Job ID = 6453385 SRX = SRX113313 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:19:47 prefetch.2.10.7: 1) Downloading 'SRR392922'... 2020-06-21T08:19:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:22:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:22:32 prefetch.2.10.7: 'SRR392922' is valid 2020-06-21T08:22:32 prefetch.2.10.7: 1) 'SRR392922' was downloaded successfully Read 17988834 spots for SRR392922/SRR392922.sra Written 17988834 spots for SRR392922/SRR392922.sra 2020-06-21T08:23:34 prefetch.2.10.7: 1) Downloading 'SRR392923'... 2020-06-21T08:23:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:48 prefetch.2.10.7: 1) 'SRR392923' was downloaded successfully Read 21633808 spots for SRR392923/SRR392923.sra Written 21633808 spots for SRR392923/SRR392923.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:47 39622642 reads; of these: 39622642 (100.00%) were unpaired; of these: 8964320 (22.62%) aligned 0 times 27455369 (69.29%) aligned exactly 1 time 3202953 (8.08%) aligned >1 times 77.38% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 10808649 / 30658322 = 0.3526 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 17:44:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.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 17:44:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:35: 1000000 INFO @ Sun, 21 Jun 2020 17:44:40: 2000000 INFO @ Sun, 21 Jun 2020 17:44:46: 3000000 INFO @ Sun, 21 Jun 2020 17:44:51: 4000000 INFO @ Sun, 21 Jun 2020 17:44:56: 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 17:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.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 17:45:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:01: 6000000 INFO @ Sun, 21 Jun 2020 17:45:05: 1000000 INFO @ Sun, 21 Jun 2020 17:45:07: 7000000 INFO @ Sun, 21 Jun 2020 17:45:09: 2000000 INFO @ Sun, 21 Jun 2020 17:45:12: 8000000 INFO @ Sun, 21 Jun 2020 17:45:14: 3000000 INFO @ Sun, 21 Jun 2020 17:45:17: 9000000 INFO @ Sun, 21 Jun 2020 17:45:19: 4000000 INFO @ Sun, 21 Jun 2020 17:45:22: 10000000 INFO @ Sun, 21 Jun 2020 17:45:24: 5000000 INFO @ Sun, 21 Jun 2020 17:45:28: 11000000 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 17:45:29: 6000000 INFO @ Sun, 21 Jun 2020 17:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.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 17:45:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:33: 12000000 INFO @ Sun, 21 Jun 2020 17:45:34: 7000000 INFO @ Sun, 21 Jun 2020 17:45:35: 1000000 INFO @ Sun, 21 Jun 2020 17:45:38: 13000000 INFO @ Sun, 21 Jun 2020 17:45:38: 8000000 INFO @ Sun, 21 Jun 2020 17:45:40: 2000000 INFO @ Sun, 21 Jun 2020 17:45:43: 14000000 INFO @ Sun, 21 Jun 2020 17:45:43: 9000000 INFO @ Sun, 21 Jun 2020 17:45:44: 3000000 INFO @ Sun, 21 Jun 2020 17:45:48: 10000000 INFO @ Sun, 21 Jun 2020 17:45:48: 15000000 INFO @ Sun, 21 Jun 2020 17:45:49: 4000000 INFO @ Sun, 21 Jun 2020 17:45:53: 11000000 INFO @ Sun, 21 Jun 2020 17:45:54: 16000000 INFO @ Sun, 21 Jun 2020 17:45:54: 5000000 INFO @ Sun, 21 Jun 2020 17:45:58: 12000000 INFO @ Sun, 21 Jun 2020 17:45:59: 6000000 INFO @ Sun, 21 Jun 2020 17:45:59: 17000000 INFO @ Sun, 21 Jun 2020 17:46:03: 13000000 INFO @ Sun, 21 Jun 2020 17:46:04: 7000000 INFO @ Sun, 21 Jun 2020 17:46:05: 18000000 INFO @ Sun, 21 Jun 2020 17:46:07: 14000000 INFO @ Sun, 21 Jun 2020 17:46:09: 8000000 INFO @ Sun, 21 Jun 2020 17:46:10: 19000000 INFO @ Sun, 21 Jun 2020 17:46:12: 15000000 INFO @ Sun, 21 Jun 2020 17:46:13: 9000000 INFO @ Sun, 21 Jun 2020 17:46:15: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:46:15: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:46:15: #1 total tags in treatment: 19849673 INFO @ Sun, 21 Jun 2020 17:46:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:15: #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 17:46:16: #1 tags after filtering in treatment: 19849666 INFO @ Sun, 21 Jun 2020 17:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:17: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 17:46:17: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:17: 16000000 INFO @ Sun, 21 Jun 2020 17:46:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:17: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:46:17: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05_model.r WARNING @ Sun, 21 Jun 2020 17:46:17: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:17: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:46:17: #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 17:46:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:18: 10000000 INFO @ Sun, 21 Jun 2020 17:46:22: 17000000 INFO @ Sun, 21 Jun 2020 17:46:23: 11000000 INFO @ Sun, 21 Jun 2020 17:46:27: 18000000 INFO @ Sun, 21 Jun 2020 17:46:28: 12000000 INFO @ Sun, 21 Jun 2020 17:46:32: 19000000 INFO @ Sun, 21 Jun 2020 17:46:32: 13000000 INFO @ Sun, 21 Jun 2020 17:46:36: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:46:36: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:46:36: #1 total tags in treatment: 19849673 INFO @ Sun, 21 Jun 2020 17:46:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:36: #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 17:46:37: #1 tags after filtering in treatment: 19849666 INFO @ Sun, 21 Jun 2020 17:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:37: 14000000 INFO @ Sun, 21 Jun 2020 17:46:38: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 17:46:38: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 17:46:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:38: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:46:38: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10_model.r WARNING @ Sun, 21 Jun 2020 17:46:38: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:38: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:46:38: #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 17:46:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:42: 15000000 INFO @ Sun, 21 Jun 2020 17:46:46: 16000000 INFO @ Sun, 21 Jun 2020 17:46:51: 17000000 INFO @ Sun, 21 Jun 2020 17:46:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:46:56: 18000000 INFO @ Sun, 21 Jun 2020 17:47:01: 19000000 INFO @ Sun, 21 Jun 2020 17:47:05: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:47:05: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:47:05: #1 total tags in treatment: 19849673 INFO @ Sun, 21 Jun 2020 17:47:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:05: #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 17:47:06: #1 tags after filtering in treatment: 19849666 INFO @ Sun, 21 Jun 2020 17:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:07: #2 number of paired peaks: 521 WARNING @ Sun, 21 Jun 2020 17:47:07: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Sun, 21 Jun 2020 17:47:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:07: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:47:07: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20_model.r WARNING @ Sun, 21 Jun 2020 17:47:07: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:07: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:47:07: #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 17:47:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:32: 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 17:47:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX113313/SRX113313.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling