Job ID = 1292418 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,982,195 reads read : 11,964,390 reads written : 5,982,195 reads 0-length : 5,982,195 spots read : 5,864,917 reads read : 11,729,834 reads written : 5,864,917 reads 0-length : 5,864,917 spots read : 5,977,025 reads read : 11,954,050 reads written : 5,977,025 reads 0-length : 5,977,025 spots read : 5,790,900 reads read : 11,581,800 reads written : 5,790,900 reads 0-length : 5,790,900 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: 00:12:40 23615037 reads; of these: 23615037 (100.00%) were unpaired; of these: 328861 (1.39%) aligned 0 times 20222049 (85.63%) aligned exactly 1 time 3064127 (12.98%) aligned >1 times 98.61% overall alignment rate Time searching: 00:12:40 Overall time: 00:12:40 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] 6472963 / 23286176 = 0.2780 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 18:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.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 18:58:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:58:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.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 18:58:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:58:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.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 18:58:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:58:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:58:50: 1000000 INFO @ Sun, 02 Jun 2019 18:58:54: 1000000 INFO @ Sun, 02 Jun 2019 18:58:54: 1000000 INFO @ Sun, 02 Jun 2019 18:59:01: 2000000 INFO @ Sun, 02 Jun 2019 18:59:09: 2000000 INFO @ Sun, 02 Jun 2019 18:59:09: 2000000 INFO @ Sun, 02 Jun 2019 18:59:12: 3000000 INFO @ Sun, 02 Jun 2019 18:59:22: 4000000 INFO @ Sun, 02 Jun 2019 18:59:24: 3000000 INFO @ Sun, 02 Jun 2019 18:59:24: 3000000 INFO @ Sun, 02 Jun 2019 18:59:33: 5000000 INFO @ Sun, 02 Jun 2019 18:59:37: 4000000 INFO @ Sun, 02 Jun 2019 18:59:38: 4000000 INFO @ Sun, 02 Jun 2019 18:59:44: 6000000 INFO @ Sun, 02 Jun 2019 18:59:51: 5000000 INFO @ Sun, 02 Jun 2019 18:59:52: 5000000 INFO @ Sun, 02 Jun 2019 18:59:55: 7000000 INFO @ Sun, 02 Jun 2019 19:00:05: 6000000 INFO @ Sun, 02 Jun 2019 19:00:06: 6000000 INFO @ Sun, 02 Jun 2019 19:00:06: 8000000 INFO @ Sun, 02 Jun 2019 19:00:17: 9000000 INFO @ Sun, 02 Jun 2019 19:00:19: 7000000 INFO @ Sun, 02 Jun 2019 19:00:20: 7000000 INFO @ Sun, 02 Jun 2019 19:00:28: 10000000 INFO @ Sun, 02 Jun 2019 19:00:33: 8000000 INFO @ Sun, 02 Jun 2019 19:00:34: 8000000 INFO @ Sun, 02 Jun 2019 19:00:38: 11000000 INFO @ Sun, 02 Jun 2019 19:00:47: 9000000 INFO @ Sun, 02 Jun 2019 19:00:48: 9000000 INFO @ Sun, 02 Jun 2019 19:00:49: 12000000 INFO @ Sun, 02 Jun 2019 19:01:00: 13000000 INFO @ Sun, 02 Jun 2019 19:01:01: 10000000 INFO @ Sun, 02 Jun 2019 19:01:02: 10000000 INFO @ Sun, 02 Jun 2019 19:01:11: 14000000 INFO @ Sun, 02 Jun 2019 19:01:15: 11000000 INFO @ Sun, 02 Jun 2019 19:01:16: 11000000 INFO @ Sun, 02 Jun 2019 19:01:21: 15000000 INFO @ Sun, 02 Jun 2019 19:01:28: 12000000 INFO @ Sun, 02 Jun 2019 19:01:29: 12000000 INFO @ Sun, 02 Jun 2019 19:01:32: 16000000 INFO @ Sun, 02 Jun 2019 19:01:41: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 19:01:41: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 19:01:41: #1 total tags in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:01:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:01:41: #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 19:01:41: #1 tags after filtering in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:01:41: #1 finished! INFO @ Sun, 02 Jun 2019 19:01:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:01:42: 13000000 INFO @ Sun, 02 Jun 2019 19:01:43: 13000000 INFO @ Sun, 02 Jun 2019 19:01:43: #2 number of paired peaks: 275 WARNING @ Sun, 02 Jun 2019 19:01:43: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sun, 02 Jun 2019 19:01:43: start model_add_line... INFO @ Sun, 02 Jun 2019 19:01:43: start X-correlation... INFO @ Sun, 02 Jun 2019 19:01:43: end of X-cor INFO @ Sun, 02 Jun 2019 19:01:43: #2 finished! INFO @ Sun, 02 Jun 2019 19:01:43: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 19:01:43: #2 alternative fragment length(s) may be 2,66,556,558,583 bps INFO @ Sun, 02 Jun 2019 19:01:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10_model.r WARNING @ Sun, 02 Jun 2019 19:01:43: #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 19:01:43: #2 You may need to consider one of the other alternative d(s): 2,66,556,558,583 WARNING @ Sun, 02 Jun 2019 19:01:43: #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 19:01:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:01:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:01:55: 14000000 INFO @ Sun, 02 Jun 2019 19:01:56: 14000000 INFO @ Sun, 02 Jun 2019 19:02:08: 15000000 INFO @ Sun, 02 Jun 2019 19:02:09: 15000000 INFO @ Sun, 02 Jun 2019 19:02:22: 16000000 INFO @ Sun, 02 Jun 2019 19:02:22: 16000000 INFO @ Sun, 02 Jun 2019 19:02:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:02:32: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 19:02:32: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 19:02:32: #1 total tags in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:02:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:02:32: #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 19:02:32: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 19:02:32: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 19:02:32: #1 total tags in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:02:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:02:32: #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 19:02:33: #1 tags after filtering in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:02:33: #1 finished! INFO @ Sun, 02 Jun 2019 19:02:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:02:33: #1 tags after filtering in treatment: 16813213 INFO @ Sun, 02 Jun 2019 19:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:02:33: #1 finished! INFO @ Sun, 02 Jun 2019 19:02:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:02:34: #2 number of paired peaks: 275 WARNING @ Sun, 02 Jun 2019 19:02:34: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sun, 02 Jun 2019 19:02:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:02:34: #2 number of paired peaks: 275 WARNING @ Sun, 02 Jun 2019 19:02:34: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Sun, 02 Jun 2019 19:02:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:02:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:02:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:02:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:02:34: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 19:02:34: #2 alternative fragment length(s) may be 2,66,556,558,583 bps INFO @ Sun, 02 Jun 2019 19:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20_model.r WARNING @ Sun, 02 Jun 2019 19:02:34: #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 19:02:34: #2 You may need to consider one of the other alternative d(s): 2,66,556,558,583 WARNING @ Sun, 02 Jun 2019 19:02:34: #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 19:02:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:02:35: start X-correlation... INFO @ Sun, 02 Jun 2019 19:02:35: end of X-cor INFO @ Sun, 02 Jun 2019 19:02:35: #2 finished! INFO @ Sun, 02 Jun 2019 19:02:35: #2 predicted fragment length is 66 bps INFO @ Sun, 02 Jun 2019 19:02:35: #2 alternative fragment length(s) may be 2,66,556,558,583 bps INFO @ Sun, 02 Jun 2019 19:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05_model.r WARNING @ Sun, 02 Jun 2019 19:02:35: #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 19:02:35: #2 You may need to consider one of the other alternative d(s): 2,66,556,558,583 WARNING @ Sun, 02 Jun 2019 19:02:35: #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 19:02:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.10_summits.bed INFO @ Sun, 02 Jun 2019 19:02:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1120 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:03:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:03:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.05_summits.bed INFO @ Sun, 02 Jun 2019 19:03:42: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (6031 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194203/SRX4194203.20_summits.bed INFO @ Sun, 02 Jun 2019 19:03:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。