Job ID = 6529706 SRX = SRX3981704 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: 00:08:40 28691459 reads; of these: 28691459 (100.00%) were unpaired; of these: 1597168 (5.57%) aligned 0 times 19465397 (67.84%) aligned exactly 1 time 7628894 (26.59%) aligned >1 times 94.43% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 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] 4351076 / 27094291 = 0.1606 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 02:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.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 02:50:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:34: 1000000 INFO @ Tue, 30 Jun 2020 02:50:39: 2000000 INFO @ Tue, 30 Jun 2020 02:50:45: 3000000 INFO @ Tue, 30 Jun 2020 02:50:50: 4000000 INFO @ Tue, 30 Jun 2020 02:50:55: 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 02:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.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 02:50:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:01: 6000000 INFO @ Tue, 30 Jun 2020 02:51:04: 1000000 INFO @ Tue, 30 Jun 2020 02:51:06: 7000000 INFO @ Tue, 30 Jun 2020 02:51:10: 2000000 INFO @ Tue, 30 Jun 2020 02:51:12: 8000000 INFO @ Tue, 30 Jun 2020 02:51:15: 3000000 INFO @ Tue, 30 Jun 2020 02:51:18: 9000000 INFO @ Tue, 30 Jun 2020 02:51:21: 4000000 INFO @ Tue, 30 Jun 2020 02:51:24: 10000000 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 02:51:27: 5000000 INFO @ Tue, 30 Jun 2020 02:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.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 02:51:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:30: 11000000 INFO @ Tue, 30 Jun 2020 02:51:32: 6000000 INFO @ Tue, 30 Jun 2020 02:51:35: 1000000 INFO @ Tue, 30 Jun 2020 02:51:36: 12000000 INFO @ Tue, 30 Jun 2020 02:51:38: 7000000 INFO @ Tue, 30 Jun 2020 02:51:41: 2000000 INFO @ Tue, 30 Jun 2020 02:51:42: 13000000 INFO @ Tue, 30 Jun 2020 02:51:44: 8000000 INFO @ Tue, 30 Jun 2020 02:51:46: 3000000 INFO @ Tue, 30 Jun 2020 02:51:47: 14000000 INFO @ Tue, 30 Jun 2020 02:51:50: 9000000 INFO @ Tue, 30 Jun 2020 02:51:52: 4000000 INFO @ Tue, 30 Jun 2020 02:51:53: 15000000 INFO @ Tue, 30 Jun 2020 02:51:56: 10000000 INFO @ Tue, 30 Jun 2020 02:51:58: 5000000 INFO @ Tue, 30 Jun 2020 02:51:59: 16000000 INFO @ Tue, 30 Jun 2020 02:52:02: 11000000 INFO @ Tue, 30 Jun 2020 02:52:04: 6000000 INFO @ Tue, 30 Jun 2020 02:52:05: 17000000 INFO @ Tue, 30 Jun 2020 02:52:08: 12000000 INFO @ Tue, 30 Jun 2020 02:52:10: 7000000 INFO @ Tue, 30 Jun 2020 02:52:11: 18000000 INFO @ Tue, 30 Jun 2020 02:52:13: 13000000 INFO @ Tue, 30 Jun 2020 02:52:16: 8000000 INFO @ Tue, 30 Jun 2020 02:52:17: 19000000 INFO @ Tue, 30 Jun 2020 02:52:19: 14000000 INFO @ Tue, 30 Jun 2020 02:52:21: 9000000 INFO @ Tue, 30 Jun 2020 02:52:23: 20000000 INFO @ Tue, 30 Jun 2020 02:52:25: 15000000 INFO @ Tue, 30 Jun 2020 02:52:27: 10000000 INFO @ Tue, 30 Jun 2020 02:52:29: 21000000 INFO @ Tue, 30 Jun 2020 02:52:31: 16000000 INFO @ Tue, 30 Jun 2020 02:52:33: 11000000 INFO @ Tue, 30 Jun 2020 02:52:35: 22000000 INFO @ Tue, 30 Jun 2020 02:52:37: 17000000 INFO @ Tue, 30 Jun 2020 02:52:39: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:52:39: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:52:39: #1 total tags in treatment: 22743215 INFO @ Tue, 30 Jun 2020 02:52:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:39: #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 02:52:39: 12000000 INFO @ Tue, 30 Jun 2020 02:52:40: #1 tags after filtering in treatment: 22743170 INFO @ Tue, 30 Jun 2020 02:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:41: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 02:52:41: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:42: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:52:42: #2 alternative fragment length(s) may be 1,53,559,589 bps INFO @ Tue, 30 Jun 2020 02:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:42: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:42: #2 You may need to consider one of the other alternative d(s): 1,53,559,589 WARNING @ Tue, 30 Jun 2020 02:52:42: #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 02:52:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:43: 18000000 INFO @ Tue, 30 Jun 2020 02:52:45: 13000000 INFO @ Tue, 30 Jun 2020 02:52:49: 19000000 INFO @ Tue, 30 Jun 2020 02:52:51: 14000000 INFO @ Tue, 30 Jun 2020 02:52:56: 20000000 INFO @ Tue, 30 Jun 2020 02:52:57: 15000000 INFO @ Tue, 30 Jun 2020 02:53:01: 21000000 INFO @ Tue, 30 Jun 2020 02:53:03: 16000000 INFO @ Tue, 30 Jun 2020 02:53:07: 22000000 INFO @ Tue, 30 Jun 2020 02:53:09: 17000000 INFO @ Tue, 30 Jun 2020 02:53:12: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:12: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:12: #1 total tags in treatment: 22743215 INFO @ Tue, 30 Jun 2020 02:53:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:12: #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 02:53:13: #1 tags after filtering in treatment: 22743170 INFO @ Tue, 30 Jun 2020 02:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:14: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 02:53:14: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:14: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:14: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:14: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:14: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:53:14: #2 alternative fragment length(s) may be 1,53,559,589 bps INFO @ Tue, 30 Jun 2020 02:53:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10_model.r WARNING @ Tue, 30 Jun 2020 02:53:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:14: #2 You may need to consider one of the other alternative d(s): 1,53,559,589 WARNING @ Tue, 30 Jun 2020 02:53:14: #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 02:53:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:15: 18000000 INFO @ Tue, 30 Jun 2020 02:53:21: 19000000 INFO @ Tue, 30 Jun 2020 02:53:27: 20000000 INFO @ Tue, 30 Jun 2020 02:53:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:53:33: 21000000 INFO @ Tue, 30 Jun 2020 02:53:39: 22000000 INFO @ Tue, 30 Jun 2020 02:53:44: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:53:44: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:53:44: #1 total tags in treatment: 22743215 INFO @ Tue, 30 Jun 2020 02:53:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:44: #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 02:53:44: #1 tags after filtering in treatment: 22743170 INFO @ Tue, 30 Jun 2020 02:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:46: #2 number of paired peaks: 406 WARNING @ Tue, 30 Jun 2020 02:53:46: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:46: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:53:46: #2 alternative fragment length(s) may be 1,53,559,589 bps INFO @ Tue, 30 Jun 2020 02:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:46: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:46: #2 You may need to consider one of the other alternative d(s): 1,53,559,589 WARNING @ Tue, 30 Jun 2020 02:53:46: #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 02:53:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:52: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (2856 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.10_summits.bed INFO @ Tue, 30 Jun 2020 02:54:23: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (1458 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:54:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981704/SRX3981704.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:55: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 9 millis CompletedMACS2peakCalling