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:34:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:34:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.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 @ Sun, 02 Jun 2019 16:34:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:34:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:34:12: 1000000 INFO @ Sun, 02 Jun 2019 16:34:12: 1000000 INFO @ Sun, 02 Jun 2019 16:34:13: 1000000 INFO @ Sun, 02 Jun 2019 16:34:18: 2000000 INFO @ Sun, 02 Jun 2019 16:34:20: 2000000 INFO @ Sun, 02 Jun 2019 16:34:20: 2000000 INFO @ Sun, 02 Jun 2019 16:34:25: 3000000 INFO @ Sun, 02 Jun 2019 16:34:27: 3000000 INFO @ Sun, 02 Jun 2019 16:34:28: 3000000 INFO @ Sun, 02 Jun 2019 16:34:32: 4000000 INFO @ Sun, 02 Jun 2019 16:34:35: 4000000 INFO @ Sun, 02 Jun 2019 16:34:35: 4000000 INFO @ Sun, 02 Jun 2019 16:34:39: 5000000 INFO @ Sun, 02 Jun 2019 16:34:43: 5000000 INFO @ Sun, 02 Jun 2019 16:34:43: 5000000 INFO @ Sun, 02 Jun 2019 16:34:45: 6000000 INFO @ Sun, 02 Jun 2019 16:34:50: 6000000 INFO @ Sun, 02 Jun 2019 16:34:51: 6000000 INFO @ Sun, 02 Jun 2019 16:34:52: 7000000 INFO @ Sun, 02 Jun 2019 16:34:57: 7000000 INFO @ Sun, 02 Jun 2019 16:34:59: 8000000 INFO @ Sun, 02 Jun 2019 16:35:00: 7000000 INFO @ Sun, 02 Jun 2019 16:35:04: 8000000 INFO @ Sun, 02 Jun 2019 16:35:06: 9000000 INFO @ Sun, 02 Jun 2019 16:35:08: 8000000 INFO @ Sun, 02 Jun 2019 16:35:11: 9000000 INFO @ Sun, 02 Jun 2019 16:35:12: 10000000 INFO @ Sun, 02 Jun 2019 16:35:16: 9000000 INFO @ Sun, 02 Jun 2019 16:35:19: 10000000 INFO @ Sun, 02 Jun 2019 16:35:19: 11000000 INFO @ Sun, 02 Jun 2019 16:35:24: 10000000 INFO @ Sun, 02 Jun 2019 16:35:26: 12000000 INFO @ Sun, 02 Jun 2019 16:35:26: 11000000 INFO @ Sun, 02 Jun 2019 16:35:32: 13000000 INFO @ Sun, 02 Jun 2019 16:35:32: 11000000 INFO @ Sun, 02 Jun 2019 16:35:33: 12000000 INFO @ Sun, 02 Jun 2019 16:35:39: 14000000 INFO @ Sun, 02 Jun 2019 16:35:40: 13000000 INFO @ Sun, 02 Jun 2019 16:35:41: 12000000 INFO @ Sun, 02 Jun 2019 16:35:46: 15000000 INFO @ Sun, 02 Jun 2019 16:35:47: 14000000 INFO @ Sun, 02 Jun 2019 16:35:49: 13000000 INFO @ Sun, 02 Jun 2019 16:35:52: 16000000 INFO @ Sun, 02 Jun 2019 16:35:54: 15000000 INFO @ Sun, 02 Jun 2019 16:35:57: 14000000 INFO @ Sun, 02 Jun 2019 16:35:59: 17000000 INFO @ Sun, 02 Jun 2019 16:36:01: 16000000 INFO @ Sun, 02 Jun 2019 16:36:05: 15000000 INFO @ Sun, 02 Jun 2019 16:36:06: 18000000 INFO @ Sun, 02 Jun 2019 16:36:09: 17000000 INFO @ Sun, 02 Jun 2019 16:36:13: 19000000 INFO @ Sun, 02 Jun 2019 16:36:13: 16000000 INFO @ Sun, 02 Jun 2019 16:36:16: 18000000 INFO @ Sun, 02 Jun 2019 16:36:19: 20000000 INFO @ Sun, 02 Jun 2019 16:36:21: 17000000 INFO @ Sun, 02 Jun 2019 16:36:23: 19000000 INFO @ Sun, 02 Jun 2019 16:36:26: 21000000 INFO @ Sun, 02 Jun 2019 16:36:29: 18000000 INFO @ Sun, 02 Jun 2019 16:36:30: 20000000 INFO @ Sun, 02 Jun 2019 16:36:33: 22000000 INFO @ Sun, 02 Jun 2019 16:36:37: 19000000 INFO @ Sun, 02 Jun 2019 16:36:37: 21000000 INFO @ Sun, 02 Jun 2019 16:36:40: 23000000 INFO @ Sun, 02 Jun 2019 16:36:44: 22000000 INFO @ Sun, 02 Jun 2019 16:36:45: 20000000 INFO @ Sun, 02 Jun 2019 16:36:46: 24000000 INFO @ Sun, 02 Jun 2019 16:36:51: 23000000 INFO @ Sun, 02 Jun 2019 16:36:53: 25000000 INFO @ Sun, 02 Jun 2019 16:36:53: 21000000 INFO @ Sun, 02 Jun 2019 16:36:55: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:36:55: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:36:55: #1 total tags in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:36:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:36:56: #1 tags after filtering in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:36:56: #1 finished! INFO @ Sun, 02 Jun 2019 16:36:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:36:58: #2 number of paired peaks: 134 WARNING @ Sun, 02 Jun 2019 16:36:58: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sun, 02 Jun 2019 16:36:58: start model_add_line... INFO @ Sun, 02 Jun 2019 16:36:58: start X-correlation... INFO @ Sun, 02 Jun 2019 16:36:58: end of X-cor INFO @ Sun, 02 Jun 2019 16:36:58: #2 finished! INFO @ Sun, 02 Jun 2019 16:36:58: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 16:36:58: #2 alternative fragment length(s) may be 1,50,66,565,588 bps INFO @ Sun, 02 Jun 2019 16:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05_model.r INFO @ Sun, 02 Jun 2019 16:36:58: 24000000 WARNING @ Sun, 02 Jun 2019 16:36:58: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:36:58: #2 You may need to consider one of the other alternative d(s): 1,50,66,565,588 WARNING @ Sun, 02 Jun 2019 16:36:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:36:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:37:01: 22000000 INFO @ Sun, 02 Jun 2019 16:37:05: 25000000 INFO @ Sun, 02 Jun 2019 16:37:08: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:37:08: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:37:08: #1 total tags in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:37:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:37:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:37:08: #1 tags after filtering in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:37:08: #1 finished! INFO @ Sun, 02 Jun 2019 16:37:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:37:09: 23000000 INFO @ Sun, 02 Jun 2019 16:37:11: #2 number of paired peaks: 134 WARNING @ Sun, 02 Jun 2019 16:37:11: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sun, 02 Jun 2019 16:37:11: start model_add_line... INFO @ Sun, 02 Jun 2019 16:37:11: start X-correlation... INFO @ Sun, 02 Jun 2019 16:37:11: end of X-cor INFO @ Sun, 02 Jun 2019 16:37:11: #2 finished! INFO @ Sun, 02 Jun 2019 16:37:11: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 16:37:11: #2 alternative fragment length(s) may be 1,50,66,565,588 bps INFO @ Sun, 02 Jun 2019 16:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20_model.r WARNING @ Sun, 02 Jun 2019 16:37:11: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:37:11: #2 You may need to consider one of the other alternative d(s): 1,50,66,565,588 WARNING @ Sun, 02 Jun 2019 16:37:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:37:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:37:17: 24000000 INFO @ Sun, 02 Jun 2019 16:37:25: 25000000 INFO @ Sun, 02 Jun 2019 16:37:27: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:37:27: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:37:27: #1 total tags in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:37:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:37:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:37:28: #1 tags after filtering in treatment: 25337051 INFO @ Sun, 02 Jun 2019 16:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:37:28: #1 finished! INFO @ Sun, 02 Jun 2019 16:37:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:37:30: #2 number of paired peaks: 134 WARNING @ Sun, 02 Jun 2019 16:37:30: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sun, 02 Jun 2019 16:37:30: start model_add_line... INFO @ Sun, 02 Jun 2019 16:37:30: start X-correlation... INFO @ Sun, 02 Jun 2019 16:37:30: end of X-cor INFO @ Sun, 02 Jun 2019 16:37:30: #2 finished! INFO @ Sun, 02 Jun 2019 16:37:30: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 16:37:30: #2 alternative fragment length(s) may be 1,50,66,565,588 bps INFO @ Sun, 02 Jun 2019 16:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10_model.r WARNING @ Sun, 02 Jun 2019 16:37:30: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:37:30: #2 You may need to consider one of the other alternative d(s): 1,50,66,565,588 WARNING @ Sun, 02 Jun 2019 16:37:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:37:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:37:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.05_summits.bed INFO @ Sun, 02 Jun 2019 16:38:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15770 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.20_summits.bed INFO @ Sun, 02 Jun 2019 16:38:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769999/SRX1769999.10_summits.bed INFO @ Sun, 02 Jun 2019 16:38:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1937 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。