Job ID = 6529456 SRX = SRX287602 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: 00:06:28 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1611543 (7.58%) aligned 0 times 13447286 (63.23%) aligned exactly 1 time 6207575 (29.19%) aligned >1 times 92.42% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 4582344 / 19654861 = 0.2331 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 02:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.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 02:10:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:52: 1000000 INFO @ Tue, 30 Jun 2020 02:10:58: 2000000 INFO @ Tue, 30 Jun 2020 02:11:04: 3000000 INFO @ Tue, 30 Jun 2020 02:11:11: 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 02:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.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 02:11:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:17: 5000000 INFO @ Tue, 30 Jun 2020 02:11:23: 1000000 INFO @ Tue, 30 Jun 2020 02:11:24: 6000000 INFO @ Tue, 30 Jun 2020 02:11:30: 2000000 INFO @ Tue, 30 Jun 2020 02:11:31: 7000000 INFO @ Tue, 30 Jun 2020 02:11:37: 3000000 INFO @ Tue, 30 Jun 2020 02:11:38: 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 @ Tue, 30 Jun 2020 02:11:44: 4000000 INFO @ Tue, 30 Jun 2020 02:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.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 02:11:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:11:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:11:45: 9000000 INFO @ Tue, 30 Jun 2020 02:11:51: 5000000 INFO @ Tue, 30 Jun 2020 02:11:53: 1000000 INFO @ Tue, 30 Jun 2020 02:11:53: 10000000 INFO @ Tue, 30 Jun 2020 02:11:59: 6000000 INFO @ Tue, 30 Jun 2020 02:12:00: 2000000 INFO @ Tue, 30 Jun 2020 02:12:00: 11000000 INFO @ Tue, 30 Jun 2020 02:12:06: 7000000 INFO @ Tue, 30 Jun 2020 02:12:07: 3000000 INFO @ Tue, 30 Jun 2020 02:12:08: 12000000 INFO @ Tue, 30 Jun 2020 02:12:13: 8000000 INFO @ Tue, 30 Jun 2020 02:12:15: 4000000 INFO @ Tue, 30 Jun 2020 02:12:16: 13000000 INFO @ Tue, 30 Jun 2020 02:12:21: 9000000 INFO @ Tue, 30 Jun 2020 02:12:22: 5000000 INFO @ Tue, 30 Jun 2020 02:12:23: 14000000 INFO @ Tue, 30 Jun 2020 02:12:28: 10000000 INFO @ Tue, 30 Jun 2020 02:12:29: 6000000 INFO @ Tue, 30 Jun 2020 02:12:31: 15000000 INFO @ Tue, 30 Jun 2020 02:12:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:32: #1 total tags in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:12:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:32: #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 02:12:32: #1 tags after filtering in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:33: #2 number of paired peaks: 719 WARNING @ Tue, 30 Jun 2020 02:12:33: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:33: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:12:33: #2 alternative fragment length(s) may be 2,35 bps INFO @ Tue, 30 Jun 2020 02:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05_model.r WARNING @ Tue, 30 Jun 2020 02:12:33: #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 02:12:33: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Tue, 30 Jun 2020 02:12:33: #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 02:12:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:35: 11000000 INFO @ Tue, 30 Jun 2020 02:12:37: 7000000 INFO @ Tue, 30 Jun 2020 02:12:43: 12000000 INFO @ Tue, 30 Jun 2020 02:12:44: 8000000 INFO @ Tue, 30 Jun 2020 02:12:50: 13000000 INFO @ Tue, 30 Jun 2020 02:12:51: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:12:58: 14000000 INFO @ Tue, 30 Jun 2020 02:12:58: 10000000 INFO @ Tue, 30 Jun 2020 02:13:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:05: 15000000 INFO @ Tue, 30 Jun 2020 02:13:05: 11000000 INFO @ Tue, 30 Jun 2020 02:13:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:05: #1 total tags in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:13:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:05: #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 02:13:06: #1 tags after filtering in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:07: #2 number of paired peaks: 719 WARNING @ Tue, 30 Jun 2020 02:13:07: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:07: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:13:07: #2 alternative fragment length(s) may be 2,35 bps INFO @ Tue, 30 Jun 2020 02:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10_model.r WARNING @ Tue, 30 Jun 2020 02:13:07: #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 02:13:07: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Tue, 30 Jun 2020 02:13:07: #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 02:13:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:12: 12000000 INFO @ Tue, 30 Jun 2020 02:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.05_summits.bed INFO @ Tue, 30 Jun 2020 02:13:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:13:18: 13000000 INFO @ Tue, 30 Jun 2020 02:13:24: 14000000 INFO @ Tue, 30 Jun 2020 02:13:30: 15000000 INFO @ Tue, 30 Jun 2020 02:13:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:31: #1 total tags in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:13:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:13:31: #1 tags after filtering in treatment: 15072517 INFO @ Tue, 30 Jun 2020 02:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:33: #2 number of paired peaks: 719 WARNING @ Tue, 30 Jun 2020 02:13:33: Fewer paired peaks (719) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 719 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:33: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:13:33: #2 alternative fragment length(s) may be 2,35 bps INFO @ Tue, 30 Jun 2020 02:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20_model.r WARNING @ Tue, 30 Jun 2020 02:13:33: #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 02:13:33: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Tue, 30 Jun 2020 02:13:33: #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 02:13:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287602/SRX287602.20_summits.bed INFO @ Tue, 30 Jun 2020 02:14:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling