Job ID = 6455151 SRX = SRX2804213 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:40 prefetch.2.10.7: 1) Downloading 'SRR5534641'... 2020-06-21T09:40:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:44 prefetch.2.10.7: 1) 'SRR5534641' was downloaded successfully 2020-06-21T09:44:44 prefetch.2.10.7: 'SRR5534641' has 0 unresolved dependencies Read 37018724 spots for SRR5534641/SRR5534641.sra Written 37018724 spots for SRR5534641/SRR5534641.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: 00:10:12 37018724 reads; of these: 37018724 (100.00%) were unpaired; of these: 1240539 (3.35%) aligned 0 times 25181043 (68.02%) aligned exactly 1 time 10597142 (28.63%) aligned >1 times 96.65% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 5611845 / 35778185 = 0.1569 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 19:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.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 19:03:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:32: 1000000 INFO @ Sun, 21 Jun 2020 19:03:38: 2000000 INFO @ Sun, 21 Jun 2020 19:03:43: 3000000 INFO @ Sun, 21 Jun 2020 19:03:49: 4000000 INFO @ Sun, 21 Jun 2020 19:03:55: 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 19:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.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 19:03:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:00: 6000000 INFO @ Sun, 21 Jun 2020 19:04:02: 1000000 INFO @ Sun, 21 Jun 2020 19:04:06: 7000000 INFO @ Sun, 21 Jun 2020 19:04:08: 2000000 INFO @ Sun, 21 Jun 2020 19:04:11: 8000000 INFO @ Sun, 21 Jun 2020 19:04:13: 3000000 INFO @ Sun, 21 Jun 2020 19:04:16: 9000000 INFO @ Sun, 21 Jun 2020 19:04:18: 4000000 INFO @ Sun, 21 Jun 2020 19:04:22: 10000000 INFO @ Sun, 21 Jun 2020 19:04:23: 5000000 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 19:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.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 19:04:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:27: 11000000 INFO @ Sun, 21 Jun 2020 19:04:28: 6000000 INFO @ Sun, 21 Jun 2020 19:04:32: 1000000 INFO @ Sun, 21 Jun 2020 19:04:33: 12000000 INFO @ Sun, 21 Jun 2020 19:04:34: 7000000 INFO @ Sun, 21 Jun 2020 19:04:38: 2000000 INFO @ Sun, 21 Jun 2020 19:04:39: 13000000 INFO @ Sun, 21 Jun 2020 19:04:39: 8000000 INFO @ Sun, 21 Jun 2020 19:04:43: 3000000 INFO @ Sun, 21 Jun 2020 19:04:44: 9000000 INFO @ Sun, 21 Jun 2020 19:04:45: 14000000 INFO @ Sun, 21 Jun 2020 19:04:48: 4000000 INFO @ Sun, 21 Jun 2020 19:04:50: 10000000 INFO @ Sun, 21 Jun 2020 19:04:51: 15000000 INFO @ Sun, 21 Jun 2020 19:04:54: 5000000 INFO @ Sun, 21 Jun 2020 19:04:55: 11000000 INFO @ Sun, 21 Jun 2020 19:04:56: 16000000 INFO @ Sun, 21 Jun 2020 19:04:59: 6000000 INFO @ Sun, 21 Jun 2020 19:05:00: 12000000 INFO @ Sun, 21 Jun 2020 19:05:02: 17000000 INFO @ Sun, 21 Jun 2020 19:05:05: 7000000 INFO @ Sun, 21 Jun 2020 19:05:06: 13000000 INFO @ Sun, 21 Jun 2020 19:05:08: 18000000 INFO @ Sun, 21 Jun 2020 19:05:10: 8000000 INFO @ Sun, 21 Jun 2020 19:05:11: 14000000 INFO @ Sun, 21 Jun 2020 19:05:14: 19000000 INFO @ Sun, 21 Jun 2020 19:05:15: 9000000 INFO @ Sun, 21 Jun 2020 19:05:16: 15000000 INFO @ Sun, 21 Jun 2020 19:05:19: 20000000 INFO @ Sun, 21 Jun 2020 19:05:20: 10000000 INFO @ Sun, 21 Jun 2020 19:05:21: 16000000 INFO @ Sun, 21 Jun 2020 19:05:25: 21000000 INFO @ Sun, 21 Jun 2020 19:05:26: 11000000 INFO @ Sun, 21 Jun 2020 19:05:27: 17000000 INFO @ Sun, 21 Jun 2020 19:05:31: 12000000 INFO @ Sun, 21 Jun 2020 19:05:31: 22000000 INFO @ Sun, 21 Jun 2020 19:05:32: 18000000 INFO @ Sun, 21 Jun 2020 19:05:36: 13000000 INFO @ Sun, 21 Jun 2020 19:05:37: 23000000 INFO @ Sun, 21 Jun 2020 19:05:37: 19000000 INFO @ Sun, 21 Jun 2020 19:05:41: 14000000 INFO @ Sun, 21 Jun 2020 19:05:42: 20000000 INFO @ Sun, 21 Jun 2020 19:05:43: 24000000 INFO @ Sun, 21 Jun 2020 19:05:46: 15000000 INFO @ Sun, 21 Jun 2020 19:05:47: 21000000 INFO @ Sun, 21 Jun 2020 19:05:49: 25000000 INFO @ Sun, 21 Jun 2020 19:05:51: 16000000 INFO @ Sun, 21 Jun 2020 19:05:52: 22000000 INFO @ Sun, 21 Jun 2020 19:05:54: 26000000 INFO @ Sun, 21 Jun 2020 19:05:56: 17000000 INFO @ Sun, 21 Jun 2020 19:05:58: 23000000 INFO @ Sun, 21 Jun 2020 19:06:00: 27000000 INFO @ Sun, 21 Jun 2020 19:06:01: 18000000 INFO @ Sun, 21 Jun 2020 19:06:03: 24000000 INFO @ Sun, 21 Jun 2020 19:06:06: 28000000 INFO @ Sun, 21 Jun 2020 19:06:06: 19000000 INFO @ Sun, 21 Jun 2020 19:06:08: 25000000 INFO @ Sun, 21 Jun 2020 19:06:12: 20000000 INFO @ Sun, 21 Jun 2020 19:06:12: 29000000 INFO @ Sun, 21 Jun 2020 19:06:13: 26000000 INFO @ Sun, 21 Jun 2020 19:06:17: 21000000 INFO @ Sun, 21 Jun 2020 19:06:18: 30000000 INFO @ Sun, 21 Jun 2020 19:06:19: 27000000 INFO @ Sun, 21 Jun 2020 19:06:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:06:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:06:19: #1 total tags in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:06:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:19: #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 19:06:20: #1 tags after filtering in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:21: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 19:06:21: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:22: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:06:22: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 19:06:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05_model.r WARNING @ Sun, 21 Jun 2020 19:06:22: #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 19:06:22: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 19:06:22: #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 19:06:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:22: 22000000 INFO @ Sun, 21 Jun 2020 19:06:24: 28000000 INFO @ Sun, 21 Jun 2020 19:06:27: 23000000 INFO @ Sun, 21 Jun 2020 19:06:29: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:06:32: 24000000 INFO @ Sun, 21 Jun 2020 19:06:34: 30000000 INFO @ Sun, 21 Jun 2020 19:06:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:06:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:06:35: #1 total tags in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:06:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:35: #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 19:06:36: #1 tags after filtering in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:37: 25000000 INFO @ Sun, 21 Jun 2020 19:06:38: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 19:06:38: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:38: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:06:38: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 19:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10_model.r WARNING @ Sun, 21 Jun 2020 19:06:38: #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 19:06:38: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 19:06:38: #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 19:06:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:42: 26000000 INFO @ Sun, 21 Jun 2020 19:06:47: 27000000 INFO @ Sun, 21 Jun 2020 19:06:52: 28000000 INFO @ Sun, 21 Jun 2020 19:06:57: 29000000 INFO @ Sun, 21 Jun 2020 19:07:02: 30000000 INFO @ Sun, 21 Jun 2020 19:07:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:07:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:07:03: #1 total tags in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:07:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:03: #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 19:07:03: #1 tags after filtering in treatment: 30166340 INFO @ Sun, 21 Jun 2020 19:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:05: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 19:07:05: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 19:07:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:05: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:07:05: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 19:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20_model.r WARNING @ Sun, 21 Jun 2020 19:07:05: #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 19:07:05: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 19:07:05: #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 19:07:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:07:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.05_summits.bed INFO @ Sun, 21 Jun 2020 19:07:27: 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 19:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804213/SRX2804213.20_summits.bed INFO @ Sun, 21 Jun 2020 19:08:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling