Job ID = 5720872 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,397,571 reads read : 41,397,571 reads written : 41,397,571 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: 00:12:11 41397571 reads; of these: 41397571 (100.00%) were unpaired; of these: 1754177 (4.24%) aligned 0 times 28066572 (67.80%) aligned exactly 1 time 11576822 (27.96%) aligned >1 times 95.76% overall alignment rate Time searching: 00:12:11 Overall time: 00:12:11 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 20 files... [bam_rmdupse_core] 6267331 / 39643394 = 0.1581 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 03:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.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 03:08:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:08:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:08:10: 1000000 INFO @ Thu, 16 Apr 2020 03:08:15: 2000000 INFO @ Thu, 16 Apr 2020 03:08:19: 3000000 INFO @ Thu, 16 Apr 2020 03:08:24: 4000000 INFO @ Thu, 16 Apr 2020 03:08:29: 5000000 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 03:08:34: 6000000 INFO @ Thu, 16 Apr 2020 03:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.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 03:08:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:08:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:08:39: 1000000 INFO @ Thu, 16 Apr 2020 03:08:40: 7000000 INFO @ Thu, 16 Apr 2020 03:08:44: 8000000 INFO @ Thu, 16 Apr 2020 03:08:44: 2000000 INFO @ Thu, 16 Apr 2020 03:08:49: 9000000 INFO @ Thu, 16 Apr 2020 03:08:49: 3000000 INFO @ Thu, 16 Apr 2020 03:08:54: 10000000 INFO @ Thu, 16 Apr 2020 03:08:54: 4000000 INFO @ Thu, 16 Apr 2020 03:09:00: 5000000 INFO @ Thu, 16 Apr 2020 03:09:00: 11000000 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 03:09:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.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 03:09:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:09:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:09:05: 6000000 INFO @ Thu, 16 Apr 2020 03:09:05: 12000000 INFO @ Thu, 16 Apr 2020 03:09:10: 7000000 INFO @ Thu, 16 Apr 2020 03:09:10: 1000000 INFO @ Thu, 16 Apr 2020 03:09:10: 13000000 INFO @ Thu, 16 Apr 2020 03:09:15: 8000000 INFO @ Thu, 16 Apr 2020 03:09:15: 14000000 INFO @ Thu, 16 Apr 2020 03:09:15: 2000000 INFO @ Thu, 16 Apr 2020 03:09:20: 9000000 INFO @ Thu, 16 Apr 2020 03:09:20: 15000000 INFO @ Thu, 16 Apr 2020 03:09:20: 3000000 INFO @ Thu, 16 Apr 2020 03:09:25: 10000000 INFO @ Thu, 16 Apr 2020 03:09:25: 16000000 INFO @ Thu, 16 Apr 2020 03:09:26: 4000000 INFO @ Thu, 16 Apr 2020 03:09:30: 11000000 INFO @ Thu, 16 Apr 2020 03:09:30: 17000000 INFO @ Thu, 16 Apr 2020 03:09:31: 5000000 INFO @ Thu, 16 Apr 2020 03:09:35: 12000000 INFO @ Thu, 16 Apr 2020 03:09:35: 18000000 INFO @ Thu, 16 Apr 2020 03:09:37: 6000000 INFO @ Thu, 16 Apr 2020 03:09:40: 13000000 INFO @ Thu, 16 Apr 2020 03:09:40: 19000000 INFO @ Thu, 16 Apr 2020 03:09:42: 7000000 INFO @ Thu, 16 Apr 2020 03:09:45: 14000000 INFO @ Thu, 16 Apr 2020 03:09:45: 20000000 INFO @ Thu, 16 Apr 2020 03:09:47: 8000000 INFO @ Thu, 16 Apr 2020 03:09:50: 15000000 INFO @ Thu, 16 Apr 2020 03:09:50: 21000000 INFO @ Thu, 16 Apr 2020 03:09:52: 9000000 INFO @ Thu, 16 Apr 2020 03:09:55: 16000000 INFO @ Thu, 16 Apr 2020 03:09:55: 22000000 INFO @ Thu, 16 Apr 2020 03:09:57: 10000000 INFO @ Thu, 16 Apr 2020 03:10:00: 17000000 INFO @ Thu, 16 Apr 2020 03:10:00: 23000000 INFO @ Thu, 16 Apr 2020 03:10:02: 11000000 INFO @ Thu, 16 Apr 2020 03:10:05: 18000000 INFO @ Thu, 16 Apr 2020 03:10:05: 24000000 INFO @ Thu, 16 Apr 2020 03:10:07: 12000000 INFO @ Thu, 16 Apr 2020 03:10:10: 19000000 INFO @ Thu, 16 Apr 2020 03:10:10: 25000000 INFO @ Thu, 16 Apr 2020 03:10:12: 13000000 INFO @ Thu, 16 Apr 2020 03:10:15: 26000000 INFO @ Thu, 16 Apr 2020 03:10:15: 20000000 INFO @ Thu, 16 Apr 2020 03:10:17: 14000000 INFO @ Thu, 16 Apr 2020 03:10:20: 27000000 INFO @ Thu, 16 Apr 2020 03:10:21: 21000000 INFO @ Thu, 16 Apr 2020 03:10:22: 15000000 INFO @ Thu, 16 Apr 2020 03:10:25: 28000000 INFO @ Thu, 16 Apr 2020 03:10:26: 22000000 INFO @ Thu, 16 Apr 2020 03:10:27: 16000000 INFO @ Thu, 16 Apr 2020 03:10:30: 29000000 INFO @ Thu, 16 Apr 2020 03:10:31: 23000000 INFO @ Thu, 16 Apr 2020 03:10:32: 17000000 INFO @ Thu, 16 Apr 2020 03:10:35: 30000000 INFO @ Thu, 16 Apr 2020 03:10:36: 24000000 INFO @ Thu, 16 Apr 2020 03:10:37: 18000000 INFO @ Thu, 16 Apr 2020 03:10:41: 31000000 INFO @ Thu, 16 Apr 2020 03:10:41: 25000000 INFO @ Thu, 16 Apr 2020 03:10:42: 19000000 INFO @ Thu, 16 Apr 2020 03:10:46: 32000000 INFO @ Thu, 16 Apr 2020 03:10:46: 26000000 INFO @ Thu, 16 Apr 2020 03:10:47: 20000000 INFO @ Thu, 16 Apr 2020 03:10:51: 33000000 INFO @ Thu, 16 Apr 2020 03:10:51: 27000000 INFO @ Thu, 16 Apr 2020 03:10:52: 21000000 INFO @ Thu, 16 Apr 2020 03:10:53: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:10:53: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:10:53: #1 total tags in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:10:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:10:53: #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 03:10:53: #1 tags after filtering in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:10:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:10:53: #1 finished! INFO @ Thu, 16 Apr 2020 03:10:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:10:55: #2 number of paired peaks: 197 WARNING @ Thu, 16 Apr 2020 03:10:55: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 16 Apr 2020 03:10:55: start model_add_line... INFO @ Thu, 16 Apr 2020 03:10:56: start X-correlation... INFO @ Thu, 16 Apr 2020 03:10:56: end of X-cor INFO @ Thu, 16 Apr 2020 03:10:56: #2 finished! INFO @ Thu, 16 Apr 2020 03:10:56: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:10:56: #2 alternative fragment length(s) may be 1,21 bps INFO @ Thu, 16 Apr 2020 03:10:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05_model.r WARNING @ Thu, 16 Apr 2020 03:10:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:10:56: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Thu, 16 Apr 2020 03:10:56: #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 03:10:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:10:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:10:56: 28000000 INFO @ Thu, 16 Apr 2020 03:10:57: 22000000 INFO @ Thu, 16 Apr 2020 03:11:01: 29000000 INFO @ Thu, 16 Apr 2020 03:11:02: 23000000 INFO @ Thu, 16 Apr 2020 03:11:06: 30000000 INFO @ Thu, 16 Apr 2020 03:11:06: 24000000 INFO @ Thu, 16 Apr 2020 03:11:11: 31000000 INFO @ Thu, 16 Apr 2020 03:11:11: 25000000 INFO @ Thu, 16 Apr 2020 03:11:15: 32000000 INFO @ Thu, 16 Apr 2020 03:11:16: 26000000 INFO @ Thu, 16 Apr 2020 03:11:20: 33000000 INFO @ Thu, 16 Apr 2020 03:11:21: 27000000 INFO @ Thu, 16 Apr 2020 03:11:23: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:11:23: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:11:23: #1 total tags in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:11:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:11:23: #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 03:11:23: #1 tags after filtering in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:11:23: #1 finished! INFO @ Thu, 16 Apr 2020 03:11:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:11:25: #2 number of paired peaks: 197 WARNING @ Thu, 16 Apr 2020 03:11:25: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 16 Apr 2020 03:11:25: start model_add_line... INFO @ Thu, 16 Apr 2020 03:11:26: start X-correlation... INFO @ Thu, 16 Apr 2020 03:11:26: end of X-cor INFO @ Thu, 16 Apr 2020 03:11:26: #2 finished! INFO @ Thu, 16 Apr 2020 03:11:26: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:11:26: #2 alternative fragment length(s) may be 1,21 bps INFO @ Thu, 16 Apr 2020 03:11:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10_model.r WARNING @ Thu, 16 Apr 2020 03:11:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:11:26: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Thu, 16 Apr 2020 03:11:26: #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 03:11:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:11:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:11:26: 28000000 INFO @ Thu, 16 Apr 2020 03:11:31: 29000000 INFO @ Thu, 16 Apr 2020 03:11:36: 30000000 INFO @ Thu, 16 Apr 2020 03:11:41: 31000000 INFO @ Thu, 16 Apr 2020 03:11:46: 32000000 INFO @ Thu, 16 Apr 2020 03:11:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:11:51: 33000000 INFO @ Thu, 16 Apr 2020 03:11:53: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:11:53: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:11:53: #1 total tags in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:11:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:11:53: #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 03:11:54: #1 tags after filtering in treatment: 33376063 INFO @ Thu, 16 Apr 2020 03:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:11:54: #1 finished! INFO @ Thu, 16 Apr 2020 03:11:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:11:56: #2 number of paired peaks: 197 WARNING @ Thu, 16 Apr 2020 03:11:56: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 16 Apr 2020 03:11:56: start model_add_line... INFO @ Thu, 16 Apr 2020 03:11:56: start X-correlation... INFO @ Thu, 16 Apr 2020 03:11:56: end of X-cor INFO @ Thu, 16 Apr 2020 03:11:56: #2 finished! INFO @ Thu, 16 Apr 2020 03:11:56: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:11:56: #2 alternative fragment length(s) may be 1,21 bps INFO @ Thu, 16 Apr 2020 03:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20_model.r WARNING @ Thu, 16 Apr 2020 03:11:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:11:56: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Thu, 16 Apr 2020 03:11:56: #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 03:11:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.05_summits.bed INFO @ Thu, 16 Apr 2020 03:12:12: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:12:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.10_summits.bed INFO @ Thu, 16 Apr 2020 03:12:42: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:12:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436058/SRX5436058.20_summits.bed INFO @ Thu, 16 Apr 2020 03:13:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。