Job ID = 5720844 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,117,836 reads read : 36,117,836 reads written : 36,117,836 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: 00:11:29 36117836 reads; of these: 36117836 (100.00%) were unpaired; of these: 1213271 (3.36%) aligned 0 times 23193570 (64.22%) aligned exactly 1 time 11710995 (32.42%) aligned >1 times 96.64% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5920886 / 34904565 = 0.1696 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 02:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.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 02:33:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:33:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:33:17: 1000000 INFO @ Thu, 16 Apr 2020 02:33:24: 2000000 INFO @ Thu, 16 Apr 2020 02:33:31: 3000000 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 02:33:38: 4000000 INFO @ Thu, 16 Apr 2020 02:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.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 02:33:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:33:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:33:45: 5000000 INFO @ Thu, 16 Apr 2020 02:33:47: 1000000 INFO @ Thu, 16 Apr 2020 02:33:53: 6000000 INFO @ Thu, 16 Apr 2020 02:33:54: 2000000 INFO @ Thu, 16 Apr 2020 02:34:01: 7000000 INFO @ Thu, 16 Apr 2020 02:34:01: 3000000 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 02:34:09: 4000000 INFO @ Thu, 16 Apr 2020 02:34:09: 8000000 INFO @ Thu, 16 Apr 2020 02:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.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 02:34:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:34:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:34:16: 5000000 INFO @ Thu, 16 Apr 2020 02:34:17: 9000000 INFO @ Thu, 16 Apr 2020 02:34:20: 1000000 INFO @ Thu, 16 Apr 2020 02:34:23: 6000000 INFO @ Thu, 16 Apr 2020 02:34:25: 10000000 INFO @ Thu, 16 Apr 2020 02:34:29: 2000000 INFO @ Thu, 16 Apr 2020 02:34:30: 7000000 INFO @ Thu, 16 Apr 2020 02:34:32: 11000000 INFO @ Thu, 16 Apr 2020 02:34:36: 3000000 INFO @ Thu, 16 Apr 2020 02:34:38: 8000000 INFO @ Thu, 16 Apr 2020 02:34:40: 12000000 INFO @ Thu, 16 Apr 2020 02:34:44: 4000000 INFO @ Thu, 16 Apr 2020 02:34:45: 9000000 INFO @ Thu, 16 Apr 2020 02:34:49: 13000000 INFO @ Thu, 16 Apr 2020 02:34:52: 5000000 INFO @ Thu, 16 Apr 2020 02:34:52: 10000000 INFO @ Thu, 16 Apr 2020 02:34:57: 14000000 INFO @ Thu, 16 Apr 2020 02:35:00: 6000000 INFO @ Thu, 16 Apr 2020 02:35:00: 11000000 INFO @ Thu, 16 Apr 2020 02:35:05: 15000000 INFO @ Thu, 16 Apr 2020 02:35:07: 7000000 INFO @ Thu, 16 Apr 2020 02:35:07: 12000000 INFO @ Thu, 16 Apr 2020 02:35:13: 16000000 INFO @ Thu, 16 Apr 2020 02:35:15: 13000000 INFO @ Thu, 16 Apr 2020 02:35:15: 8000000 INFO @ Thu, 16 Apr 2020 02:35:21: 17000000 INFO @ Thu, 16 Apr 2020 02:35:22: 14000000 INFO @ Thu, 16 Apr 2020 02:35:22: 9000000 INFO @ Thu, 16 Apr 2020 02:35:29: 18000000 INFO @ Thu, 16 Apr 2020 02:35:29: 15000000 INFO @ Thu, 16 Apr 2020 02:35:30: 10000000 INFO @ Thu, 16 Apr 2020 02:35:37: 16000000 INFO @ Thu, 16 Apr 2020 02:35:37: 19000000 INFO @ Thu, 16 Apr 2020 02:35:38: 11000000 INFO @ Thu, 16 Apr 2020 02:35:44: 17000000 INFO @ Thu, 16 Apr 2020 02:35:45: 20000000 INFO @ Thu, 16 Apr 2020 02:35:46: 12000000 INFO @ Thu, 16 Apr 2020 02:35:52: 18000000 INFO @ Thu, 16 Apr 2020 02:35:53: 21000000 INFO @ Thu, 16 Apr 2020 02:35:54: 13000000 INFO @ Thu, 16 Apr 2020 02:35:59: 19000000 INFO @ Thu, 16 Apr 2020 02:36:00: 22000000 INFO @ Thu, 16 Apr 2020 02:36:02: 14000000 INFO @ Thu, 16 Apr 2020 02:36:06: 20000000 INFO @ Thu, 16 Apr 2020 02:36:08: 23000000 INFO @ Thu, 16 Apr 2020 02:36:10: 15000000 INFO @ Thu, 16 Apr 2020 02:36:13: 21000000 INFO @ Thu, 16 Apr 2020 02:36:16: 24000000 INFO @ Thu, 16 Apr 2020 02:36:18: 16000000 INFO @ Thu, 16 Apr 2020 02:36:21: 22000000 INFO @ Thu, 16 Apr 2020 02:36:24: 25000000 INFO @ Thu, 16 Apr 2020 02:36:26: 17000000 INFO @ Thu, 16 Apr 2020 02:36:28: 23000000 INFO @ Thu, 16 Apr 2020 02:36:32: 26000000 INFO @ Thu, 16 Apr 2020 02:36:34: 18000000 INFO @ Thu, 16 Apr 2020 02:36:35: 24000000 INFO @ Thu, 16 Apr 2020 02:36:40: 27000000 INFO @ Thu, 16 Apr 2020 02:36:42: 19000000 INFO @ Thu, 16 Apr 2020 02:36:42: 25000000 INFO @ Thu, 16 Apr 2020 02:36:48: 28000000 INFO @ Thu, 16 Apr 2020 02:36:50: 20000000 INFO @ Thu, 16 Apr 2020 02:36:50: 26000000 INFO @ Thu, 16 Apr 2020 02:36:56: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:36:56: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:36:56: #1 total tags in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:36:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:36:56: #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 02:36:57: #1 tags after filtering in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:36:57: #1 finished! INFO @ Thu, 16 Apr 2020 02:36:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:36:57: 27000000 INFO @ Thu, 16 Apr 2020 02:36:58: 21000000 INFO @ Thu, 16 Apr 2020 02:36:59: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 02:36:59: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 02:36:59: start model_add_line... INFO @ Thu, 16 Apr 2020 02:36:59: start X-correlation... INFO @ Thu, 16 Apr 2020 02:36:59: end of X-cor INFO @ Thu, 16 Apr 2020 02:36:59: #2 finished! INFO @ Thu, 16 Apr 2020 02:36:59: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:36:59: #2 alternative fragment length(s) may be 1,10,37,549,586,596,598 bps INFO @ Thu, 16 Apr 2020 02:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05_model.r WARNING @ Thu, 16 Apr 2020 02:36:59: #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 02:36:59: #2 You may need to consider one of the other alternative d(s): 1,10,37,549,586,596,598 WARNING @ Thu, 16 Apr 2020 02:36:59: #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 02:36:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:37:05: 28000000 INFO @ Thu, 16 Apr 2020 02:37:05: 22000000 INFO @ Thu, 16 Apr 2020 02:37:12: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:37:12: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:37:12: #1 total tags in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:37:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:37:12: #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 02:37:12: #1 tags after filtering in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:37:12: #1 finished! INFO @ Thu, 16 Apr 2020 02:37:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:37:13: 23000000 INFO @ Thu, 16 Apr 2020 02:37:14: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 02:37:14: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 02:37:14: start model_add_line... INFO @ Thu, 16 Apr 2020 02:37:14: start X-correlation... INFO @ Thu, 16 Apr 2020 02:37:14: end of X-cor INFO @ Thu, 16 Apr 2020 02:37:14: #2 finished! INFO @ Thu, 16 Apr 2020 02:37:14: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:37:14: #2 alternative fragment length(s) may be 1,10,37,549,586,596,598 bps INFO @ Thu, 16 Apr 2020 02:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10_model.r WARNING @ Thu, 16 Apr 2020 02:37:14: #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 02:37:14: #2 You may need to consider one of the other alternative d(s): 1,10,37,549,586,596,598 WARNING @ Thu, 16 Apr 2020 02:37:14: #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 02:37:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:37:21: 24000000 INFO @ Thu, 16 Apr 2020 02:37:28: 25000000 INFO @ Thu, 16 Apr 2020 02:37:35: 26000000 INFO @ Thu, 16 Apr 2020 02:37:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:37:43: 27000000 INFO @ Thu, 16 Apr 2020 02:37:50: 28000000 INFO @ Thu, 16 Apr 2020 02:37:57: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:37:57: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:37:57: #1 total tags in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:37:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:37:57: #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 02:37:57: #1 tags after filtering in treatment: 28983679 INFO @ Thu, 16 Apr 2020 02:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:37:57: #1 finished! INFO @ Thu, 16 Apr 2020 02:37:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:37:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:37:59: #2 number of paired peaks: 420 WARNING @ Thu, 16 Apr 2020 02:37:59: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 16 Apr 2020 02:37:59: start model_add_line... INFO @ Thu, 16 Apr 2020 02:37:59: start X-correlation... INFO @ Thu, 16 Apr 2020 02:38:00: end of X-cor INFO @ Thu, 16 Apr 2020 02:38:00: #2 finished! INFO @ Thu, 16 Apr 2020 02:38:00: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:38:00: #2 alternative fragment length(s) may be 1,10,37,549,586,596,598 bps INFO @ Thu, 16 Apr 2020 02:38:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20_model.r WARNING @ Thu, 16 Apr 2020 02:38:00: #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 02:38:00: #2 You may need to consider one of the other alternative d(s): 1,10,37,549,586,596,598 WARNING @ Thu, 16 Apr 2020 02:38:00: #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 02:38:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:38:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:38:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:38:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:38:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.05_summits.bed INFO @ Thu, 16 Apr 2020 02:38:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.10_summits.bed INFO @ Thu, 16 Apr 2020 02:38:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:38:44: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:39:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:39:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:39:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436037/SRX5436037.20_summits.bed INFO @ Thu, 16 Apr 2020 02:39:04: Done! pass1 - making usageList (0 chroms): 1 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。