Job ID = 6456594 SRX = SRX3663163 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:58:16 prefetch.2.10.7: 1) Downloading 'SRR6686973'... 2020-06-21T10:58:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:30 prefetch.2.10.7: 1) 'SRR6686973' was downloaded successfully Read 51920217 spots for SRR6686973/SRR6686973.sra Written 51920217 spots for SRR6686973/SRR6686973.sra 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: 00:12:05 51920217 reads; of these: 51920217 (100.00%) were unpaired; of these: 4354213 (8.39%) aligned 0 times 40146254 (77.32%) aligned exactly 1 time 7419750 (14.29%) aligned >1 times 91.61% overall alignment rate Time searching: 00:12:05 Overall time: 00:12:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 9023033 / 47566004 = 0.1897 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 @ Sun, 21 Jun 2020 20:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.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 @ Sun, 21 Jun 2020 20:30:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:20: 1000000 INFO @ Sun, 21 Jun 2020 20:30:27: 2000000 INFO @ Sun, 21 Jun 2020 20:30:34: 3000000 INFO @ Sun, 21 Jun 2020 20:30:40: 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 @ Sun, 21 Jun 2020 20:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.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 @ Sun, 21 Jun 2020 20:30:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:47: 5000000 INFO @ Sun, 21 Jun 2020 20:30:49: 1000000 INFO @ Sun, 21 Jun 2020 20:30:55: 6000000 INFO @ Sun, 21 Jun 2020 20:30:55: 2000000 INFO @ Sun, 21 Jun 2020 20:31:02: 7000000 INFO @ Sun, 21 Jun 2020 20:31:02: 3000000 INFO @ Sun, 21 Jun 2020 20:31:08: 4000000 INFO @ Sun, 21 Jun 2020 20:31:09: 8000000 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 @ Sun, 21 Jun 2020 20:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.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 @ Sun, 21 Jun 2020 20:31:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:15: 5000000 INFO @ Sun, 21 Jun 2020 20:31:16: 9000000 INFO @ Sun, 21 Jun 2020 20:31:20: 1000000 INFO @ Sun, 21 Jun 2020 20:31:21: 6000000 INFO @ Sun, 21 Jun 2020 20:31:23: 10000000 INFO @ Sun, 21 Jun 2020 20:31:27: 2000000 INFO @ Sun, 21 Jun 2020 20:31:27: 7000000 INFO @ Sun, 21 Jun 2020 20:31:30: 11000000 INFO @ Sun, 21 Jun 2020 20:31:34: 8000000 INFO @ Sun, 21 Jun 2020 20:31:35: 3000000 INFO @ Sun, 21 Jun 2020 20:31:38: 12000000 INFO @ Sun, 21 Jun 2020 20:31:40: 9000000 INFO @ Sun, 21 Jun 2020 20:31:42: 4000000 INFO @ Sun, 21 Jun 2020 20:31:45: 13000000 INFO @ Sun, 21 Jun 2020 20:31:47: 10000000 INFO @ Sun, 21 Jun 2020 20:31:49: 5000000 INFO @ Sun, 21 Jun 2020 20:31:52: 14000000 INFO @ Sun, 21 Jun 2020 20:31:53: 11000000 INFO @ Sun, 21 Jun 2020 20:31:57: 6000000 INFO @ Sun, 21 Jun 2020 20:31:59: 15000000 INFO @ Sun, 21 Jun 2020 20:31:59: 12000000 INFO @ Sun, 21 Jun 2020 20:32:04: 7000000 INFO @ Sun, 21 Jun 2020 20:32:06: 13000000 INFO @ Sun, 21 Jun 2020 20:32:06: 16000000 INFO @ Sun, 21 Jun 2020 20:32:11: 8000000 INFO @ Sun, 21 Jun 2020 20:32:12: 14000000 INFO @ Sun, 21 Jun 2020 20:32:13: 17000000 INFO @ Sun, 21 Jun 2020 20:32:18: 9000000 INFO @ Sun, 21 Jun 2020 20:32:18: 15000000 INFO @ Sun, 21 Jun 2020 20:32:21: 18000000 INFO @ Sun, 21 Jun 2020 20:32:25: 16000000 INFO @ Sun, 21 Jun 2020 20:32:25: 10000000 INFO @ Sun, 21 Jun 2020 20:32:28: 19000000 INFO @ Sun, 21 Jun 2020 20:32:31: 17000000 INFO @ Sun, 21 Jun 2020 20:32:32: 11000000 INFO @ Sun, 21 Jun 2020 20:32:35: 20000000 INFO @ Sun, 21 Jun 2020 20:32:37: 18000000 INFO @ Sun, 21 Jun 2020 20:32:39: 12000000 INFO @ Sun, 21 Jun 2020 20:32:42: 21000000 INFO @ Sun, 21 Jun 2020 20:32:44: 19000000 INFO @ Sun, 21 Jun 2020 20:32:46: 13000000 INFO @ Sun, 21 Jun 2020 20:32:49: 22000000 INFO @ Sun, 21 Jun 2020 20:32:50: 20000000 INFO @ Sun, 21 Jun 2020 20:32:54: 14000000 INFO @ Sun, 21 Jun 2020 20:32:56: 23000000 INFO @ Sun, 21 Jun 2020 20:32:56: 21000000 INFO @ Sun, 21 Jun 2020 20:33:01: 15000000 INFO @ Sun, 21 Jun 2020 20:33:03: 22000000 INFO @ Sun, 21 Jun 2020 20:33:03: 24000000 INFO @ Sun, 21 Jun 2020 20:33:08: 16000000 INFO @ Sun, 21 Jun 2020 20:33:09: 23000000 INFO @ Sun, 21 Jun 2020 20:33:10: 25000000 INFO @ Sun, 21 Jun 2020 20:33:15: 17000000 INFO @ Sun, 21 Jun 2020 20:33:15: 24000000 INFO @ Sun, 21 Jun 2020 20:33:17: 26000000 INFO @ Sun, 21 Jun 2020 20:33:22: 25000000 INFO @ Sun, 21 Jun 2020 20:33:22: 18000000 INFO @ Sun, 21 Jun 2020 20:33:25: 27000000 INFO @ Sun, 21 Jun 2020 20:33:28: 26000000 INFO @ Sun, 21 Jun 2020 20:33:29: 19000000 INFO @ Sun, 21 Jun 2020 20:33:32: 28000000 INFO @ Sun, 21 Jun 2020 20:33:34: 27000000 INFO @ Sun, 21 Jun 2020 20:33:36: 20000000 INFO @ Sun, 21 Jun 2020 20:33:39: 29000000 INFO @ Sun, 21 Jun 2020 20:33:41: 28000000 INFO @ Sun, 21 Jun 2020 20:33:44: 21000000 INFO @ Sun, 21 Jun 2020 20:33:46: 30000000 INFO @ Sun, 21 Jun 2020 20:33:47: 29000000 INFO @ Sun, 21 Jun 2020 20:33:51: 22000000 INFO @ Sun, 21 Jun 2020 20:33:54: 31000000 INFO @ Sun, 21 Jun 2020 20:33:54: 30000000 INFO @ Sun, 21 Jun 2020 20:33:58: 23000000 INFO @ Sun, 21 Jun 2020 20:34:00: 31000000 INFO @ Sun, 21 Jun 2020 20:34:01: 32000000 INFO @ Sun, 21 Jun 2020 20:34:05: 24000000 INFO @ Sun, 21 Jun 2020 20:34:07: 32000000 INFO @ Sun, 21 Jun 2020 20:34:08: 33000000 INFO @ Sun, 21 Jun 2020 20:34:12: 25000000 INFO @ Sun, 21 Jun 2020 20:34:13: 33000000 INFO @ Sun, 21 Jun 2020 20:34:15: 34000000 INFO @ Sun, 21 Jun 2020 20:34:19: 26000000 INFO @ Sun, 21 Jun 2020 20:34:20: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:34:22: 35000000 INFO @ Sun, 21 Jun 2020 20:34:26: 35000000 INFO @ Sun, 21 Jun 2020 20:34:26: 27000000 INFO @ Sun, 21 Jun 2020 20:34:29: 36000000 INFO @ Sun, 21 Jun 2020 20:34:33: 36000000 INFO @ Sun, 21 Jun 2020 20:34:34: 28000000 INFO @ Sun, 21 Jun 2020 20:34:37: 37000000 INFO @ Sun, 21 Jun 2020 20:34:39: 37000000 INFO @ Sun, 21 Jun 2020 20:34:41: 29000000 INFO @ Sun, 21 Jun 2020 20:34:44: 38000000 INFO @ Sun, 21 Jun 2020 20:34:46: 38000000 INFO @ Sun, 21 Jun 2020 20:34:48: 30000000 INFO @ Sun, 21 Jun 2020 20:34:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:48: #1 total tags in treatment: 38542971 INFO @ Sun, 21 Jun 2020 20:34:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:34:49: #1 tags after filtering in treatment: 38542916 INFO @ Sun, 21 Jun 2020 20:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:50: #1 total tags in treatment: 38542971 INFO @ Sun, 21 Jun 2020 20:34:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:34:51: #1 tags after filtering in treatment: 38542916 INFO @ Sun, 21 Jun 2020 20:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:52: #2 number of paired peaks: 108 WARNING @ Sun, 21 Jun 2020 20:34:52: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:52: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:34:52: #2 alternative fragment length(s) may be 1,20,44,84,110,217,433,453,583 bps INFO @ Sun, 21 Jun 2020 20:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05_model.r WARNING @ Sun, 21 Jun 2020 20:34:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:52: #2 You may need to consider one of the other alternative d(s): 1,20,44,84,110,217,433,453,583 WARNING @ Sun, 21 Jun 2020 20:34:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:34:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:53: #2 number of paired peaks: 108 WARNING @ Sun, 21 Jun 2020 20:34:53: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:53: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:53: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:53: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:53: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:34:53: #2 alternative fragment length(s) may be 1,20,44,84,110,217,433,453,583 bps INFO @ Sun, 21 Jun 2020 20:34:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10_model.r WARNING @ Sun, 21 Jun 2020 20:34:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:53: #2 You may need to consider one of the other alternative d(s): 1,20,44,84,110,217,433,453,583 WARNING @ Sun, 21 Jun 2020 20:34:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:34:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:55: 31000000 INFO @ Sun, 21 Jun 2020 20:35:02: 32000000 INFO @ Sun, 21 Jun 2020 20:35:09: 33000000 INFO @ Sun, 21 Jun 2020 20:35:15: 34000000 INFO @ Sun, 21 Jun 2020 20:35:22: 35000000 INFO @ Sun, 21 Jun 2020 20:35:29: 36000000 INFO @ Sun, 21 Jun 2020 20:35:35: 37000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:35:42: 38000000 INFO @ Sun, 21 Jun 2020 20:35:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:35:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:35:46: #1 total tags in treatment: 38542971 INFO @ Sun, 21 Jun 2020 20:35:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:35:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:47: #1 tags after filtering in treatment: 38542916 INFO @ Sun, 21 Jun 2020 20:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:49: #2 number of paired peaks: 108 WARNING @ Sun, 21 Jun 2020 20:35:49: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 21 Jun 2020 20:35:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:49: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:35:49: #2 alternative fragment length(s) may be 1,20,44,84,110,217,433,453,583 bps INFO @ Sun, 21 Jun 2020 20:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20_model.r WARNING @ Sun, 21 Jun 2020 20:35:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:35:49: #2 You may need to consider one of the other alternative d(s): 1,20,44,84,110,217,433,453,583 WARNING @ Sun, 21 Jun 2020 20:35:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:35:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.05_summits.bed INFO @ Sun, 21 Jun 2020 20:36:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.10_summits.bed INFO @ Sun, 21 Jun 2020 20:36:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:36:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3663163/SRX3663163.20_summits.bed INFO @ Sun, 21 Jun 2020 20:37:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling