Job ID = 16439467 SRX = SRX13227896 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: 00:13:11 36033252 reads; of these: 36033252 (100.00%) were unpaired; of these: 1109142 (3.08%) aligned 0 times 25224416 (70.00%) aligned exactly 1 time 9699694 (26.92%) aligned >1 times 96.92% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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 16 files... [bam_rmdupse_core] 5675513 / 34924110 = 0.1625 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.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, 02 Aug 2022 15:38:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:38:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:38:25: 1000000 INFO @ Tue, 02 Aug 2022 15:38:31: 2000000 INFO @ Tue, 02 Aug 2022 15:38:37: 3000000 INFO @ Tue, 02 Aug 2022 15:38:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:38:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.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, 02 Aug 2022 15:38:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:38:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:38:50: 5000000 INFO @ Tue, 02 Aug 2022 15:38:55: 1000000 INFO @ Tue, 02 Aug 2022 15:38:58: 6000000 INFO @ Tue, 02 Aug 2022 15:39:02: 2000000 INFO @ Tue, 02 Aug 2022 15:39:05: 7000000 INFO @ Tue, 02 Aug 2022 15:39:09: 3000000 INFO @ Tue, 02 Aug 2022 15:39:12: 8000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 15:39:16: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:39:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.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, 02 Aug 2022 15:39:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:39:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:39:19: 9000000 INFO @ Tue, 02 Aug 2022 15:39:23: 5000000 INFO @ Tue, 02 Aug 2022 15:39:25: 1000000 INFO @ Tue, 02 Aug 2022 15:39:26: 10000000 INFO @ Tue, 02 Aug 2022 15:39:30: 6000000 INFO @ Tue, 02 Aug 2022 15:39:33: 2000000 INFO @ Tue, 02 Aug 2022 15:39:33: 11000000 INFO @ Tue, 02 Aug 2022 15:39:37: 7000000 INFO @ Tue, 02 Aug 2022 15:39:40: 3000000 INFO @ Tue, 02 Aug 2022 15:39:41: 12000000 INFO @ Tue, 02 Aug 2022 15:39:45: 8000000 INFO @ Tue, 02 Aug 2022 15:39:47: 4000000 INFO @ Tue, 02 Aug 2022 15:39:48: 13000000 INFO @ Tue, 02 Aug 2022 15:39:52: 9000000 INFO @ Tue, 02 Aug 2022 15:39:55: 5000000 INFO @ Tue, 02 Aug 2022 15:39:56: 14000000 INFO @ Tue, 02 Aug 2022 15:39:59: 10000000 INFO @ Tue, 02 Aug 2022 15:40:02: 6000000 INFO @ Tue, 02 Aug 2022 15:40:03: 15000000 INFO @ Tue, 02 Aug 2022 15:40:06: 11000000 INFO @ Tue, 02 Aug 2022 15:40:09: 7000000 INFO @ Tue, 02 Aug 2022 15:40:10: 16000000 INFO @ Tue, 02 Aug 2022 15:40:14: 12000000 INFO @ Tue, 02 Aug 2022 15:40:17: 8000000 INFO @ Tue, 02 Aug 2022 15:40:17: 17000000 INFO @ Tue, 02 Aug 2022 15:40:21: 13000000 INFO @ Tue, 02 Aug 2022 15:40:24: 9000000 INFO @ Tue, 02 Aug 2022 15:40:25: 18000000 INFO @ Tue, 02 Aug 2022 15:40:28: 14000000 INFO @ Tue, 02 Aug 2022 15:40:31: 10000000 INFO @ Tue, 02 Aug 2022 15:40:32: 19000000 INFO @ Tue, 02 Aug 2022 15:40:35: 15000000 INFO @ Tue, 02 Aug 2022 15:40:39: 11000000 INFO @ Tue, 02 Aug 2022 15:40:39: 20000000 INFO @ Tue, 02 Aug 2022 15:40:42: 16000000 INFO @ Tue, 02 Aug 2022 15:40:46: 12000000 INFO @ Tue, 02 Aug 2022 15:40:46: 21000000 INFO @ Tue, 02 Aug 2022 15:40:49: 17000000 INFO @ Tue, 02 Aug 2022 15:40:53: 13000000 INFO @ Tue, 02 Aug 2022 15:40:54: 22000000 INFO @ Tue, 02 Aug 2022 15:40:56: 18000000 INFO @ Tue, 02 Aug 2022 15:41:00: 14000000 INFO @ Tue, 02 Aug 2022 15:41:01: 23000000 INFO @ Tue, 02 Aug 2022 15:41:03: 19000000 INFO @ Tue, 02 Aug 2022 15:41:08: 15000000 INFO @ Tue, 02 Aug 2022 15:41:09: 24000000 INFO @ Tue, 02 Aug 2022 15:41:10: 20000000 INFO @ Tue, 02 Aug 2022 15:41:15: 16000000 INFO @ Tue, 02 Aug 2022 15:41:16: 25000000 INFO @ Tue, 02 Aug 2022 15:41:18: 21000000 INFO @ Tue, 02 Aug 2022 15:41:22: 17000000 INFO @ Tue, 02 Aug 2022 15:41:23: 26000000 INFO @ Tue, 02 Aug 2022 15:41:25: 22000000 INFO @ Tue, 02 Aug 2022 15:41:29: 18000000 INFO @ Tue, 02 Aug 2022 15:41:31: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:41:32: 23000000 INFO @ Tue, 02 Aug 2022 15:41:37: 19000000 INFO @ Tue, 02 Aug 2022 15:41:38: 28000000 INFO @ Tue, 02 Aug 2022 15:41:40: 24000000 INFO @ Tue, 02 Aug 2022 15:41:44: 20000000 INFO @ Tue, 02 Aug 2022 15:41:46: 29000000 INFO @ Tue, 02 Aug 2022 15:41:48: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:41:48: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:41:48: #1 total tags in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:41:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:41:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:41:48: 25000000 INFO @ Tue, 02 Aug 2022 15:41:48: #1 tags after filtering in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:41:48: #1 finished! INFO @ Tue, 02 Aug 2022 15:41:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:41:50: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 15:41:50: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 15:41:50: start model_add_line... INFO @ Tue, 02 Aug 2022 15:41:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:41:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:41:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:41:50: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:41:50: #2 alternative fragment length(s) may be 3,31 bps INFO @ Tue, 02 Aug 2022 15:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05_model.r WARNING @ Tue, 02 Aug 2022 15:41:51: #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, 02 Aug 2022 15:41:51: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Tue, 02 Aug 2022 15:41:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:41:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:41:52: 21000000 INFO @ Tue, 02 Aug 2022 15:41:55: 26000000 INFO @ Tue, 02 Aug 2022 15:41:59: 22000000 INFO @ Tue, 02 Aug 2022 15:42:03: 27000000 INFO @ Tue, 02 Aug 2022 15:42:07: 23000000 INFO @ Tue, 02 Aug 2022 15:42:10: 28000000 INFO @ Tue, 02 Aug 2022 15:42:14: 24000000 INFO @ Tue, 02 Aug 2022 15:42:17: 29000000 INFO @ Tue, 02 Aug 2022 15:42:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:42:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:42:19: #1 total tags in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:42:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:42:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:42:20: #1 tags after filtering in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:42:20: #1 finished! INFO @ Tue, 02 Aug 2022 15:42:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:42:22: 25000000 INFO @ Tue, 02 Aug 2022 15:42:22: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 15:42:22: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 15:42:22: start model_add_line... INFO @ Tue, 02 Aug 2022 15:42:22: start X-correlation... INFO @ Tue, 02 Aug 2022 15:42:22: end of X-cor INFO @ Tue, 02 Aug 2022 15:42:22: #2 finished! INFO @ Tue, 02 Aug 2022 15:42:22: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:42:22: #2 alternative fragment length(s) may be 3,31 bps INFO @ Tue, 02 Aug 2022 15:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10_model.r WARNING @ Tue, 02 Aug 2022 15:42:22: #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, 02 Aug 2022 15:42:22: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Tue, 02 Aug 2022 15:42:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:42:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:42:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:42:29: 26000000 INFO @ Tue, 02 Aug 2022 15:42:36: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:42:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:42:42: 28000000 INFO @ Tue, 02 Aug 2022 15:42:50: 29000000 INFO @ Tue, 02 Aug 2022 15:42:52: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:42:52: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:42:52: #1 total tags in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:42:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:42:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:42:53: #1 tags after filtering in treatment: 29248597 INFO @ Tue, 02 Aug 2022 15:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:42:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:42:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:42:55: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 15:42:55: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 15:42:55: start model_add_line... INFO @ Tue, 02 Aug 2022 15:42:55: start X-correlation... INFO @ Tue, 02 Aug 2022 15:42:55: end of X-cor INFO @ Tue, 02 Aug 2022 15:42:55: #2 finished! INFO @ Tue, 02 Aug 2022 15:42:55: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:42:55: #2 alternative fragment length(s) may be 3,31 bps INFO @ Tue, 02 Aug 2022 15:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20_model.r WARNING @ Tue, 02 Aug 2022 15:42:55: #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, 02 Aug 2022 15:42:55: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Tue, 02 Aug 2022 15:42:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:42:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:43:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.05_summits.bed INFO @ Tue, 02 Aug 2022 15:43:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:43:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.10_summits.bed INFO @ Tue, 02 Aug 2022 15:43:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:43:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227896/SRX13227896.20_summits.bed INFO @ Tue, 02 Aug 2022 15:44:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling