Job ID = 6456704 SRX = SRX3981612 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:02:32 prefetch.2.10.7: 1) Downloading 'SRR7050220'... 2020-06-21T11:02:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:04:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:04:40 prefetch.2.10.7: 'SRR7050220' is valid 2020-06-21T11:04:40 prefetch.2.10.7: 1) 'SRR7050220' was downloaded successfully 2020-06-21T11:04:41 prefetch.2.10.7: 'SRR7050220' has 0 unresolved dependencies Read 13536788 spots for SRR7050220/SRR7050220.sra Written 13536788 spots for SRR7050220/SRR7050220.sra 2020-06-21T11:05:33 prefetch.2.10.7: 1) Downloading 'SRR7050221'... 2020-06-21T11:05:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:22 prefetch.2.10.7: 'SRR7050221' is valid 2020-06-21T11:07:22 prefetch.2.10.7: 1) 'SRR7050221' was downloaded successfully 2020-06-21T11:07:22 prefetch.2.10.7: 'SRR7050221' has 0 unresolved dependencies Read 13320276 spots for SRR7050221/SRR7050221.sra Written 13320276 spots for SRR7050221/SRR7050221.sra 2020-06-21T11:08:12 prefetch.2.10.7: 1) Downloading 'SRR7050222'... 2020-06-21T11:08:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:49 prefetch.2.10.7: 'SRR7050222' is valid 2020-06-21T11:09:49 prefetch.2.10.7: 1) 'SRR7050222' was downloaded successfully 2020-06-21T11:09:49 prefetch.2.10.7: 'SRR7050222' has 0 unresolved dependencies Read 13518222 spots for SRR7050222/SRR7050222.sra Written 13518222 spots for SRR7050222/SRR7050222.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: 00:10:30 40375286 reads; of these: 40375286 (100.00%) were unpaired; of these: 1350762 (3.35%) aligned 0 times 28443061 (70.45%) aligned exactly 1 time 10581463 (26.21%) aligned >1 times 96.65% overall alignment rate Time searching: 00:10:30 Overall time: 00:10:30 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 16 files... [bam_rmdupse_core] 5420293 / 39024524 = 0.1389 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 20:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.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 20:29:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:14: 1000000 INFO @ Sun, 21 Jun 2020 20:29:19: 2000000 INFO @ Sun, 21 Jun 2020 20:29:25: 3000000 INFO @ Sun, 21 Jun 2020 20:29:30: 4000000 INFO @ Sun, 21 Jun 2020 20:29:36: 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 @ Sun, 21 Jun 2020 20:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.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 20:29:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:41: 6000000 INFO @ Sun, 21 Jun 2020 20:29:45: 1000000 INFO @ Sun, 21 Jun 2020 20:29:47: 7000000 INFO @ Sun, 21 Jun 2020 20:29:51: 2000000 INFO @ Sun, 21 Jun 2020 20:29:54: 8000000 INFO @ Sun, 21 Jun 2020 20:29:57: 3000000 INFO @ Sun, 21 Jun 2020 20:30:00: 9000000 INFO @ Sun, 21 Jun 2020 20:30:03: 4000000 INFO @ Sun, 21 Jun 2020 20:30:06: 10000000 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 20:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.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 20:30:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:09: 5000000 INFO @ Sun, 21 Jun 2020 20:30:12: 11000000 INFO @ Sun, 21 Jun 2020 20:30:15: 1000000 INFO @ Sun, 21 Jun 2020 20:30:16: 6000000 INFO @ Sun, 21 Jun 2020 20:30:19: 12000000 INFO @ Sun, 21 Jun 2020 20:30:22: 2000000 INFO @ Sun, 21 Jun 2020 20:30:23: 7000000 INFO @ Sun, 21 Jun 2020 20:30:25: 13000000 INFO @ Sun, 21 Jun 2020 20:30:28: 3000000 INFO @ Sun, 21 Jun 2020 20:30:29: 8000000 INFO @ Sun, 21 Jun 2020 20:30:32: 14000000 INFO @ Sun, 21 Jun 2020 20:30:35: 4000000 INFO @ Sun, 21 Jun 2020 20:30:36: 9000000 INFO @ Sun, 21 Jun 2020 20:30:38: 15000000 INFO @ Sun, 21 Jun 2020 20:30:41: 5000000 INFO @ Sun, 21 Jun 2020 20:30:42: 10000000 INFO @ Sun, 21 Jun 2020 20:30:44: 16000000 INFO @ Sun, 21 Jun 2020 20:30:48: 6000000 INFO @ Sun, 21 Jun 2020 20:30:49: 11000000 INFO @ Sun, 21 Jun 2020 20:30:51: 17000000 INFO @ Sun, 21 Jun 2020 20:30:54: 7000000 INFO @ Sun, 21 Jun 2020 20:30:55: 12000000 INFO @ Sun, 21 Jun 2020 20:30:57: 18000000 INFO @ Sun, 21 Jun 2020 20:31:01: 8000000 INFO @ Sun, 21 Jun 2020 20:31:01: 13000000 INFO @ Sun, 21 Jun 2020 20:31:03: 19000000 INFO @ Sun, 21 Jun 2020 20:31:07: 9000000 INFO @ Sun, 21 Jun 2020 20:31:08: 14000000 INFO @ Sun, 21 Jun 2020 20:31:09: 20000000 INFO @ Sun, 21 Jun 2020 20:31:13: 10000000 INFO @ Sun, 21 Jun 2020 20:31:14: 15000000 INFO @ Sun, 21 Jun 2020 20:31:16: 21000000 INFO @ Sun, 21 Jun 2020 20:31:20: 11000000 INFO @ Sun, 21 Jun 2020 20:31:20: 16000000 INFO @ Sun, 21 Jun 2020 20:31:22: 22000000 INFO @ Sun, 21 Jun 2020 20:31:26: 12000000 INFO @ Sun, 21 Jun 2020 20:31:26: 17000000 INFO @ Sun, 21 Jun 2020 20:31:28: 23000000 INFO @ Sun, 21 Jun 2020 20:31:32: 13000000 INFO @ Sun, 21 Jun 2020 20:31:33: 18000000 INFO @ Sun, 21 Jun 2020 20:31:34: 24000000 INFO @ Sun, 21 Jun 2020 20:31:38: 14000000 INFO @ Sun, 21 Jun 2020 20:31:39: 19000000 INFO @ Sun, 21 Jun 2020 20:31:40: 25000000 INFO @ Sun, 21 Jun 2020 20:31:45: 15000000 INFO @ Sun, 21 Jun 2020 20:31:45: 20000000 INFO @ Sun, 21 Jun 2020 20:31:47: 26000000 INFO @ Sun, 21 Jun 2020 20:31:51: 16000000 INFO @ Sun, 21 Jun 2020 20:31:51: 21000000 INFO @ Sun, 21 Jun 2020 20:31:53: 27000000 INFO @ Sun, 21 Jun 2020 20:31:57: 17000000 INFO @ Sun, 21 Jun 2020 20:31:57: 22000000 INFO @ Sun, 21 Jun 2020 20:31:59: 28000000 INFO @ Sun, 21 Jun 2020 20:32:03: 18000000 INFO @ Sun, 21 Jun 2020 20:32:03: 23000000 INFO @ Sun, 21 Jun 2020 20:32:06: 29000000 INFO @ Sun, 21 Jun 2020 20:32:09: 19000000 INFO @ Sun, 21 Jun 2020 20:32:10: 24000000 INFO @ Sun, 21 Jun 2020 20:32:12: 30000000 INFO @ Sun, 21 Jun 2020 20:32:15: 20000000 INFO @ Sun, 21 Jun 2020 20:32:16: 25000000 INFO @ Sun, 21 Jun 2020 20:32:18: 31000000 INFO @ Sun, 21 Jun 2020 20:32:21: 21000000 INFO @ Sun, 21 Jun 2020 20:32:22: 26000000 INFO @ Sun, 21 Jun 2020 20:32:24: 32000000 INFO @ Sun, 21 Jun 2020 20:32:28: 22000000 INFO @ Sun, 21 Jun 2020 20:32:29: 27000000 INFO @ Sun, 21 Jun 2020 20:32:31: 33000000 INFO @ Sun, 21 Jun 2020 20:32:34: 23000000 INFO @ Sun, 21 Jun 2020 20:32:35: 28000000 INFO @ Sun, 21 Jun 2020 20:32:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:35: #1 total tags in treatment: 33604231 INFO @ Sun, 21 Jun 2020 20:32:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:35: #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 20:32:36: #1 tags after filtering in treatment: 33604179 INFO @ Sun, 21 Jun 2020 20:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:38: #2 number of paired peaks: 207 WARNING @ Sun, 21 Jun 2020 20:32:38: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:38: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:32:38: #2 alternative fragment length(s) may be 1,34,49,583 bps INFO @ Sun, 21 Jun 2020 20:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05_model.r WARNING @ Sun, 21 Jun 2020 20:32:38: #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 20:32:38: #2 You may need to consider one of the other alternative d(s): 1,34,49,583 WARNING @ Sun, 21 Jun 2020 20:32:38: #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 20:32:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:40: 24000000 INFO @ Sun, 21 Jun 2020 20:32:42: 29000000 INFO @ Sun, 21 Jun 2020 20:32:46: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:48: 30000000 INFO @ Sun, 21 Jun 2020 20:32:53: 26000000 INFO @ Sun, 21 Jun 2020 20:32:54: 31000000 INFO @ Sun, 21 Jun 2020 20:32:59: 27000000 INFO @ Sun, 21 Jun 2020 20:33:01: 32000000 INFO @ Sun, 21 Jun 2020 20:33:05: 28000000 INFO @ Sun, 21 Jun 2020 20:33:07: 33000000 INFO @ Sun, 21 Jun 2020 20:33:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:11: #1 total tags in treatment: 33604231 INFO @ Sun, 21 Jun 2020 20:33:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:11: #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 20:33:12: #1 tags after filtering in treatment: 33604179 INFO @ Sun, 21 Jun 2020 20:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:12: 29000000 INFO @ Sun, 21 Jun 2020 20:33:14: #2 number of paired peaks: 207 WARNING @ Sun, 21 Jun 2020 20:33:14: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:14: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:33:14: #2 alternative fragment length(s) may be 1,34,49,583 bps INFO @ Sun, 21 Jun 2020 20:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10_model.r WARNING @ Sun, 21 Jun 2020 20:33:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:14: #2 You may need to consider one of the other alternative d(s): 1,34,49,583 WARNING @ Sun, 21 Jun 2020 20:33:14: #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 20:33:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:18: 30000000 INFO @ Sun, 21 Jun 2020 20:33:24: 31000000 INFO @ Sun, 21 Jun 2020 20:33:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:29: 32000000 INFO @ Sun, 21 Jun 2020 20:33:35: 33000000 INFO @ Sun, 21 Jun 2020 20:33:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:33:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:33:39: #1 total tags in treatment: 33604231 INFO @ Sun, 21 Jun 2020 20:33:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:39: #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 20:33:40: #1 tags after filtering in treatment: 33604179 INFO @ Sun, 21 Jun 2020 20:33:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:42: #2 number of paired peaks: 207 WARNING @ Sun, 21 Jun 2020 20:33:42: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 21 Jun 2020 20:33:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:42: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:33:42: #2 alternative fragment length(s) may be 1,34,49,583 bps INFO @ Sun, 21 Jun 2020 20:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20_model.r WARNING @ Sun, 21 Jun 2020 20:33:42: #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 20:33:42: #2 You may need to consider one of the other alternative d(s): 1,34,49,583 WARNING @ Sun, 21 Jun 2020 20:33:42: #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 20:33:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.05_summits.bed INFO @ Sun, 21 Jun 2020 20:33:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:34:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.10_summits.bed INFO @ Sun, 21 Jun 2020 20:34:23: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:34:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981612/SRX3981612.20_summits.bed INFO @ Sun, 21 Jun 2020 20:34:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling