Job ID = 6529840 SRX = SRX495785 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: 00:06:06 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 1075745 (6.10%) aligned 0 times 11627022 (65.90%) aligned exactly 1 time 4941166 (28.00%) aligned >1 times 93.90% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 4021244 / 16568188 = 0.2427 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 03:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.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 03:12:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:18: 1000000 INFO @ Tue, 30 Jun 2020 03:12:25: 2000000 INFO @ Tue, 30 Jun 2020 03:12:32: 3000000 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 03:12:39: 4000000 INFO @ Tue, 30 Jun 2020 03:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.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 03:12:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:47: 5000000 INFO @ Tue, 30 Jun 2020 03:12:49: 1000000 INFO @ Tue, 30 Jun 2020 03:12:56: 6000000 INFO @ Tue, 30 Jun 2020 03:12:57: 2000000 INFO @ Tue, 30 Jun 2020 03:13:04: 7000000 INFO @ Tue, 30 Jun 2020 03:13:05: 3000000 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 03:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.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 03:13:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:12: 8000000 INFO @ Tue, 30 Jun 2020 03:13:14: 4000000 INFO @ Tue, 30 Jun 2020 03:13:19: 1000000 INFO @ Tue, 30 Jun 2020 03:13:20: 9000000 INFO @ Tue, 30 Jun 2020 03:13:22: 5000000 INFO @ Tue, 30 Jun 2020 03:13:28: 2000000 INFO @ Tue, 30 Jun 2020 03:13:29: 10000000 INFO @ Tue, 30 Jun 2020 03:13:30: 6000000 INFO @ Tue, 30 Jun 2020 03:13:37: 3000000 INFO @ Tue, 30 Jun 2020 03:13:37: 11000000 INFO @ Tue, 30 Jun 2020 03:13:39: 7000000 INFO @ Tue, 30 Jun 2020 03:13:45: 12000000 INFO @ Tue, 30 Jun 2020 03:13:45: 4000000 INFO @ Tue, 30 Jun 2020 03:13:47: 8000000 INFO @ Tue, 30 Jun 2020 03:13:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:13:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:13:50: #1 total tags in treatment: 12546944 INFO @ Tue, 30 Jun 2020 03:13:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:50: #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 03:13:50: #1 tags after filtering in treatment: 12546856 INFO @ Tue, 30 Jun 2020 03:13:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:51: #2 number of paired peaks: 213 WARNING @ Tue, 30 Jun 2020 03:13:51: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:51: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:13:51: #2 alternative fragment length(s) may be 3,13,25,43,517 bps INFO @ Tue, 30 Jun 2020 03:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05_model.r WARNING @ Tue, 30 Jun 2020 03:13:51: #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 03:13:51: #2 You may need to consider one of the other alternative d(s): 3,13,25,43,517 WARNING @ Tue, 30 Jun 2020 03:13:51: #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 03:13:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:54: 5000000 INFO @ Tue, 30 Jun 2020 03:13:56: 9000000 INFO @ Tue, 30 Jun 2020 03:14:03: 6000000 INFO @ Tue, 30 Jun 2020 03:14:04: 10000000 INFO @ Tue, 30 Jun 2020 03:14:11: 7000000 INFO @ Tue, 30 Jun 2020 03:14:12: 11000000 INFO @ Tue, 30 Jun 2020 03:14:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:19: 8000000 INFO @ Tue, 30 Jun 2020 03:14:20: 12000000 INFO @ Tue, 30 Jun 2020 03:14:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:14:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:14:25: #1 total tags in treatment: 12546944 INFO @ Tue, 30 Jun 2020 03:14:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:25: #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 03:14:25: #1 tags after filtering in treatment: 12546856 INFO @ Tue, 30 Jun 2020 03:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:25: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:26: #2 number of paired peaks: 213 WARNING @ Tue, 30 Jun 2020 03:14:26: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:26: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:26: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:26: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:26: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:26: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:14:26: #2 alternative fragment length(s) may be 3,13,25,43,517 bps INFO @ Tue, 30 Jun 2020 03:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10_model.r WARNING @ Tue, 30 Jun 2020 03:14:26: #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 03:14:26: #2 You may need to consider one of the other alternative d(s): 3,13,25,43,517 WARNING @ Tue, 30 Jun 2020 03:14:26: #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 03:14:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:28: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:36: 10000000 INFO @ Tue, 30 Jun 2020 03:14:43: 11000000 INFO @ Tue, 30 Jun 2020 03:14:51: 12000000 INFO @ Tue, 30 Jun 2020 03:14:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:14:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:14:55: #1 total tags in treatment: 12546944 INFO @ Tue, 30 Jun 2020 03:14:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:55: #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 03:14:56: #1 tags after filtering in treatment: 12546856 INFO @ Tue, 30 Jun 2020 03:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:57: #2 number of paired peaks: 213 WARNING @ Tue, 30 Jun 2020 03:14:57: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:57: #2 predicted fragment length is 3 bps INFO @ Tue, 30 Jun 2020 03:14:57: #2 alternative fragment length(s) may be 3,13,25,43,517 bps INFO @ Tue, 30 Jun 2020 03:14:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20_model.r WARNING @ Tue, 30 Jun 2020 03:14:57: #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 03:14:57: #2 You may need to consider one of the other alternative d(s): 3,13,25,43,517 WARNING @ Tue, 30 Jun 2020 03:14:57: #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 03:14:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:15:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.10_summits.bed INFO @ Tue, 30 Jun 2020 03:15:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:15:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495785/SRX495785.20_summits.bed INFO @ Tue, 30 Jun 2020 03:15:34: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling