Job ID = 6529118 SRX = ERX1266821 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: 00:07:39 26582460 reads; of these: 26582460 (100.00%) were unpaired; of these: 3505655 (13.19%) aligned 0 times 14373114 (54.07%) aligned exactly 1 time 8703691 (32.74%) aligned >1 times 86.81% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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] 5254955 / 23076805 = 0.2277 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 01:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.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 01:38:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:38:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:38:13: 1000000 INFO @ Tue, 30 Jun 2020 01:38:19: 2000000 INFO @ Tue, 30 Jun 2020 01:38:25: 3000000 INFO @ Tue, 30 Jun 2020 01:38:30: 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 @ Tue, 30 Jun 2020 01:38:36: 5000000 INFO @ Tue, 30 Jun 2020 01:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.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 01:38:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:38:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:38:42: 6000000 INFO @ Tue, 30 Jun 2020 01:38:43: 1000000 INFO @ Tue, 30 Jun 2020 01:38:48: 7000000 INFO @ Tue, 30 Jun 2020 01:38:49: 2000000 INFO @ Tue, 30 Jun 2020 01:38:54: 8000000 INFO @ Tue, 30 Jun 2020 01:38:55: 3000000 INFO @ Tue, 30 Jun 2020 01:39:00: 9000000 INFO @ Tue, 30 Jun 2020 01:39:01: 4000000 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 01:39:06: 10000000 INFO @ Tue, 30 Jun 2020 01:39:07: 5000000 INFO @ Tue, 30 Jun 2020 01:39:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.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 01:39:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:39:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:39:12: 11000000 INFO @ Tue, 30 Jun 2020 01:39:13: 1000000 INFO @ Tue, 30 Jun 2020 01:39:13: 6000000 INFO @ Tue, 30 Jun 2020 01:39:18: 12000000 INFO @ Tue, 30 Jun 2020 01:39:18: 2000000 INFO @ Tue, 30 Jun 2020 01:39:19: 7000000 INFO @ Tue, 30 Jun 2020 01:39:24: 3000000 INFO @ Tue, 30 Jun 2020 01:39:24: 13000000 INFO @ Tue, 30 Jun 2020 01:39:25: 8000000 INFO @ Tue, 30 Jun 2020 01:39:29: 4000000 INFO @ Tue, 30 Jun 2020 01:39:30: 14000000 INFO @ Tue, 30 Jun 2020 01:39:31: 9000000 INFO @ Tue, 30 Jun 2020 01:39:34: 5000000 INFO @ Tue, 30 Jun 2020 01:39:36: 15000000 INFO @ Tue, 30 Jun 2020 01:39:37: 10000000 INFO @ Tue, 30 Jun 2020 01:39:40: 6000000 INFO @ Tue, 30 Jun 2020 01:39:41: 16000000 INFO @ Tue, 30 Jun 2020 01:39:43: 11000000 INFO @ Tue, 30 Jun 2020 01:39:45: 7000000 INFO @ Tue, 30 Jun 2020 01:39:47: 17000000 INFO @ Tue, 30 Jun 2020 01:39:48: 12000000 INFO @ Tue, 30 Jun 2020 01:39:50: 8000000 INFO @ Tue, 30 Jun 2020 01:39:52: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:39:52: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:39:52: #1 total tags in treatment: 17821850 INFO @ Tue, 30 Jun 2020 01:39:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:39:52: #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 01:39:53: #1 tags after filtering in treatment: 17821849 INFO @ Tue, 30 Jun 2020 01:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:39:53: #1 finished! INFO @ Tue, 30 Jun 2020 01:39:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:39:54: 13000000 INFO @ Tue, 30 Jun 2020 01:39:54: #2 number of paired peaks: 798 WARNING @ Tue, 30 Jun 2020 01:39:54: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 30 Jun 2020 01:39:54: start model_add_line... INFO @ Tue, 30 Jun 2020 01:39:54: start X-correlation... INFO @ Tue, 30 Jun 2020 01:39:54: end of X-cor INFO @ Tue, 30 Jun 2020 01:39:54: #2 finished! INFO @ Tue, 30 Jun 2020 01:39:54: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:39:54: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 01:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05_model.r WARNING @ Tue, 30 Jun 2020 01:39:54: #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 01:39:54: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 01:39:54: #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 01:39:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:39:56: 9000000 INFO @ Tue, 30 Jun 2020 01:40:00: 14000000 INFO @ Tue, 30 Jun 2020 01:40:01: 10000000 INFO @ Tue, 30 Jun 2020 01:40:06: 15000000 INFO @ Tue, 30 Jun 2020 01:40:06: 11000000 INFO @ Tue, 30 Jun 2020 01:40:11: 12000000 INFO @ Tue, 30 Jun 2020 01:40:12: 16000000 INFO @ Tue, 30 Jun 2020 01:40:16: 13000000 INFO @ Tue, 30 Jun 2020 01:40:17: 17000000 INFO @ Tue, 30 Jun 2020 01:40:22: 14000000 INFO @ Tue, 30 Jun 2020 01:40:22: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:40:22: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:40:22: #1 total tags in treatment: 17821850 INFO @ Tue, 30 Jun 2020 01:40:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:40:22: #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 01:40:23: #1 tags after filtering in treatment: 17821849 INFO @ Tue, 30 Jun 2020 01:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:40:23: #1 finished! INFO @ Tue, 30 Jun 2020 01:40:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:40:24: #2 number of paired peaks: 798 WARNING @ Tue, 30 Jun 2020 01:40:24: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 30 Jun 2020 01:40:24: start model_add_line... INFO @ Tue, 30 Jun 2020 01:40:24: start X-correlation... INFO @ Tue, 30 Jun 2020 01:40:24: end of X-cor INFO @ Tue, 30 Jun 2020 01:40:24: #2 finished! INFO @ Tue, 30 Jun 2020 01:40:24: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:40:24: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 01:40:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10_model.r WARNING @ Tue, 30 Jun 2020 01:40:24: #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 01:40:24: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 01:40:24: #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 01:40:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:40:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:40:27: 15000000 INFO @ Tue, 30 Jun 2020 01:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:40:32: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:40:37: 17000000 INFO @ Tue, 30 Jun 2020 01:40:42: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:40:42: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:40:42: #1 total tags in treatment: 17821850 INFO @ Tue, 30 Jun 2020 01:40:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:40:42: #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 01:40:42: #1 tags after filtering in treatment: 17821849 INFO @ Tue, 30 Jun 2020 01:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:40:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:40:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:40:44: #2 number of paired peaks: 798 WARNING @ Tue, 30 Jun 2020 01:40:44: Fewer paired peaks (798) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 798 pairs to build model! INFO @ Tue, 30 Jun 2020 01:40:44: start model_add_line... INFO @ Tue, 30 Jun 2020 01:40:44: start X-correlation... INFO @ Tue, 30 Jun 2020 01:40:44: end of X-cor INFO @ Tue, 30 Jun 2020 01:40:44: #2 finished! INFO @ Tue, 30 Jun 2020 01:40:44: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:40:44: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 01:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20_model.r WARNING @ Tue, 30 Jun 2020 01:40:44: #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 01:40:44: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 01:40:44: #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 01:40:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:40:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.05_summits.bed INFO @ Tue, 30 Jun 2020 01:40:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:41:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.10_summits.bed INFO @ Tue, 30 Jun 2020 01:41:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:41:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1266821/ERX1266821.20_summits.bed INFO @ Tue, 30 Jun 2020 01:41:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling