Job ID = 6529323 SRX = SRX182774 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: 00:07:22 27246731 reads; of these: 27246731 (100.00%) were unpaired; of these: 1474941 (5.41%) aligned 0 times 17785230 (65.27%) aligned exactly 1 time 7986560 (29.31%) aligned >1 times 94.59% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 5182075 / 25771790 = 0.2011 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 02:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.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 02:00:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:00:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:00:52: 1000000 INFO @ Tue, 30 Jun 2020 02:00:57: 2000000 INFO @ Tue, 30 Jun 2020 02:01:02: 3000000 INFO @ Tue, 30 Jun 2020 02:01:07: 4000000 INFO @ Tue, 30 Jun 2020 02:01:12: 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 @ Tue, 30 Jun 2020 02:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.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 02:01:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:17: 6000000 INFO @ Tue, 30 Jun 2020 02:01:22: 1000000 INFO @ Tue, 30 Jun 2020 02:01:22: 7000000 INFO @ Tue, 30 Jun 2020 02:01:27: 8000000 INFO @ Tue, 30 Jun 2020 02:01:27: 2000000 INFO @ Tue, 30 Jun 2020 02:01:32: 9000000 INFO @ Tue, 30 Jun 2020 02:01:32: 3000000 INFO @ Tue, 30 Jun 2020 02:01:37: 10000000 INFO @ Tue, 30 Jun 2020 02:01:37: 4000000 INFO @ Tue, 30 Jun 2020 02:01:42: 11000000 INFO @ Tue, 30 Jun 2020 02:01:43: 5000000 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 02:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.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 02:01:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:47: 12000000 INFO @ Tue, 30 Jun 2020 02:01:48: 6000000 INFO @ Tue, 30 Jun 2020 02:01:53: 1000000 INFO @ Tue, 30 Jun 2020 02:01:53: 13000000 INFO @ Tue, 30 Jun 2020 02:01:53: 7000000 INFO @ Tue, 30 Jun 2020 02:01:58: 14000000 INFO @ Tue, 30 Jun 2020 02:01:59: 8000000 INFO @ Tue, 30 Jun 2020 02:01:59: 2000000 INFO @ Tue, 30 Jun 2020 02:02:03: 15000000 INFO @ Tue, 30 Jun 2020 02:02:04: 9000000 INFO @ Tue, 30 Jun 2020 02:02:05: 3000000 INFO @ Tue, 30 Jun 2020 02:02:08: 16000000 INFO @ Tue, 30 Jun 2020 02:02:09: 10000000 INFO @ Tue, 30 Jun 2020 02:02:11: 4000000 INFO @ Tue, 30 Jun 2020 02:02:14: 17000000 INFO @ Tue, 30 Jun 2020 02:02:15: 11000000 INFO @ Tue, 30 Jun 2020 02:02:17: 5000000 INFO @ Tue, 30 Jun 2020 02:02:19: 18000000 INFO @ Tue, 30 Jun 2020 02:02:20: 12000000 INFO @ Tue, 30 Jun 2020 02:02:23: 6000000 INFO @ Tue, 30 Jun 2020 02:02:25: 19000000 INFO @ Tue, 30 Jun 2020 02:02:25: 13000000 INFO @ Tue, 30 Jun 2020 02:02:29: 7000000 INFO @ Tue, 30 Jun 2020 02:02:30: 20000000 INFO @ Tue, 30 Jun 2020 02:02:31: 14000000 INFO @ Tue, 30 Jun 2020 02:02:33: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:02:33: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:02:33: #1 total tags in treatment: 20589715 INFO @ Tue, 30 Jun 2020 02:02:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:33: #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 02:02:34: #1 tags after filtering in treatment: 20589714 INFO @ Tue, 30 Jun 2020 02:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:34: 8000000 INFO @ Tue, 30 Jun 2020 02:02:35: #2 number of paired peaks: 550 WARNING @ Tue, 30 Jun 2020 02:02:35: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:36: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:02:36: #2 alternative fragment length(s) may be 2,32 bps INFO @ Tue, 30 Jun 2020 02:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05_model.r WARNING @ Tue, 30 Jun 2020 02:02:36: #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 02:02:36: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Tue, 30 Jun 2020 02:02:36: #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 02:02:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:36: 15000000 INFO @ Tue, 30 Jun 2020 02:02:40: 9000000 INFO @ Tue, 30 Jun 2020 02:02:41: 16000000 INFO @ Tue, 30 Jun 2020 02:02:46: 10000000 INFO @ Tue, 30 Jun 2020 02:02:47: 17000000 INFO @ Tue, 30 Jun 2020 02:02:52: 11000000 INFO @ Tue, 30 Jun 2020 02:02:52: 18000000 INFO @ Tue, 30 Jun 2020 02:02:57: 19000000 INFO @ Tue, 30 Jun 2020 02:02:58: 12000000 INFO @ Tue, 30 Jun 2020 02:03:03: 20000000 INFO @ Tue, 30 Jun 2020 02:03:03: 13000000 INFO @ Tue, 30 Jun 2020 02:03:06: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:03:06: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:03:06: #1 total tags in treatment: 20589715 INFO @ Tue, 30 Jun 2020 02:03:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:06: #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 02:03:07: #1 tags after filtering in treatment: 20589714 INFO @ Tue, 30 Jun 2020 02:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:08: #2 number of paired peaks: 550 WARNING @ Tue, 30 Jun 2020 02:03:08: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:03:08: #2 alternative fragment length(s) may be 2,32 bps INFO @ Tue, 30 Jun 2020 02:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10_model.r WARNING @ Tue, 30 Jun 2020 02:03:08: #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 02:03:08: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Tue, 30 Jun 2020 02:03:08: #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 02:03:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:09: 14000000 INFO @ Tue, 30 Jun 2020 02:03:11: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:03:15: 15000000 INFO @ Tue, 30 Jun 2020 02:03:20: 16000000 INFO @ Tue, 30 Jun 2020 02:03:26: 17000000 INFO @ Tue, 30 Jun 2020 02:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.05_summits.bed INFO @ Tue, 30 Jun 2020 02:03:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:32: 18000000 INFO @ Tue, 30 Jun 2020 02:03:37: 19000000 INFO @ Tue, 30 Jun 2020 02:03:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:43: 20000000 INFO @ Tue, 30 Jun 2020 02:03:47: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:03:47: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:03:47: #1 total tags in treatment: 20589715 INFO @ Tue, 30 Jun 2020 02:03:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:47: #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 02:03:47: #1 tags after filtering in treatment: 20589714 INFO @ Tue, 30 Jun 2020 02:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:48: #2 number of paired peaks: 550 WARNING @ Tue, 30 Jun 2020 02:03:48: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:48: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:49: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:03:49: #2 alternative fragment length(s) may be 2,32 bps INFO @ Tue, 30 Jun 2020 02:03:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20_model.r WARNING @ Tue, 30 Jun 2020 02:03:49: #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 02:03:49: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Tue, 30 Jun 2020 02:03:49: #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 02:03:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.10_summits.bed INFO @ Tue, 30 Jun 2020 02:03:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:04:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182774/SRX182774.20_summits.bed INFO @ Tue, 30 Jun 2020 02:04:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling