Job ID = 6455171 SRX = SRX2804229 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:55:10 prefetch.2.10.7: 1) Downloading 'SRR5534657'... 2020-06-21T09:55:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:58:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:58:24 prefetch.2.10.7: 1) 'SRR5534657' was downloaded successfully 2020-06-21T09:58:24 prefetch.2.10.7: 'SRR5534657' has 0 unresolved dependencies Read 31202456 spots for SRR5534657/SRR5534657.sra Written 31202456 spots for SRR5534657/SRR5534657.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: 00:09:04 31202456 reads; of these: 31202456 (100.00%) were unpaired; of these: 2625247 (8.41%) aligned 0 times 19105861 (61.23%) aligned exactly 1 time 9471348 (30.35%) aligned >1 times 91.59% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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 12 files... [bam_rmdupse_core] 5383046 / 28577209 = 0.1884 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 19:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.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 19:14:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:51: 1000000 INFO @ Sun, 21 Jun 2020 19:14:58: 2000000 INFO @ Sun, 21 Jun 2020 19:15:04: 3000000 INFO @ Sun, 21 Jun 2020 19:15:10: 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 19:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.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 19:15:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:17: 5000000 INFO @ Sun, 21 Jun 2020 19:15:21: 1000000 INFO @ Sun, 21 Jun 2020 19:15:23: 6000000 INFO @ Sun, 21 Jun 2020 19:15:28: 2000000 INFO @ Sun, 21 Jun 2020 19:15:30: 7000000 INFO @ Sun, 21 Jun 2020 19:15:35: 3000000 INFO @ Sun, 21 Jun 2020 19:15:37: 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 19:15:42: 4000000 INFO @ Sun, 21 Jun 2020 19:15:44: 9000000 INFO @ Sun, 21 Jun 2020 19:15:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.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 19:15:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:49: 5000000 INFO @ Sun, 21 Jun 2020 19:15:50: 10000000 INFO @ Sun, 21 Jun 2020 19:15:51: 1000000 INFO @ Sun, 21 Jun 2020 19:15:56: 6000000 INFO @ Sun, 21 Jun 2020 19:15:57: 11000000 INFO @ Sun, 21 Jun 2020 19:15:58: 2000000 INFO @ Sun, 21 Jun 2020 19:16:03: 7000000 INFO @ Sun, 21 Jun 2020 19:16:04: 12000000 INFO @ Sun, 21 Jun 2020 19:16:05: 3000000 INFO @ Sun, 21 Jun 2020 19:16:11: 8000000 INFO @ Sun, 21 Jun 2020 19:16:11: 13000000 INFO @ Sun, 21 Jun 2020 19:16:12: 4000000 INFO @ Sun, 21 Jun 2020 19:16:17: 14000000 INFO @ Sun, 21 Jun 2020 19:16:18: 9000000 INFO @ Sun, 21 Jun 2020 19:16:19: 5000000 INFO @ Sun, 21 Jun 2020 19:16:24: 15000000 INFO @ Sun, 21 Jun 2020 19:16:25: 10000000 INFO @ Sun, 21 Jun 2020 19:16:26: 6000000 INFO @ Sun, 21 Jun 2020 19:16:31: 16000000 INFO @ Sun, 21 Jun 2020 19:16:31: 11000000 INFO @ Sun, 21 Jun 2020 19:16:33: 7000000 INFO @ Sun, 21 Jun 2020 19:16:37: 17000000 INFO @ Sun, 21 Jun 2020 19:16:38: 12000000 INFO @ Sun, 21 Jun 2020 19:16:40: 8000000 INFO @ Sun, 21 Jun 2020 19:16:44: 18000000 INFO @ Sun, 21 Jun 2020 19:16:45: 13000000 INFO @ Sun, 21 Jun 2020 19:16:47: 9000000 INFO @ Sun, 21 Jun 2020 19:16:51: 19000000 INFO @ Sun, 21 Jun 2020 19:16:52: 14000000 INFO @ Sun, 21 Jun 2020 19:16:54: 10000000 INFO @ Sun, 21 Jun 2020 19:16:58: 15000000 INFO @ Sun, 21 Jun 2020 19:16:58: 20000000 INFO @ Sun, 21 Jun 2020 19:17:01: 11000000 INFO @ Sun, 21 Jun 2020 19:17:05: 16000000 INFO @ Sun, 21 Jun 2020 19:17:05: 21000000 INFO @ Sun, 21 Jun 2020 19:17:07: 12000000 INFO @ Sun, 21 Jun 2020 19:17:12: 22000000 INFO @ Sun, 21 Jun 2020 19:17:12: 17000000 INFO @ Sun, 21 Jun 2020 19:17:14: 13000000 INFO @ Sun, 21 Jun 2020 19:17:18: 23000000 INFO @ Sun, 21 Jun 2020 19:17:19: 18000000 INFO @ Sun, 21 Jun 2020 19:17:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:17:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:17:20: #1 total tags in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:17:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:20: #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 19:17:20: #1 tags after filtering in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:21: 14000000 INFO @ Sun, 21 Jun 2020 19:17:22: #2 number of paired peaks: 623 WARNING @ Sun, 21 Jun 2020 19:17:22: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:22: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:17:22: #2 alternative fragment length(s) may be 1,43 bps INFO @ Sun, 21 Jun 2020 19:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05_model.r WARNING @ Sun, 21 Jun 2020 19:17:22: #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 19:17:22: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Sun, 21 Jun 2020 19:17:22: #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 19:17:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:17:26: 19000000 INFO @ Sun, 21 Jun 2020 19:17:27: 15000000 INFO @ Sun, 21 Jun 2020 19:17:33: 20000000 INFO @ Sun, 21 Jun 2020 19:17:34: 16000000 INFO @ Sun, 21 Jun 2020 19:17:39: 21000000 INFO @ Sun, 21 Jun 2020 19:17:40: 17000000 INFO @ Sun, 21 Jun 2020 19:17:46: 22000000 INFO @ Sun, 21 Jun 2020 19:17:47: 18000000 INFO @ Sun, 21 Jun 2020 19:17:53: 23000000 INFO @ Sun, 21 Jun 2020 19:17:54: 19000000 INFO @ Sun, 21 Jun 2020 19:17:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:17:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:17:54: #1 total tags in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:17:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:54: #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 19:17:55: #1 tags after filtering in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:56: #2 number of paired peaks: 623 WARNING @ Sun, 21 Jun 2020 19:17:56: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:56: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:17:56: #2 alternative fragment length(s) may be 1,43 bps INFO @ Sun, 21 Jun 2020 19:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10_model.r WARNING @ Sun, 21 Jun 2020 19:17:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:56: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Sun, 21 Jun 2020 19:17:56: #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 19:17:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:00: 20000000 INFO @ Sun, 21 Jun 2020 19:18:06: 21000000 INFO @ Sun, 21 Jun 2020 19:18:13: 22000000 INFO @ Sun, 21 Jun 2020 19:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.05_summits.bed INFO @ Sun, 21 Jun 2020 19:18:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:19: 23000000 INFO @ Sun, 21 Jun 2020 19:18:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:18:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:18:20: #1 total tags in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:18:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:20: #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 19:18:21: #1 tags after filtering in treatment: 23194163 INFO @ Sun, 21 Jun 2020 19:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:21: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:22: #2 number of paired peaks: 623 WARNING @ Sun, 21 Jun 2020 19:18:22: Fewer paired peaks (623) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 623 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:22: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:18:22: #2 alternative fragment length(s) may be 1,43 bps INFO @ Sun, 21 Jun 2020 19:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20_model.r WARNING @ Sun, 21 Jun 2020 19:18:22: #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 19:18:22: #2 You may need to consider one of the other alternative d(s): 1,43 WARNING @ Sun, 21 Jun 2020 19:18:22: #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 19:18:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:18:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804229/SRX2804229.20_summits.bed INFO @ Sun, 21 Jun 2020 19:19:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling