Job ID = 6529469 SRX = SRX287693 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:28 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1567425 (6.81%) aligned 0 times 14607445 (63.49%) aligned exactly 1 time 6833213 (29.70%) aligned >1 times 93.19% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 4171288 / 21440658 = 0.1946 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 @ Tue, 30 Jun 2020 02:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.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 @ Tue, 30 Jun 2020 02:20:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:14: 1000000 INFO @ Tue, 30 Jun 2020 02:20:22: 2000000 INFO @ Tue, 30 Jun 2020 02:20:31: 3000000 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 @ Tue, 30 Jun 2020 02:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.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 @ Tue, 30 Jun 2020 02:20:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:39: 4000000 INFO @ Tue, 30 Jun 2020 02:20:45: 1000000 INFO @ Tue, 30 Jun 2020 02:20:48: 5000000 INFO @ Tue, 30 Jun 2020 02:20:53: 2000000 INFO @ Tue, 30 Jun 2020 02:20:58: 6000000 INFO @ Tue, 30 Jun 2020 02:21:01: 3000000 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 @ Tue, 30 Jun 2020 02:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.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 @ Tue, 30 Jun 2020 02:21:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:07: 7000000 INFO @ Tue, 30 Jun 2020 02:21:09: 4000000 INFO @ Tue, 30 Jun 2020 02:21:15: 1000000 INFO @ Tue, 30 Jun 2020 02:21:17: 8000000 INFO @ Tue, 30 Jun 2020 02:21:18: 5000000 INFO @ Tue, 30 Jun 2020 02:21:25: 2000000 INFO @ Tue, 30 Jun 2020 02:21:26: 6000000 INFO @ Tue, 30 Jun 2020 02:21:27: 9000000 INFO @ Tue, 30 Jun 2020 02:21:34: 7000000 INFO @ Tue, 30 Jun 2020 02:21:34: 3000000 INFO @ Tue, 30 Jun 2020 02:21:37: 10000000 INFO @ Tue, 30 Jun 2020 02:21:42: 8000000 INFO @ Tue, 30 Jun 2020 02:21:44: 4000000 INFO @ Tue, 30 Jun 2020 02:21:46: 11000000 INFO @ Tue, 30 Jun 2020 02:21:50: 9000000 INFO @ Tue, 30 Jun 2020 02:21:54: 5000000 INFO @ Tue, 30 Jun 2020 02:21:56: 12000000 INFO @ Tue, 30 Jun 2020 02:21:58: 10000000 INFO @ Tue, 30 Jun 2020 02:22:03: 6000000 INFO @ Tue, 30 Jun 2020 02:22:05: 13000000 INFO @ Tue, 30 Jun 2020 02:22:06: 11000000 INFO @ Tue, 30 Jun 2020 02:22:13: 7000000 INFO @ Tue, 30 Jun 2020 02:22:14: 12000000 INFO @ Tue, 30 Jun 2020 02:22:15: 14000000 INFO @ Tue, 30 Jun 2020 02:22:22: 8000000 INFO @ Tue, 30 Jun 2020 02:22:22: 13000000 INFO @ Tue, 30 Jun 2020 02:22:25: 15000000 INFO @ Tue, 30 Jun 2020 02:22:31: 14000000 INFO @ Tue, 30 Jun 2020 02:22:32: 9000000 INFO @ Tue, 30 Jun 2020 02:22:35: 16000000 INFO @ Tue, 30 Jun 2020 02:22:39: 15000000 INFO @ Tue, 30 Jun 2020 02:22:42: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:22:45: 17000000 INFO @ Tue, 30 Jun 2020 02:22:47: 16000000 INFO @ Tue, 30 Jun 2020 02:22:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:22:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:22:48: #1 total tags in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:22:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:22:48: #1 tags after filtering in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:49: #2 number of paired peaks: 684 WARNING @ Tue, 30 Jun 2020 02:22:49: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:50: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:22:50: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05_model.r WARNING @ Tue, 30 Jun 2020 02:22:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:50: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:22:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:22:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:52: 11000000 INFO @ Tue, 30 Jun 2020 02:22:55: 17000000 INFO @ Tue, 30 Jun 2020 02:22:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:22:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:22:57: #1 total tags in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:22:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:22:58: #1 tags after filtering in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:59: #2 number of paired peaks: 684 WARNING @ Tue, 30 Jun 2020 02:22:59: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:59: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:22:59: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10_model.r WARNING @ Tue, 30 Jun 2020 02:22:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:59: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:22:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:22:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:00: 12000000 INFO @ Tue, 30 Jun 2020 02:23:08: 13000000 INFO @ Tue, 30 Jun 2020 02:23:17: 14000000 INFO @ Tue, 30 Jun 2020 02:23:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:25: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:23:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:34: 16000000 INFO @ Tue, 30 Jun 2020 02:23:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.05_summits.bed INFO @ Tue, 30 Jun 2020 02:23:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:23:43: 17000000 INFO @ Tue, 30 Jun 2020 02:23:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:23:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:23:45: #1 total tags in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:23:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:23:46: #1 tags after filtering in treatment: 17269370 INFO @ Tue, 30 Jun 2020 02:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:47: #2 number of paired peaks: 684 WARNING @ Tue, 30 Jun 2020 02:23:47: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:47: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:23:47: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20_model.r WARNING @ Tue, 30 Jun 2020 02:23:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:23:47: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:23:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:23:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.10_summits.bed INFO @ Tue, 30 Jun 2020 02:23:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287693/SRX287693.20_summits.bed INFO @ Tue, 30 Jun 2020 02:24:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling