Job ID = 6454997 SRX = SRX2618545 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR5319099'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:35 prefetch.2.10.7: 'SRR5319099' is valid 2020-06-21T09:50:35 prefetch.2.10.7: 1) 'SRR5319099' was downloaded successfully 2020-06-21T09:50:35 prefetch.2.10.7: 'SRR5319099' has 0 unresolved dependencies Read 19539289 spots for SRR5319099/SRR5319099.sra Written 19539289 spots for SRR5319099/SRR5319099.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: 00:05:17 19539289 reads; of these: 19539289 (100.00%) were unpaired; of these: 1979638 (10.13%) aligned 0 times 11779408 (60.29%) aligned exactly 1 time 5780243 (29.58%) aligned >1 times 89.87% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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 8 files... [bam_rmdupse_core] 2592754 / 17559651 = 0.1477 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 19:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.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 19:02:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:12: 1000000 INFO @ Sun, 21 Jun 2020 19:02:18: 2000000 INFO @ Sun, 21 Jun 2020 19:02:23: 3000000 INFO @ Sun, 21 Jun 2020 19:02:29: 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 19:02:35: 5000000 INFO @ Sun, 21 Jun 2020 19:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.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 19:02:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:40: 6000000 INFO @ Sun, 21 Jun 2020 19:02:42: 1000000 INFO @ Sun, 21 Jun 2020 19:02:46: 7000000 INFO @ Sun, 21 Jun 2020 19:02:48: 2000000 INFO @ Sun, 21 Jun 2020 19:02:52: 8000000 INFO @ Sun, 21 Jun 2020 19:02:54: 3000000 INFO @ Sun, 21 Jun 2020 19:02:58: 9000000 INFO @ Sun, 21 Jun 2020 19:02:59: 4000000 INFO @ Sun, 21 Jun 2020 19:03:03: 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 19:03:05: 5000000 INFO @ Sun, 21 Jun 2020 19:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.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 19:03:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:09: 11000000 INFO @ Sun, 21 Jun 2020 19:03:11: 6000000 INFO @ Sun, 21 Jun 2020 19:03:12: 1000000 INFO @ Sun, 21 Jun 2020 19:03:16: 12000000 INFO @ Sun, 21 Jun 2020 19:03:17: 7000000 INFO @ Sun, 21 Jun 2020 19:03:18: 2000000 INFO @ Sun, 21 Jun 2020 19:03:21: 13000000 INFO @ Sun, 21 Jun 2020 19:03:23: 8000000 INFO @ Sun, 21 Jun 2020 19:03:24: 3000000 INFO @ Sun, 21 Jun 2020 19:03:27: 14000000 INFO @ Sun, 21 Jun 2020 19:03:28: 9000000 INFO @ Sun, 21 Jun 2020 19:03:30: 4000000 INFO @ Sun, 21 Jun 2020 19:03:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:33: #1 total tags in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:03:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:33: #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 19:03:33: #1 tags after filtering in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:34: 10000000 INFO @ Sun, 21 Jun 2020 19:03:34: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 19:03:34: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:34: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:03:34: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 19:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05_model.r WARNING @ Sun, 21 Jun 2020 19:03:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:34: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 19:03:34: #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 19:03:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:35: 5000000 INFO @ Sun, 21 Jun 2020 19:03:40: 11000000 INFO @ Sun, 21 Jun 2020 19:03:41: 6000000 INFO @ Sun, 21 Jun 2020 19:03:46: 12000000 INFO @ Sun, 21 Jun 2020 19:03:47: 7000000 INFO @ Sun, 21 Jun 2020 19:03:52: 13000000 INFO @ Sun, 21 Jun 2020 19:03:53: 8000000 INFO @ Sun, 21 Jun 2020 19:03:57: 14000000 INFO @ Sun, 21 Jun 2020 19:03:58: 9000000 INFO @ Sun, 21 Jun 2020 19:04:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:03: #1 total tags in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:04:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:03: #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 19:04:03: #1 tags after filtering in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:04: 10000000 INFO @ Sun, 21 Jun 2020 19:04:05: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 19:04:05: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:05: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:04:05: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 19:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:05: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 19:04:05: #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 19:04:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:10: 11000000 INFO @ Sun, 21 Jun 2020 19:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:16: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:21: 13000000 INFO @ Sun, 21 Jun 2020 19:04:27: 14000000 INFO @ Sun, 21 Jun 2020 19:04:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:33: #1 total tags in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:04:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:33: #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 19:04:33: #1 tags after filtering in treatment: 14966897 INFO @ Sun, 21 Jun 2020 19:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:34: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 19:04:34: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:35: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:04:35: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 19:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20_model.r WARNING @ Sun, 21 Jun 2020 19:04:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:35: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 19:04:35: #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 19:04:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.10_summits.bed INFO @ Sun, 21 Jun 2020 19:04:45: 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 19:05:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618545/SRX2618545.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:16: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling