Job ID = 6529687 SRX = SRX3981664 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: 00:11:33 37423185 reads; of these: 37423185 (100.00%) were unpaired; of these: 1473880 (3.94%) aligned 0 times 26676690 (71.28%) aligned exactly 1 time 9272615 (24.78%) aligned >1 times 96.06% overall alignment rate Time searching: 00:11:33 Overall time: 00:11:33 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] 4571157 / 35949305 = 0.1272 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 02:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.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 02:58:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:26: 1000000 INFO @ Tue, 30 Jun 2020 02:58:32: 2000000 INFO @ Tue, 30 Jun 2020 02:58:38: 3000000 INFO @ Tue, 30 Jun 2020 02:58:44: 4000000 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 02:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.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 02:58:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:50: 5000000 INFO @ Tue, 30 Jun 2020 02:58:57: 1000000 INFO @ Tue, 30 Jun 2020 02:58:58: 6000000 INFO @ Tue, 30 Jun 2020 02:59:03: 2000000 INFO @ Tue, 30 Jun 2020 02:59:05: 7000000 INFO @ Tue, 30 Jun 2020 02:59:10: 3000000 INFO @ Tue, 30 Jun 2020 02:59:12: 8000000 INFO @ Tue, 30 Jun 2020 02:59:17: 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 02:59:18: 9000000 INFO @ Tue, 30 Jun 2020 02:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.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 02:59:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:24: 5000000 INFO @ Tue, 30 Jun 2020 02:59:26: 10000000 INFO @ Tue, 30 Jun 2020 02:59:27: 1000000 INFO @ Tue, 30 Jun 2020 02:59:32: 6000000 INFO @ Tue, 30 Jun 2020 02:59:33: 11000000 INFO @ Tue, 30 Jun 2020 02:59:34: 2000000 INFO @ Tue, 30 Jun 2020 02:59:39: 7000000 INFO @ Tue, 30 Jun 2020 02:59:40: 3000000 INFO @ Tue, 30 Jun 2020 02:59:40: 12000000 INFO @ Tue, 30 Jun 2020 02:59:46: 8000000 INFO @ Tue, 30 Jun 2020 02:59:47: 4000000 INFO @ Tue, 30 Jun 2020 02:59:48: 13000000 INFO @ Tue, 30 Jun 2020 02:59:54: 9000000 INFO @ Tue, 30 Jun 2020 02:59:54: 5000000 INFO @ Tue, 30 Jun 2020 02:59:55: 14000000 INFO @ Tue, 30 Jun 2020 03:00:01: 6000000 INFO @ Tue, 30 Jun 2020 03:00:02: 10000000 INFO @ Tue, 30 Jun 2020 03:00:02: 15000000 INFO @ Tue, 30 Jun 2020 03:00:08: 7000000 INFO @ Tue, 30 Jun 2020 03:00:09: 16000000 INFO @ Tue, 30 Jun 2020 03:00:10: 11000000 INFO @ Tue, 30 Jun 2020 03:00:15: 8000000 INFO @ Tue, 30 Jun 2020 03:00:16: 17000000 INFO @ Tue, 30 Jun 2020 03:00:18: 12000000 INFO @ Tue, 30 Jun 2020 03:00:22: 9000000 INFO @ Tue, 30 Jun 2020 03:00:23: 18000000 INFO @ Tue, 30 Jun 2020 03:00:26: 13000000 INFO @ Tue, 30 Jun 2020 03:00:29: 10000000 INFO @ Tue, 30 Jun 2020 03:00:31: 19000000 INFO @ Tue, 30 Jun 2020 03:00:33: 14000000 INFO @ Tue, 30 Jun 2020 03:00:37: 11000000 INFO @ Tue, 30 Jun 2020 03:00:38: 20000000 INFO @ Tue, 30 Jun 2020 03:00:41: 15000000 INFO @ Tue, 30 Jun 2020 03:00:44: 12000000 INFO @ Tue, 30 Jun 2020 03:00:45: 21000000 INFO @ Tue, 30 Jun 2020 03:00:49: 16000000 INFO @ Tue, 30 Jun 2020 03:00:51: 13000000 INFO @ Tue, 30 Jun 2020 03:00:52: 22000000 INFO @ Tue, 30 Jun 2020 03:00:56: 17000000 INFO @ Tue, 30 Jun 2020 03:00:58: 14000000 INFO @ Tue, 30 Jun 2020 03:00:59: 23000000 INFO @ Tue, 30 Jun 2020 03:01:04: 18000000 INFO @ Tue, 30 Jun 2020 03:01:04: 15000000 INFO @ Tue, 30 Jun 2020 03:01:06: 24000000 INFO @ Tue, 30 Jun 2020 03:01:11: 16000000 INFO @ Tue, 30 Jun 2020 03:01:11: 19000000 INFO @ Tue, 30 Jun 2020 03:01:13: 25000000 INFO @ Tue, 30 Jun 2020 03:01:18: 17000000 INFO @ Tue, 30 Jun 2020 03:01:19: 20000000 INFO @ Tue, 30 Jun 2020 03:01:20: 26000000 INFO @ Tue, 30 Jun 2020 03:01:25: 18000000 INFO @ Tue, 30 Jun 2020 03:01:26: 21000000 INFO @ Tue, 30 Jun 2020 03:01:27: 27000000 INFO @ Tue, 30 Jun 2020 03:01:32: 19000000 INFO @ Tue, 30 Jun 2020 03:01:34: 28000000 INFO @ Tue, 30 Jun 2020 03:01:34: 22000000 INFO @ Tue, 30 Jun 2020 03:01:39: 20000000 INFO @ Tue, 30 Jun 2020 03:01:41: 29000000 INFO @ Tue, 30 Jun 2020 03:01:42: 23000000 INFO @ Tue, 30 Jun 2020 03:01:46: 21000000 INFO @ Tue, 30 Jun 2020 03:01:48: 30000000 INFO @ Tue, 30 Jun 2020 03:01:49: 24000000 INFO @ Tue, 30 Jun 2020 03:01:53: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:01:55: 31000000 INFO @ Tue, 30 Jun 2020 03:01:57: 25000000 INFO @ Tue, 30 Jun 2020 03:01:58: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:01:58: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:01:58: #1 total tags in treatment: 31378148 INFO @ Tue, 30 Jun 2020 03:01:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:01:58: #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 03:01:59: #1 tags after filtering in treatment: 31378101 INFO @ Tue, 30 Jun 2020 03:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:01:59: #1 finished! INFO @ Tue, 30 Jun 2020 03:01:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:01:59: 23000000 INFO @ Tue, 30 Jun 2020 03:02:01: #2 number of paired peaks: 180 WARNING @ Tue, 30 Jun 2020 03:02:01: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:01: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:02:01: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05_model.r WARNING @ Tue, 30 Jun 2020 03:02:01: #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 03:02:01: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:02:01: #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 03:02:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:04: 26000000 INFO @ Tue, 30 Jun 2020 03:02:06: 24000000 INFO @ Tue, 30 Jun 2020 03:02:12: 27000000 INFO @ Tue, 30 Jun 2020 03:02:13: 25000000 INFO @ Tue, 30 Jun 2020 03:02:19: 28000000 INFO @ Tue, 30 Jun 2020 03:02:20: 26000000 INFO @ Tue, 30 Jun 2020 03:02:27: 29000000 INFO @ Tue, 30 Jun 2020 03:02:27: 27000000 INFO @ Tue, 30 Jun 2020 03:02:34: 28000000 INFO @ Tue, 30 Jun 2020 03:02:34: 30000000 INFO @ Tue, 30 Jun 2020 03:02:41: 29000000 INFO @ Tue, 30 Jun 2020 03:02:42: 31000000 INFO @ Tue, 30 Jun 2020 03:02:45: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:02:45: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:02:45: #1 total tags in treatment: 31378148 INFO @ Tue, 30 Jun 2020 03:02:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:45: #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 03:02:46: #1 tags after filtering in treatment: 31378101 INFO @ Tue, 30 Jun 2020 03:02:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:46: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:02:48: 30000000 INFO @ Tue, 30 Jun 2020 03:02:49: #2 number of paired peaks: 180 WARNING @ Tue, 30 Jun 2020 03:02:49: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 30 Jun 2020 03:02:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:02:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:02:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:02:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:02:49: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:02:49: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10_model.r WARNING @ Tue, 30 Jun 2020 03:02:49: #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 03:02:49: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:02:49: #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 03:02:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:02:55: 31000000 INFO @ Tue, 30 Jun 2020 03:02:58: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:02:58: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:02:58: #1 total tags in treatment: 31378148 INFO @ Tue, 30 Jun 2020 03:02:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:02:58: #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 03:02:58: #1 tags after filtering in treatment: 31378101 INFO @ Tue, 30 Jun 2020 03:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:02:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:02:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:03:01: #2 number of paired peaks: 180 WARNING @ Tue, 30 Jun 2020 03:03:01: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 30 Jun 2020 03:03:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:03:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:03:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:03:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:03:01: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:03:01: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20_model.r WARNING @ Tue, 30 Jun 2020 03:03:01: #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 03:03:01: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:03:01: #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 03:03:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:03:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.05_summits.bed INFO @ Tue, 30 Jun 2020 03:03:36: Done! pass1 - making usageList (660 chroms): 2 millis pass2 - checking and writing primary data (3330 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:03:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:04:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.10_summits.bed INFO @ Tue, 30 Jun 2020 03:04:21: Done! pass1 - making usageList (495 chroms): 2 millis pass2 - checking and writing primary data (1685 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981664/SRX3981664.20_summits.bed INFO @ Tue, 30 Jun 2020 03:04:33: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 9 millis CompletedMACS2peakCalling