Job ID = 6529841 SRX = SRX495786 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: 00:08:37 25341638 reads; of these: 25341638 (100.00%) were unpaired; of these: 8991372 (35.48%) aligned 0 times 8908306 (35.15%) aligned exactly 1 time 7441960 (29.37%) aligned >1 times 64.52% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 8054172 / 16350266 = 0.4926 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 03:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.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 03:17:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:17:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:17:41: 1000000 INFO @ Tue, 30 Jun 2020 03:17:47: 2000000 INFO @ Tue, 30 Jun 2020 03:17:53: 3000000 INFO @ Tue, 30 Jun 2020 03:17:59: 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 03:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.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 03:18:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:05: 5000000 INFO @ Tue, 30 Jun 2020 03:18:11: 1000000 INFO @ Tue, 30 Jun 2020 03:18:12: 6000000 INFO @ Tue, 30 Jun 2020 03:18:18: 2000000 INFO @ Tue, 30 Jun 2020 03:18:19: 7000000 INFO @ Tue, 30 Jun 2020 03:18:24: 3000000 INFO @ Tue, 30 Jun 2020 03:18:26: 8000000 INFO @ Tue, 30 Jun 2020 03:18:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:18:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:18:29: #1 total tags in treatment: 8296094 INFO @ Tue, 30 Jun 2020 03:18:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:29: #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 03:18:29: #1 tags after filtering in treatment: 8296005 INFO @ Tue, 30 Jun 2020 03:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:18:30: #2 number of paired peaks: 2293 INFO @ Tue, 30 Jun 2020 03:18:30: start model_add_line... INFO @ Tue, 30 Jun 2020 03:18:30: start X-correlation... INFO @ Tue, 30 Jun 2020 03:18:30: end of X-cor INFO @ Tue, 30 Jun 2020 03:18:30: #2 finished! INFO @ Tue, 30 Jun 2020 03:18:30: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:18:30: #2 alternative fragment length(s) may be 3,52,92,134,180,223,266,405,451,496,540,589 bps INFO @ Tue, 30 Jun 2020 03:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05_model.r WARNING @ Tue, 30 Jun 2020 03:18:30: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:18:30: #2 You may need to consider one of the other alternative d(s): 3,52,92,134,180,223,266,405,451,496,540,589 WARNING @ Tue, 30 Jun 2020 03:18:30: #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 03:18:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:18:31: 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 03:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.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 03:18:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:37: 5000000 INFO @ Tue, 30 Jun 2020 03:18:41: 1000000 INFO @ Tue, 30 Jun 2020 03:18:43: 6000000 INFO @ Tue, 30 Jun 2020 03:18:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:48: 2000000 INFO @ Tue, 30 Jun 2020 03:18:50: 7000000 INFO @ Tue, 30 Jun 2020 03:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.05_summits.bed INFO @ Tue, 30 Jun 2020 03:18:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:54: 3000000 INFO @ Tue, 30 Jun 2020 03:18:56: 8000000 INFO @ Tue, 30 Jun 2020 03:18:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:18:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:18:58: #1 total tags in treatment: 8296094 INFO @ Tue, 30 Jun 2020 03:18:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:58: #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 03:18:59: #1 tags after filtering in treatment: 8296005 INFO @ Tue, 30 Jun 2020 03:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:59: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:00: #2 number of paired peaks: 2293 INFO @ Tue, 30 Jun 2020 03:19:00: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:00: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:00: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:00: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:00: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:19:00: #2 alternative fragment length(s) may be 3,52,92,134,180,223,266,405,451,496,540,589 bps INFO @ Tue, 30 Jun 2020 03:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10_model.r WARNING @ Tue, 30 Jun 2020 03:19:00: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:00: #2 You may need to consider one of the other alternative d(s): 3,52,92,134,180,223,266,405,451,496,540,589 WARNING @ Tue, 30 Jun 2020 03:19:00: #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 03:19:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:01: 4000000 INFO @ Tue, 30 Jun 2020 03:19:07: 5000000 INFO @ Tue, 30 Jun 2020 03:19:14: 6000000 INFO @ Tue, 30 Jun 2020 03:19:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:19:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:19:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.10_summits.bed INFO @ Tue, 30 Jun 2020 03:19:23: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:19:28: 8000000 INFO @ Tue, 30 Jun 2020 03:19:30: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:19:30: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:19:30: #1 total tags in treatment: 8296094 INFO @ Tue, 30 Jun 2020 03:19:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:30: #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 03:19:30: #1 tags after filtering in treatment: 8296005 INFO @ Tue, 30 Jun 2020 03:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:31: #2 number of paired peaks: 2293 INFO @ Tue, 30 Jun 2020 03:19:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:31: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:19:31: #2 alternative fragment length(s) may be 3,52,92,134,180,223,266,405,451,496,540,589 bps INFO @ Tue, 30 Jun 2020 03:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20_model.r WARNING @ Tue, 30 Jun 2020 03:19:31: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:31: #2 You may need to consider one of the other alternative d(s): 3,52,92,134,180,223,266,405,451,496,540,589 WARNING @ Tue, 30 Jun 2020 03:19:31: #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 03:19:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:19:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495786/SRX495786.20_summits.bed INFO @ Tue, 30 Jun 2020 03:19:54: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling