Job ID = 6529733 SRX = SRX4580640 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: 00:07:36 32140314 reads; of these: 32140314 (100.00%) were unpaired; of these: 2764185 (8.60%) aligned 0 times 24048170 (74.82%) aligned exactly 1 time 5327959 (16.58%) aligned >1 times 91.40% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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 12 files... [bam_rmdupse_core] 3158028 / 29376129 = 0.1075 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 02:51:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.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 02:51:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:20: 1000000 INFO @ Tue, 30 Jun 2020 02:51:25: 2000000 INFO @ Tue, 30 Jun 2020 02:51:31: 3000000 INFO @ Tue, 30 Jun 2020 02:51:36: 4000000 INFO @ Tue, 30 Jun 2020 02:51:42: 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 02:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.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 02:51:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:48: 6000000 INFO @ Tue, 30 Jun 2020 02:51:50: 1000000 INFO @ Tue, 30 Jun 2020 02:51:54: 7000000 INFO @ Tue, 30 Jun 2020 02:51:56: 2000000 INFO @ Tue, 30 Jun 2020 02:52:00: 8000000 INFO @ Tue, 30 Jun 2020 02:52:02: 3000000 INFO @ Tue, 30 Jun 2020 02:52:06: 9000000 INFO @ Tue, 30 Jun 2020 02:52:08: 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 02:52:12: 10000000 INFO @ Tue, 30 Jun 2020 02:52:14: 5000000 INFO @ Tue, 30 Jun 2020 02:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.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 02:52:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:18: 11000000 INFO @ Tue, 30 Jun 2020 02:52:19: 6000000 INFO @ Tue, 30 Jun 2020 02:52:20: 1000000 INFO @ Tue, 30 Jun 2020 02:52:25: 12000000 INFO @ Tue, 30 Jun 2020 02:52:25: 7000000 INFO @ Tue, 30 Jun 2020 02:52:26: 2000000 INFO @ Tue, 30 Jun 2020 02:52:31: 13000000 INFO @ Tue, 30 Jun 2020 02:52:31: 8000000 INFO @ Tue, 30 Jun 2020 02:52:32: 3000000 INFO @ Tue, 30 Jun 2020 02:52:37: 14000000 INFO @ Tue, 30 Jun 2020 02:52:37: 9000000 INFO @ Tue, 30 Jun 2020 02:52:38: 4000000 INFO @ Tue, 30 Jun 2020 02:52:43: 15000000 INFO @ Tue, 30 Jun 2020 02:52:43: 10000000 INFO @ Tue, 30 Jun 2020 02:52:44: 5000000 INFO @ Tue, 30 Jun 2020 02:52:49: 16000000 INFO @ Tue, 30 Jun 2020 02:52:49: 11000000 INFO @ Tue, 30 Jun 2020 02:52:50: 6000000 INFO @ Tue, 30 Jun 2020 02:52:55: 17000000 INFO @ Tue, 30 Jun 2020 02:52:55: 12000000 INFO @ Tue, 30 Jun 2020 02:52:56: 7000000 INFO @ Tue, 30 Jun 2020 02:53:01: 13000000 INFO @ Tue, 30 Jun 2020 02:53:01: 18000000 INFO @ Tue, 30 Jun 2020 02:53:02: 8000000 INFO @ Tue, 30 Jun 2020 02:53:07: 14000000 INFO @ Tue, 30 Jun 2020 02:53:08: 19000000 INFO @ Tue, 30 Jun 2020 02:53:08: 9000000 INFO @ Tue, 30 Jun 2020 02:53:13: 15000000 INFO @ Tue, 30 Jun 2020 02:53:14: 20000000 INFO @ Tue, 30 Jun 2020 02:53:14: 10000000 INFO @ Tue, 30 Jun 2020 02:53:19: 16000000 INFO @ Tue, 30 Jun 2020 02:53:20: 11000000 INFO @ Tue, 30 Jun 2020 02:53:20: 21000000 INFO @ Tue, 30 Jun 2020 02:53:25: 17000000 INFO @ Tue, 30 Jun 2020 02:53:26: 12000000 INFO @ Tue, 30 Jun 2020 02:53:26: 22000000 INFO @ Tue, 30 Jun 2020 02:53:31: 18000000 INFO @ Tue, 30 Jun 2020 02:53:32: 13000000 INFO @ Tue, 30 Jun 2020 02:53:33: 23000000 INFO @ Tue, 30 Jun 2020 02:53:37: 19000000 INFO @ Tue, 30 Jun 2020 02:53:38: 14000000 INFO @ Tue, 30 Jun 2020 02:53:39: 24000000 INFO @ Tue, 30 Jun 2020 02:53:43: 20000000 INFO @ Tue, 30 Jun 2020 02:53:44: 15000000 INFO @ Tue, 30 Jun 2020 02:53:45: 25000000 INFO @ Tue, 30 Jun 2020 02:53:50: 16000000 INFO @ Tue, 30 Jun 2020 02:53:50: 21000000 INFO @ Tue, 30 Jun 2020 02:53:51: 26000000 INFO @ Tue, 30 Jun 2020 02:53:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:53: #1 total tags in treatment: 26218101 INFO @ Tue, 30 Jun 2020 02:53:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:53: #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 02:53:53: #1 tags after filtering in treatment: 26218017 INFO @ Tue, 30 Jun 2020 02:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:55: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:53:55: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:55: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:53:55: #2 alternative fragment length(s) may be 1,50,521,551 bps INFO @ Tue, 30 Jun 2020 02:53:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05_model.r WARNING @ Tue, 30 Jun 2020 02:53:55: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:55: #2 You may need to consider one of the other alternative d(s): 1,50,521,551 WARNING @ Tue, 30 Jun 2020 02:53:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:53:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:56: 17000000 INFO @ Tue, 30 Jun 2020 02:53:56: 22000000 INFO @ Tue, 30 Jun 2020 02:54:02: 18000000 INFO @ Tue, 30 Jun 2020 02:54:02: 23000000 INFO @ Tue, 30 Jun 2020 02:54:07: 19000000 INFO @ Tue, 30 Jun 2020 02:54:08: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:54:13: 20000000 INFO @ Tue, 30 Jun 2020 02:54:14: 25000000 INFO @ Tue, 30 Jun 2020 02:54:20: 21000000 INFO @ Tue, 30 Jun 2020 02:54:20: 26000000 INFO @ Tue, 30 Jun 2020 02:54:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:21: #1 total tags in treatment: 26218101 INFO @ Tue, 30 Jun 2020 02:54:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:21: #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 02:54:22: #1 tags after filtering in treatment: 26218017 INFO @ Tue, 30 Jun 2020 02:54:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:24: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:54:24: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:24: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:54:24: #2 alternative fragment length(s) may be 1,50,521,551 bps INFO @ Tue, 30 Jun 2020 02:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10_model.r WARNING @ Tue, 30 Jun 2020 02:54:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:24: #2 You may need to consider one of the other alternative d(s): 1,50,521,551 WARNING @ Tue, 30 Jun 2020 02:54:24: #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 02:54:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:25: 22000000 INFO @ Tue, 30 Jun 2020 02:54:31: 23000000 INFO @ Tue, 30 Jun 2020 02:54:36: 24000000 INFO @ Tue, 30 Jun 2020 02:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:42: 25000000 INFO @ Tue, 30 Jun 2020 02:54:48: 26000000 INFO @ Tue, 30 Jun 2020 02:54:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:49: #1 total tags in treatment: 26218101 INFO @ Tue, 30 Jun 2020 02:54:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:49: #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 02:54:50: #1 tags after filtering in treatment: 26218017 INFO @ Tue, 30 Jun 2020 02:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:51: #2 number of paired peaks: 196 WARNING @ Tue, 30 Jun 2020 02:54:51: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:51: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:54:51: #2 alternative fragment length(s) may be 1,50,521,551 bps INFO @ Tue, 30 Jun 2020 02:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20_model.r WARNING @ Tue, 30 Jun 2020 02:54:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:54:51: #2 You may need to consider one of the other alternative d(s): 1,50,521,551 WARNING @ Tue, 30 Jun 2020 02:54:51: #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 02:54:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.05_summits.bed INFO @ Tue, 30 Jun 2020 02:54:59: Done! pass1 - making usageList (483 chroms): 1 millis pass2 - checking and writing primary data (2098 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:55:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:27: Done! pass1 - making usageList (358 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580640/SRX4580640.20_summits.bed INFO @ Tue, 30 Jun 2020 02:55:55: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 7 millis CompletedMACS2peakCalling