Job ID = 2590243 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,270,696 reads read : 22,270,696 reads written : 22,270,696 rm: cannot remove ‘[DSE]RR*’: 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: 00:07:51 22270696 reads; of these: 22270696 (100.00%) were unpaired; of these: 1239577 (5.57%) aligned 0 times 17679855 (79.39%) aligned exactly 1 time 3351264 (15.05%) aligned >1 times 94.43% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 2205651 / 21031119 = 0.1049 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 20:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.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 20:45:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.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 20:45:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.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 20:45:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:51: 1000000 INFO @ Mon, 12 Aug 2019 20:45:54: 1000000 INFO @ Mon, 12 Aug 2019 20:45:54: 1000000 INFO @ Mon, 12 Aug 2019 20:46:00: 2000000 INFO @ Mon, 12 Aug 2019 20:46:04: 2000000 INFO @ Mon, 12 Aug 2019 20:46:06: 2000000 INFO @ Mon, 12 Aug 2019 20:46:08: 3000000 INFO @ Mon, 12 Aug 2019 20:46:13: 3000000 INFO @ Mon, 12 Aug 2019 20:46:17: 3000000 INFO @ Mon, 12 Aug 2019 20:46:17: 4000000 INFO @ Mon, 12 Aug 2019 20:46:22: 4000000 INFO @ Mon, 12 Aug 2019 20:46:26: 5000000 INFO @ Mon, 12 Aug 2019 20:46:28: 4000000 INFO @ Mon, 12 Aug 2019 20:46:32: 5000000 INFO @ Mon, 12 Aug 2019 20:46:35: 6000000 INFO @ Mon, 12 Aug 2019 20:46:39: 5000000 INFO @ Mon, 12 Aug 2019 20:46:42: 6000000 INFO @ Mon, 12 Aug 2019 20:46:44: 7000000 INFO @ Mon, 12 Aug 2019 20:46:49: 6000000 INFO @ Mon, 12 Aug 2019 20:46:51: 7000000 INFO @ Mon, 12 Aug 2019 20:46:53: 8000000 INFO @ Mon, 12 Aug 2019 20:47:00: 7000000 INFO @ Mon, 12 Aug 2019 20:47:00: 8000000 INFO @ Mon, 12 Aug 2019 20:47:02: 9000000 INFO @ Mon, 12 Aug 2019 20:47:09: 9000000 INFO @ Mon, 12 Aug 2019 20:47:10: 10000000 INFO @ Mon, 12 Aug 2019 20:47:11: 8000000 INFO @ Mon, 12 Aug 2019 20:47:19: 10000000 INFO @ Mon, 12 Aug 2019 20:47:19: 11000000 INFO @ Mon, 12 Aug 2019 20:47:22: 9000000 INFO @ Mon, 12 Aug 2019 20:47:28: 12000000 INFO @ Mon, 12 Aug 2019 20:47:28: 11000000 INFO @ Mon, 12 Aug 2019 20:47:33: 10000000 INFO @ Mon, 12 Aug 2019 20:47:37: 13000000 INFO @ Mon, 12 Aug 2019 20:47:38: 12000000 INFO @ Mon, 12 Aug 2019 20:47:44: 11000000 INFO @ Mon, 12 Aug 2019 20:47:46: 14000000 INFO @ Mon, 12 Aug 2019 20:47:47: 13000000 INFO @ Mon, 12 Aug 2019 20:47:55: 15000000 INFO @ Mon, 12 Aug 2019 20:47:55: 12000000 INFO @ Mon, 12 Aug 2019 20:47:57: 14000000 INFO @ Mon, 12 Aug 2019 20:48:03: 16000000 INFO @ Mon, 12 Aug 2019 20:48:06: 15000000 INFO @ Mon, 12 Aug 2019 20:48:07: 13000000 INFO @ Mon, 12 Aug 2019 20:48:12: 17000000 INFO @ Mon, 12 Aug 2019 20:48:15: 16000000 INFO @ Mon, 12 Aug 2019 20:48:18: 14000000 INFO @ Mon, 12 Aug 2019 20:48:20: 18000000 INFO @ Mon, 12 Aug 2019 20:48:24: 17000000 INFO @ Mon, 12 Aug 2019 20:48:28: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:48:28: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:48:28: #1 total tags in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:48:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:48:28: #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 20:48:28: #1 tags after filtering in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:48:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:48:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:48:29: 15000000 INFO @ Mon, 12 Aug 2019 20:48:30: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 20:48:30: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 20:48:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:48:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:48:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:48:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:48:30: #2 predicted fragment length is 74 bps INFO @ Mon, 12 Aug 2019 20:48:30: #2 alternative fragment length(s) may be 2,48,74,564 bps INFO @ Mon, 12 Aug 2019 20:48:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05_model.r WARNING @ Mon, 12 Aug 2019 20:48:30: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:48:30: #2 You may need to consider one of the other alternative d(s): 2,48,74,564 WARNING @ Mon, 12 Aug 2019 20:48:30: #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 20:48:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:48:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:48:34: 18000000 INFO @ Mon, 12 Aug 2019 20:48:40: 16000000 INFO @ Mon, 12 Aug 2019 20:48:41: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:48:41: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:48:41: #1 total tags in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:48:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:48:41: #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 20:48:42: #1 tags after filtering in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:48:42: #1 finished! INFO @ Mon, 12 Aug 2019 20:48:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:48:43: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 20:48:43: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 20:48:43: start model_add_line... INFO @ Mon, 12 Aug 2019 20:48:43: start X-correlation... INFO @ Mon, 12 Aug 2019 20:48:43: end of X-cor INFO @ Mon, 12 Aug 2019 20:48:43: #2 finished! INFO @ Mon, 12 Aug 2019 20:48:43: #2 predicted fragment length is 74 bps INFO @ Mon, 12 Aug 2019 20:48:43: #2 alternative fragment length(s) may be 2,48,74,564 bps INFO @ Mon, 12 Aug 2019 20:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20_model.r WARNING @ Mon, 12 Aug 2019 20:48:43: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:48:43: #2 You may need to consider one of the other alternative d(s): 2,48,74,564 WARNING @ Mon, 12 Aug 2019 20:48:43: #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 20:48:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:48:51: 17000000 INFO @ Mon, 12 Aug 2019 20:49:01: 18000000 INFO @ Mon, 12 Aug 2019 20:49:10: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:49:10: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:49:10: #1 total tags in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:49:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:49:10: #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 20:49:11: #1 tags after filtering in treatment: 18825468 INFO @ Mon, 12 Aug 2019 20:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:49:11: #1 finished! INFO @ Mon, 12 Aug 2019 20:49:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:49:12: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 20:49:12: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 20:49:12: start model_add_line... INFO @ Mon, 12 Aug 2019 20:49:12: start X-correlation... INFO @ Mon, 12 Aug 2019 20:49:12: end of X-cor INFO @ Mon, 12 Aug 2019 20:49:12: #2 finished! INFO @ Mon, 12 Aug 2019 20:49:12: #2 predicted fragment length is 74 bps INFO @ Mon, 12 Aug 2019 20:49:12: #2 alternative fragment length(s) may be 2,48,74,564 bps INFO @ Mon, 12 Aug 2019 20:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10_model.r WARNING @ Mon, 12 Aug 2019 20:49:12: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:49:12: #2 You may need to consider one of the other alternative d(s): 2,48,74,564 WARNING @ Mon, 12 Aug 2019 20:49:12: #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 20:49:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:49:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:49:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.05_summits.bed INFO @ Mon, 12 Aug 2019 20:49:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:49:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:49:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:49:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.20_summits.bed INFO @ Mon, 12 Aug 2019 20:49:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:49:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:50:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:50:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:50:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985675/SRX5985675.10_summits.bed INFO @ Mon, 12 Aug 2019 20:50:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (442 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。