Job ID = 6529681 SRX = SRX3981657 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: 00:10:32 34931412 reads; of these: 34931412 (100.00%) were unpaired; of these: 1405212 (4.02%) aligned 0 times 25226211 (72.22%) aligned exactly 1 time 8299989 (23.76%) aligned >1 times 95.98% overall alignment rate Time searching: 00:10:32 Overall time: 00:10:32 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] 3909433 / 33526200 = 0.1166 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 02:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.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 02:52:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:25: 1000000 INFO @ Tue, 30 Jun 2020 02:52:33: 2000000 INFO @ Tue, 30 Jun 2020 02:52:40: 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 02:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.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 02:52:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:48: 4000000 INFO @ Tue, 30 Jun 2020 02:52:55: 1000000 INFO @ Tue, 30 Jun 2020 02:52:56: 5000000 INFO @ Tue, 30 Jun 2020 02:53:03: 2000000 INFO @ Tue, 30 Jun 2020 02:53:05: 6000000 INFO @ Tue, 30 Jun 2020 02:53:11: 3000000 INFO @ Tue, 30 Jun 2020 02:53:13: 7000000 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 02:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.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 02:53:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:19: 4000000 INFO @ Tue, 30 Jun 2020 02:53:21: 8000000 INFO @ Tue, 30 Jun 2020 02:53:26: 1000000 INFO @ Tue, 30 Jun 2020 02:53:27: 5000000 INFO @ Tue, 30 Jun 2020 02:53:30: 9000000 INFO @ Tue, 30 Jun 2020 02:53:35: 6000000 INFO @ Tue, 30 Jun 2020 02:53:36: 2000000 INFO @ Tue, 30 Jun 2020 02:53:40: 10000000 INFO @ Tue, 30 Jun 2020 02:53:43: 7000000 INFO @ Tue, 30 Jun 2020 02:53:45: 3000000 INFO @ Tue, 30 Jun 2020 02:53:48: 11000000 INFO @ Tue, 30 Jun 2020 02:53:51: 8000000 INFO @ Tue, 30 Jun 2020 02:53:53: 4000000 INFO @ Tue, 30 Jun 2020 02:53:57: 12000000 INFO @ Tue, 30 Jun 2020 02:53:59: 9000000 INFO @ Tue, 30 Jun 2020 02:54:02: 5000000 INFO @ Tue, 30 Jun 2020 02:54:05: 13000000 INFO @ Tue, 30 Jun 2020 02:54:07: 10000000 INFO @ Tue, 30 Jun 2020 02:54:11: 6000000 INFO @ Tue, 30 Jun 2020 02:54:14: 14000000 INFO @ Tue, 30 Jun 2020 02:54:15: 11000000 INFO @ Tue, 30 Jun 2020 02:54:19: 7000000 INFO @ Tue, 30 Jun 2020 02:54:22: 15000000 INFO @ Tue, 30 Jun 2020 02:54:23: 12000000 INFO @ Tue, 30 Jun 2020 02:54:28: 8000000 INFO @ Tue, 30 Jun 2020 02:54:30: 16000000 INFO @ Tue, 30 Jun 2020 02:54:30: 13000000 INFO @ Tue, 30 Jun 2020 02:54:37: 9000000 INFO @ Tue, 30 Jun 2020 02:54:38: 14000000 INFO @ Tue, 30 Jun 2020 02:54:38: 17000000 INFO @ Tue, 30 Jun 2020 02:54:45: 10000000 INFO @ Tue, 30 Jun 2020 02:54:46: 15000000 INFO @ Tue, 30 Jun 2020 02:54:47: 18000000 INFO @ Tue, 30 Jun 2020 02:54:53: 16000000 INFO @ Tue, 30 Jun 2020 02:54:54: 11000000 INFO @ Tue, 30 Jun 2020 02:54:55: 19000000 INFO @ Tue, 30 Jun 2020 02:55:01: 17000000 INFO @ Tue, 30 Jun 2020 02:55:02: 12000000 INFO @ Tue, 30 Jun 2020 02:55:03: 20000000 INFO @ Tue, 30 Jun 2020 02:55:09: 18000000 INFO @ Tue, 30 Jun 2020 02:55:10: 13000000 INFO @ Tue, 30 Jun 2020 02:55:11: 21000000 INFO @ Tue, 30 Jun 2020 02:55:16: 19000000 INFO @ Tue, 30 Jun 2020 02:55:18: 14000000 INFO @ Tue, 30 Jun 2020 02:55:19: 22000000 INFO @ Tue, 30 Jun 2020 02:55:24: 20000000 INFO @ Tue, 30 Jun 2020 02:55:26: 15000000 INFO @ Tue, 30 Jun 2020 02:55:27: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:55:32: 21000000 INFO @ Tue, 30 Jun 2020 02:55:34: 16000000 INFO @ Tue, 30 Jun 2020 02:55:34: 24000000 INFO @ Tue, 30 Jun 2020 02:55:39: 22000000 INFO @ Tue, 30 Jun 2020 02:55:42: 17000000 INFO @ Tue, 30 Jun 2020 02:55:42: 25000000 INFO @ Tue, 30 Jun 2020 02:55:47: 23000000 INFO @ Tue, 30 Jun 2020 02:55:50: 18000000 INFO @ Tue, 30 Jun 2020 02:55:51: 26000000 INFO @ Tue, 30 Jun 2020 02:55:55: 24000000 INFO @ Tue, 30 Jun 2020 02:55:57: 19000000 INFO @ Tue, 30 Jun 2020 02:55:58: 27000000 INFO @ Tue, 30 Jun 2020 02:56:02: 25000000 INFO @ Tue, 30 Jun 2020 02:56:05: 20000000 INFO @ Tue, 30 Jun 2020 02:56:06: 28000000 INFO @ Tue, 30 Jun 2020 02:56:10: 26000000 INFO @ Tue, 30 Jun 2020 02:56:13: 21000000 INFO @ Tue, 30 Jun 2020 02:56:14: 29000000 INFO @ Tue, 30 Jun 2020 02:56:18: 27000000 INFO @ Tue, 30 Jun 2020 02:56:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:56:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:56:19: #1 total tags in treatment: 29616767 INFO @ Tue, 30 Jun 2020 02:56:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:19: #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 02:56:20: #1 tags after filtering in treatment: 29616717 INFO @ Tue, 30 Jun 2020 02:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:21: 22000000 INFO @ Tue, 30 Jun 2020 02:56:22: #2 number of paired peaks: 193 WARNING @ Tue, 30 Jun 2020 02:56:22: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:22: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:56:22: #2 alternative fragment length(s) may be 1,57 bps INFO @ Tue, 30 Jun 2020 02:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05_model.r WARNING @ Tue, 30 Jun 2020 02:56:22: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:22: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Tue, 30 Jun 2020 02:56:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:56:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:25: 28000000 INFO @ Tue, 30 Jun 2020 02:56:29: 23000000 INFO @ Tue, 30 Jun 2020 02:56:33: 29000000 INFO @ Tue, 30 Jun 2020 02:56:36: 24000000 INFO @ Tue, 30 Jun 2020 02:56:38: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:56:38: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:56:38: #1 total tags in treatment: 29616767 INFO @ Tue, 30 Jun 2020 02:56:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:38: #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 02:56:39: #1 tags after filtering in treatment: 29616717 INFO @ Tue, 30 Jun 2020 02:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:39: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:56:41: #2 number of paired peaks: 193 WARNING @ Tue, 30 Jun 2020 02:56:41: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:41: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:56:41: #2 alternative fragment length(s) may be 1,57 bps INFO @ Tue, 30 Jun 2020 02:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10_model.r WARNING @ Tue, 30 Jun 2020 02:56:41: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:41: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Tue, 30 Jun 2020 02:56:41: #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 02:56:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:44: 25000000 INFO @ Tue, 30 Jun 2020 02:56:51: 26000000 INFO @ Tue, 30 Jun 2020 02:56:58: 27000000 INFO @ Tue, 30 Jun 2020 02:57:05: 28000000 INFO @ Tue, 30 Jun 2020 02:57:12: 29000000 INFO @ Tue, 30 Jun 2020 02:57:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:57:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:57:17: #1 total tags in treatment: 29616767 INFO @ Tue, 30 Jun 2020 02:57:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:17: #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 02:57:17: #1 tags after filtering in treatment: 29616717 INFO @ Tue, 30 Jun 2020 02:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:19: #2 number of paired peaks: 193 WARNING @ Tue, 30 Jun 2020 02:57:19: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:20: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 02:57:20: #2 alternative fragment length(s) may be 1,57 bps INFO @ Tue, 30 Jun 2020 02:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20_model.r WARNING @ Tue, 30 Jun 2020 02:57:20: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:20: #2 You may need to consider one of the other alternative d(s): 1,57 WARNING @ Tue, 30 Jun 2020 02:57:20: #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 02:57:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.05_summits.bed INFO @ Tue, 30 Jun 2020 02:57:42: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (3150 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.10_summits.bed INFO @ Tue, 30 Jun 2020 02:58:03: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1843 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:58:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981657/SRX3981657.20_summits.bed INFO @ Tue, 30 Jun 2020 02:58:41: Done! pass1 - making usageList (270 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 9 millis CompletedMACS2peakCalling