Job ID = 6529761 SRX = SRX467096 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: 00:06:32 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1594029 (7.21%) aligned 0 times 13930149 (63.00%) aligned exactly 1 time 6585553 (29.79%) aligned >1 times 92.79% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 4221683 / 20515702 = 0.2058 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 02:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.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 02:46:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:36: 1000000 INFO @ Tue, 30 Jun 2020 02:46:42: 2000000 INFO @ Tue, 30 Jun 2020 02:46:48: 3000000 INFO @ Tue, 30 Jun 2020 02:46:54: 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 02:46:59: 5000000 INFO @ Tue, 30 Jun 2020 02:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.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 02:47:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:06: 6000000 INFO @ Tue, 30 Jun 2020 02:47:06: 1000000 INFO @ Tue, 30 Jun 2020 02:47:12: 7000000 INFO @ Tue, 30 Jun 2020 02:47:13: 2000000 INFO @ Tue, 30 Jun 2020 02:47:18: 8000000 INFO @ Tue, 30 Jun 2020 02:47:19: 3000000 INFO @ Tue, 30 Jun 2020 02:47:24: 9000000 INFO @ Tue, 30 Jun 2020 02:47:25: 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 02:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.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 02:47:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:30: 10000000 INFO @ Tue, 30 Jun 2020 02:47:31: 5000000 INFO @ Tue, 30 Jun 2020 02:47:36: 1000000 INFO @ Tue, 30 Jun 2020 02:47:37: 11000000 INFO @ Tue, 30 Jun 2020 02:47:38: 6000000 INFO @ Tue, 30 Jun 2020 02:47:43: 2000000 INFO @ Tue, 30 Jun 2020 02:47:43: 12000000 INFO @ Tue, 30 Jun 2020 02:47:44: 7000000 INFO @ Tue, 30 Jun 2020 02:47:49: 3000000 INFO @ Tue, 30 Jun 2020 02:47:49: 13000000 INFO @ Tue, 30 Jun 2020 02:47:50: 8000000 INFO @ Tue, 30 Jun 2020 02:47:56: 4000000 INFO @ Tue, 30 Jun 2020 02:47:56: 14000000 INFO @ Tue, 30 Jun 2020 02:47:56: 9000000 INFO @ Tue, 30 Jun 2020 02:48:02: 5000000 INFO @ Tue, 30 Jun 2020 02:48:02: 15000000 INFO @ Tue, 30 Jun 2020 02:48:03: 10000000 INFO @ Tue, 30 Jun 2020 02:48:08: 6000000 INFO @ Tue, 30 Jun 2020 02:48:09: 16000000 INFO @ Tue, 30 Jun 2020 02:48:09: 11000000 INFO @ Tue, 30 Jun 2020 02:48:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:11: #1 total tags in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:48:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:11: #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 02:48:11: #1 tags after filtering in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:11: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:13: #2 number of paired peaks: 708 WARNING @ Tue, 30 Jun 2020 02:48:13: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:13: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:48:13: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05_model.r WARNING @ Tue, 30 Jun 2020 02:48:13: #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 02:48:13: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:48:13: #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 02:48:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:15: 7000000 INFO @ Tue, 30 Jun 2020 02:48:15: 12000000 INFO @ Tue, 30 Jun 2020 02:48:21: 8000000 INFO @ Tue, 30 Jun 2020 02:48:22: 13000000 INFO @ Tue, 30 Jun 2020 02:48:27: 9000000 INFO @ Tue, 30 Jun 2020 02:48:29: 14000000 INFO @ Tue, 30 Jun 2020 02:48:34: 10000000 INFO @ Tue, 30 Jun 2020 02:48:35: 15000000 INFO @ Tue, 30 Jun 2020 02:48:40: 11000000 INFO @ Tue, 30 Jun 2020 02:48:42: 16000000 INFO @ Tue, 30 Jun 2020 02:48:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:44: #1 total tags in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:48:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:44: #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 02:48:44: #1 tags after filtering in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:48:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:46: #2 number of paired peaks: 708 WARNING @ Tue, 30 Jun 2020 02:48:46: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:46: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:48:46: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:46: #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 02:48:46: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:48:46: #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 02:48:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:48:53: 13000000 INFO @ Tue, 30 Jun 2020 02:48:59: 14000000 INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.05_summits.bed INFO @ Tue, 30 Jun 2020 02:49:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:05: 15000000 INFO @ Tue, 30 Jun 2020 02:49:12: 16000000 INFO @ Tue, 30 Jun 2020 02:49:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:14: #1 total tags in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:49:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:14: #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 02:49:14: #1 tags after filtering in treatment: 16294019 INFO @ Tue, 30 Jun 2020 02:49:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:16: #2 number of paired peaks: 708 WARNING @ Tue, 30 Jun 2020 02:49:16: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:16: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:49:16: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20_model.r WARNING @ Tue, 30 Jun 2020 02:49:16: #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 02:49:16: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:49:16: #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 02:49:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.10_summits.bed INFO @ Tue, 30 Jun 2020 02:49:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467096/SRX467096.20_summits.bed INFO @ Tue, 30 Jun 2020 02:50:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling