Job ID = 5720696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,237,743 reads read : 34,237,743 reads written : 34,237,743 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: 00:08:01 34237743 reads; of these: 34237743 (100.00%) were unpaired; of these: 2625127 (7.67%) aligned 0 times 25979897 (75.88%) aligned exactly 1 time 5632719 (16.45%) aligned >1 times 92.33% overall alignment rate Time searching: 00:08:01 Overall time: 00:08:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 4504379 / 31612616 = 0.1425 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:26:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:26:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:26:24: 1000000 INFO @ Thu, 16 Apr 2020 01:26:30: 2000000 INFO @ Thu, 16 Apr 2020 01:26:36: 3000000 INFO @ Thu, 16 Apr 2020 01:26:41: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:26:47: 5000000 INFO @ Thu, 16 Apr 2020 01:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:26:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:26:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:26:53: 6000000 INFO @ Thu, 16 Apr 2020 01:26:56: 1000000 INFO @ Thu, 16 Apr 2020 01:27:00: 7000000 INFO @ Thu, 16 Apr 2020 01:27:03: 2000000 INFO @ Thu, 16 Apr 2020 01:27:07: 8000000 INFO @ Thu, 16 Apr 2020 01:27:11: 3000000 INFO @ Thu, 16 Apr 2020 01:27:14: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 01:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:27:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:19: 4000000 INFO @ Thu, 16 Apr 2020 01:27:21: 10000000 INFO @ Thu, 16 Apr 2020 01:27:26: 5000000 INFO @ Thu, 16 Apr 2020 01:27:27: 1000000 INFO @ Thu, 16 Apr 2020 01:27:27: 11000000 INFO @ Thu, 16 Apr 2020 01:27:34: 6000000 INFO @ Thu, 16 Apr 2020 01:27:34: 2000000 INFO @ Thu, 16 Apr 2020 01:27:35: 12000000 INFO @ Thu, 16 Apr 2020 01:27:41: 7000000 INFO @ Thu, 16 Apr 2020 01:27:41: 13000000 INFO @ Thu, 16 Apr 2020 01:27:42: 3000000 INFO @ Thu, 16 Apr 2020 01:27:48: 14000000 INFO @ Thu, 16 Apr 2020 01:27:49: 8000000 INFO @ Thu, 16 Apr 2020 01:27:50: 4000000 INFO @ Thu, 16 Apr 2020 01:27:55: 15000000 INFO @ Thu, 16 Apr 2020 01:27:57: 9000000 INFO @ Thu, 16 Apr 2020 01:27:57: 5000000 INFO @ Thu, 16 Apr 2020 01:28:02: 16000000 INFO @ Thu, 16 Apr 2020 01:28:04: 10000000 INFO @ Thu, 16 Apr 2020 01:28:07: 6000000 INFO @ Thu, 16 Apr 2020 01:28:09: 17000000 INFO @ Thu, 16 Apr 2020 01:28:12: 11000000 INFO @ Thu, 16 Apr 2020 01:28:14: 7000000 INFO @ Thu, 16 Apr 2020 01:28:17: 18000000 INFO @ Thu, 16 Apr 2020 01:28:20: 12000000 INFO @ Thu, 16 Apr 2020 01:28:22: 8000000 INFO @ Thu, 16 Apr 2020 01:28:23: 19000000 INFO @ Thu, 16 Apr 2020 01:28:27: 13000000 INFO @ Thu, 16 Apr 2020 01:28:30: 9000000 INFO @ Thu, 16 Apr 2020 01:28:30: 20000000 INFO @ Thu, 16 Apr 2020 01:28:35: 14000000 INFO @ Thu, 16 Apr 2020 01:28:37: 21000000 INFO @ Thu, 16 Apr 2020 01:28:38: 10000000 INFO @ Thu, 16 Apr 2020 01:28:43: 15000000 INFO @ Thu, 16 Apr 2020 01:28:44: 22000000 INFO @ Thu, 16 Apr 2020 01:28:45: 11000000 INFO @ Thu, 16 Apr 2020 01:28:50: 16000000 INFO @ Thu, 16 Apr 2020 01:28:51: 23000000 INFO @ Thu, 16 Apr 2020 01:28:53: 12000000 INFO @ Thu, 16 Apr 2020 01:28:58: 17000000 INFO @ Thu, 16 Apr 2020 01:28:58: 24000000 INFO @ Thu, 16 Apr 2020 01:29:01: 13000000 INFO @ Thu, 16 Apr 2020 01:29:05: 25000000 INFO @ Thu, 16 Apr 2020 01:29:06: 18000000 INFO @ Thu, 16 Apr 2020 01:29:08: 14000000 INFO @ Thu, 16 Apr 2020 01:29:12: 26000000 INFO @ Thu, 16 Apr 2020 01:29:13: 19000000 INFO @ Thu, 16 Apr 2020 01:29:16: 15000000 INFO @ Thu, 16 Apr 2020 01:29:19: 27000000 INFO @ Thu, 16 Apr 2020 01:29:21: 20000000 INFO @ Thu, 16 Apr 2020 01:29:21: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:29:21: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:29:21: #1 total tags in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:29:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:29:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:29:21: #1 tags after filtering in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:29:21: #1 finished! INFO @ Thu, 16 Apr 2020 01:29:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:29:23: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 01:29:23: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 01:29:23: start model_add_line... INFO @ Thu, 16 Apr 2020 01:29:23: start X-correlation... INFO @ Thu, 16 Apr 2020 01:29:23: end of X-cor INFO @ Thu, 16 Apr 2020 01:29:23: #2 finished! INFO @ Thu, 16 Apr 2020 01:29:23: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:29:23: #2 alternative fragment length(s) may be 47,110,131,162,188,257,294,310,410,431,487,500,549,567 bps INFO @ Thu, 16 Apr 2020 01:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05_model.r WARNING @ Thu, 16 Apr 2020 01:29:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:29:23: #2 You may need to consider one of the other alternative d(s): 47,110,131,162,188,257,294,310,410,431,487,500,549,567 WARNING @ Thu, 16 Apr 2020 01:29:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:29:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:29:24: 16000000 INFO @ Thu, 16 Apr 2020 01:29:28: 21000000 INFO @ Thu, 16 Apr 2020 01:29:31: 17000000 INFO @ Thu, 16 Apr 2020 01:29:36: 22000000 INFO @ Thu, 16 Apr 2020 01:29:39: 18000000 INFO @ Thu, 16 Apr 2020 01:29:44: 23000000 INFO @ Thu, 16 Apr 2020 01:29:46: 19000000 INFO @ Thu, 16 Apr 2020 01:29:51: 24000000 INFO @ Thu, 16 Apr 2020 01:29:53: 20000000 INFO @ Thu, 16 Apr 2020 01:29:59: 25000000 INFO @ Thu, 16 Apr 2020 01:30:01: 21000000 INFO @ Thu, 16 Apr 2020 01:30:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:30:07: 26000000 INFO @ Thu, 16 Apr 2020 01:30:09: 22000000 INFO @ Thu, 16 Apr 2020 01:30:14: 27000000 INFO @ Thu, 16 Apr 2020 01:30:15: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:30:15: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:30:15: #1 total tags in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:30:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:30:15: #1 tags after filtering in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:30:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:15: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:16: 23000000 INFO @ Thu, 16 Apr 2020 01:30:17: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 01:30:17: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:17: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:17: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:17: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:17: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:17: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:30:17: #2 alternative fragment length(s) may be 47,110,131,162,188,257,294,310,410,431,487,500,549,567 bps INFO @ Thu, 16 Apr 2020 01:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10_model.r WARNING @ Thu, 16 Apr 2020 01:30:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:17: #2 You may need to consider one of the other alternative d(s): 47,110,131,162,188,257,294,310,410,431,487,500,549,567 WARNING @ Thu, 16 Apr 2020 01:30:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:30:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:24: 24000000 INFO @ Thu, 16 Apr 2020 01:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.05_summits.bed INFO @ Thu, 16 Apr 2020 01:30:27: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (767 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:30:31: 25000000 INFO @ Thu, 16 Apr 2020 01:30:38: 26000000 INFO @ Thu, 16 Apr 2020 01:30:45: 27000000 INFO @ Thu, 16 Apr 2020 01:30:46: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:30:46: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:30:46: #1 total tags in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:30:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:30:46: #1 tags after filtering in treatment: 27108237 INFO @ Thu, 16 Apr 2020 01:30:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:46: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:48: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 01:30:48: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:48: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:30:48: #2 alternative fragment length(s) may be 47,110,131,162,188,257,294,310,410,431,487,500,549,567 bps INFO @ Thu, 16 Apr 2020 01:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20_model.r WARNING @ Thu, 16 Apr 2020 01:30:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:48: #2 You may need to consider one of the other alternative d(s): 47,110,131,162,188,257,294,310,410,431,487,500,549,567 WARNING @ Thu, 16 Apr 2020 01:30:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:30:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.10_summits.bed INFO @ Thu, 16 Apr 2020 01:31:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:31:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158161/SRX4158161.20_summits.bed INFO @ Thu, 16 Apr 2020 01:31:51: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。