Job ID = 16439177 SRX = SRX15312100 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: 00:18:01 40258128 reads; of these: 40258128 (100.00%) were unpaired; of these: 1060370 (2.63%) aligned 0 times 31798243 (78.99%) aligned exactly 1 time 7399515 (18.38%) aligned >1 times 97.37% overall alignment rate Time searching: 00:18:01 Overall time: 00:18:01 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] 4886747 / 39197758 = 0.1247 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 15:14:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.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 15:14:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:09: 1000000 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 15:15:23: 2000000 INFO @ Tue, 02 Aug 2022 15:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.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 15:15:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:36: 1000000 INFO @ Tue, 02 Aug 2022 15:15:36: 3000000 INFO @ Tue, 02 Aug 2022 15:15:46: 2000000 INFO @ Tue, 02 Aug 2022 15:15:49: 4000000 BedGraph に変換中... 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 15:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.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 15:15:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:57: 3000000 INFO @ Tue, 02 Aug 2022 15:16:03: 5000000 INFO @ Tue, 02 Aug 2022 15:16:07: 4000000 INFO @ Tue, 02 Aug 2022 15:16:08: 1000000 INFO @ Tue, 02 Aug 2022 15:16:16: 6000000 INFO @ Tue, 02 Aug 2022 15:16:18: 5000000 INFO @ Tue, 02 Aug 2022 15:16:21: 2000000 INFO @ Tue, 02 Aug 2022 15:16:29: 6000000 INFO @ Tue, 02 Aug 2022 15:16:29: 7000000 INFO @ Tue, 02 Aug 2022 15:16:33: 3000000 INFO @ Tue, 02 Aug 2022 15:16:39: 7000000 INFO @ Tue, 02 Aug 2022 15:16:43: 8000000 INFO @ Tue, 02 Aug 2022 15:16:45: 4000000 INFO @ Tue, 02 Aug 2022 15:16:50: 8000000 INFO @ Tue, 02 Aug 2022 15:16:56: 9000000 INFO @ Tue, 02 Aug 2022 15:16:58: 5000000 INFO @ Tue, 02 Aug 2022 15:17:00: 9000000 INFO @ Tue, 02 Aug 2022 15:17:10: 10000000 INFO @ Tue, 02 Aug 2022 15:17:10: 10000000 INFO @ Tue, 02 Aug 2022 15:17:10: 6000000 INFO @ Tue, 02 Aug 2022 15:17:20: 11000000 INFO @ Tue, 02 Aug 2022 15:17:22: 7000000 INFO @ Tue, 02 Aug 2022 15:17:23: 11000000 INFO @ Tue, 02 Aug 2022 15:17:30: 12000000 INFO @ Tue, 02 Aug 2022 15:17:34: 8000000 INFO @ Tue, 02 Aug 2022 15:17:36: 12000000 INFO @ Tue, 02 Aug 2022 15:17:41: 13000000 INFO @ Tue, 02 Aug 2022 15:17:46: 9000000 INFO @ Tue, 02 Aug 2022 15:17:50: 13000000 INFO @ Tue, 02 Aug 2022 15:17:51: 14000000 INFO @ Tue, 02 Aug 2022 15:17:58: 10000000 INFO @ Tue, 02 Aug 2022 15:18:00: 15000000 INFO @ Tue, 02 Aug 2022 15:18:03: 14000000 INFO @ Tue, 02 Aug 2022 15:18:11: 11000000 INFO @ Tue, 02 Aug 2022 15:18:11: 16000000 INFO @ Tue, 02 Aug 2022 15:18:16: 15000000 INFO @ Tue, 02 Aug 2022 15:18:21: 17000000 INFO @ Tue, 02 Aug 2022 15:18:23: 12000000 INFO @ Tue, 02 Aug 2022 15:18:30: 16000000 INFO @ Tue, 02 Aug 2022 15:18:31: 18000000 INFO @ Tue, 02 Aug 2022 15:18:35: 13000000 INFO @ Tue, 02 Aug 2022 15:18:42: 19000000 INFO @ Tue, 02 Aug 2022 15:18:43: 17000000 INFO @ Tue, 02 Aug 2022 15:18:47: 14000000 INFO @ Tue, 02 Aug 2022 15:18:52: 20000000 INFO @ Tue, 02 Aug 2022 15:18:56: 18000000 INFO @ Tue, 02 Aug 2022 15:18:59: 15000000 INFO @ Tue, 02 Aug 2022 15:19:03: 21000000 INFO @ Tue, 02 Aug 2022 15:19:09: 19000000 INFO @ Tue, 02 Aug 2022 15:19:11: 16000000 INFO @ Tue, 02 Aug 2022 15:19:13: 22000000 INFO @ Tue, 02 Aug 2022 15:19:22: 20000000 INFO @ Tue, 02 Aug 2022 15:19:23: 23000000 INFO @ Tue, 02 Aug 2022 15:19:23: 17000000 INFO @ Tue, 02 Aug 2022 15:19:33: 24000000 INFO @ Tue, 02 Aug 2022 15:19:35: 21000000 INFO @ Tue, 02 Aug 2022 15:19:35: 18000000 INFO @ Tue, 02 Aug 2022 15:19:43: 25000000 INFO @ Tue, 02 Aug 2022 15:19:47: 19000000 INFO @ Tue, 02 Aug 2022 15:19:48: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:19:53: 26000000 INFO @ Tue, 02 Aug 2022 15:19:59: 20000000 INFO @ Tue, 02 Aug 2022 15:20:01: 23000000 INFO @ Tue, 02 Aug 2022 15:20:03: 27000000 INFO @ Tue, 02 Aug 2022 15:20:11: 21000000 INFO @ Tue, 02 Aug 2022 15:20:14: 28000000 INFO @ Tue, 02 Aug 2022 15:20:14: 24000000 INFO @ Tue, 02 Aug 2022 15:20:23: 22000000 INFO @ Tue, 02 Aug 2022 15:20:24: 29000000 INFO @ Tue, 02 Aug 2022 15:20:26: 25000000 INFO @ Tue, 02 Aug 2022 15:20:34: 30000000 INFO @ Tue, 02 Aug 2022 15:20:36: 23000000 INFO @ Tue, 02 Aug 2022 15:20:39: 26000000 INFO @ Tue, 02 Aug 2022 15:20:45: 31000000 INFO @ Tue, 02 Aug 2022 15:20:48: 24000000 INFO @ Tue, 02 Aug 2022 15:20:51: 27000000 INFO @ Tue, 02 Aug 2022 15:20:57: 32000000 INFO @ Tue, 02 Aug 2022 15:21:01: 25000000 INFO @ Tue, 02 Aug 2022 15:21:04: 28000000 INFO @ Tue, 02 Aug 2022 15:21:07: 33000000 INFO @ Tue, 02 Aug 2022 15:21:13: 26000000 INFO @ Tue, 02 Aug 2022 15:21:18: 29000000 INFO @ Tue, 02 Aug 2022 15:21:18: 34000000 INFO @ Tue, 02 Aug 2022 15:21:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:21:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:21:22: #1 total tags in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:21:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:21:22: #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 15:21:23: #1 tags after filtering in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:21:23: #1 finished! INFO @ Tue, 02 Aug 2022 15:21:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:21:24: 27000000 INFO @ Tue, 02 Aug 2022 15:21:25: #2 number of paired peaks: 103 WARNING @ Tue, 02 Aug 2022 15:21:25: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 02 Aug 2022 15:21:25: start model_add_line... INFO @ Tue, 02 Aug 2022 15:21:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:21:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:21:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:21:26: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 15:21:26: #2 alternative fragment length(s) may be 1,18,66 bps INFO @ Tue, 02 Aug 2022 15:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10_model.r WARNING @ Tue, 02 Aug 2022 15:21:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:21:26: #2 You may need to consider one of the other alternative d(s): 1,18,66 WARNING @ Tue, 02 Aug 2022 15:21:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:21:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:21:31: 30000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:21:37: 28000000 INFO @ Tue, 02 Aug 2022 15:21:44: 31000000 INFO @ Tue, 02 Aug 2022 15:21:49: 29000000 INFO @ Tue, 02 Aug 2022 15:21:56: 32000000 INFO @ Tue, 02 Aug 2022 15:22:00: 30000000 INFO @ Tue, 02 Aug 2022 15:22:08: 33000000 INFO @ Tue, 02 Aug 2022 15:22:11: 31000000 INFO @ Tue, 02 Aug 2022 15:22:21: 34000000 INFO @ Tue, 02 Aug 2022 15:22:22: 32000000 INFO @ Tue, 02 Aug 2022 15:22:25: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:22:25: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:22:25: #1 total tags in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:22:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:22:25: #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 15:22:26: #1 tags after filtering in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:22:26: #1 finished! INFO @ Tue, 02 Aug 2022 15:22:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:22:29: #2 number of paired peaks: 103 WARNING @ Tue, 02 Aug 2022 15:22:29: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 02 Aug 2022 15:22:29: start model_add_line... INFO @ Tue, 02 Aug 2022 15:22:29: start X-correlation... INFO @ Tue, 02 Aug 2022 15:22:29: end of X-cor INFO @ Tue, 02 Aug 2022 15:22:29: #2 finished! INFO @ Tue, 02 Aug 2022 15:22:29: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 15:22:29: #2 alternative fragment length(s) may be 1,18,66 bps INFO @ Tue, 02 Aug 2022 15:22:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05_model.r WARNING @ Tue, 02 Aug 2022 15:22:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:22:29: #2 You may need to consider one of the other alternative d(s): 1,18,66 WARNING @ Tue, 02 Aug 2022 15:22:29: #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 15:22:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:22:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:22:33: 33000000 INFO @ Tue, 02 Aug 2022 15:22:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:22:44: 34000000 INFO @ Tue, 02 Aug 2022 15:22:48: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:22:48: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:22:48: #1 total tags in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:22:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:22:48: #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 15:22:49: #1 tags after filtering in treatment: 34311011 INFO @ Tue, 02 Aug 2022 15:22:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:22:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:22:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:22:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:22:52: #2 number of paired peaks: 103 WARNING @ Tue, 02 Aug 2022 15:22:52: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 02 Aug 2022 15:22:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:22:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:22:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:22:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:22:52: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 15:22:52: #2 alternative fragment length(s) may be 1,18,66 bps INFO @ Tue, 02 Aug 2022 15:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20_model.r WARNING @ Tue, 02 Aug 2022 15:22:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:22:52: #2 You may need to consider one of the other alternative d(s): 1,18,66 WARNING @ Tue, 02 Aug 2022 15:22:52: #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 15:22:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.10_summits.bed INFO @ Tue, 02 Aug 2022 15:23:07: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:23:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:24:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:24:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:24:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.05_summits.bed INFO @ Tue, 02 Aug 2022 15:24:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:24:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:24:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:24:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15312100/SRX15312100.20_summits.bed INFO @ Tue, 02 Aug 2022 15:24:35: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling