Job ID = 5721088 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,339,406 reads read : 88,678,812 reads written : 44,339,406 reads 0-length : 44,339,406 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:17:00 44339406 reads; of these: 44339406 (100.00%) were unpaired; of these: 2085632 (4.70%) aligned 0 times 33033454 (74.50%) aligned exactly 1 time 9220320 (20.79%) aligned >1 times 95.30% overall alignment rate Time searching: 00:17:00 Overall time: 00:17:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 19507895 / 42253774 = 0.4617 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 @ Thu, 16 Apr 2020 05:08:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.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 @ Thu, 16 Apr 2020 05:08:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:08:57: 1000000 INFO @ Thu, 16 Apr 2020 05:09:03: 2000000 INFO @ Thu, 16 Apr 2020 05:09:09: 3000000 INFO @ Thu, 16 Apr 2020 05:09:14: 4000000 INFO @ Thu, 16 Apr 2020 05:09:20: 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 @ Thu, 16 Apr 2020 05:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.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 @ Thu, 16 Apr 2020 05:09:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:26: 6000000 INFO @ Thu, 16 Apr 2020 05:09:28: 1000000 INFO @ Thu, 16 Apr 2020 05:09:31: 7000000 INFO @ Thu, 16 Apr 2020 05:09:34: 2000000 INFO @ Thu, 16 Apr 2020 05:09:38: 8000000 INFO @ Thu, 16 Apr 2020 05:09:40: 3000000 INFO @ Thu, 16 Apr 2020 05:09:44: 9000000 INFO @ Thu, 16 Apr 2020 05:09:46: 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 @ Thu, 16 Apr 2020 05:09:50: 10000000 INFO @ Thu, 16 Apr 2020 05:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.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 @ Thu, 16 Apr 2020 05:09:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:52: 5000000 INFO @ Thu, 16 Apr 2020 05:09:56: 11000000 INFO @ Thu, 16 Apr 2020 05:09:58: 6000000 INFO @ Thu, 16 Apr 2020 05:09:59: 1000000 INFO @ Thu, 16 Apr 2020 05:10:02: 12000000 INFO @ Thu, 16 Apr 2020 05:10:05: 7000000 INFO @ Thu, 16 Apr 2020 05:10:06: 2000000 INFO @ Thu, 16 Apr 2020 05:10:09: 13000000 INFO @ Thu, 16 Apr 2020 05:10:11: 8000000 INFO @ Thu, 16 Apr 2020 05:10:13: 3000000 INFO @ Thu, 16 Apr 2020 05:10:15: 14000000 INFO @ Thu, 16 Apr 2020 05:10:17: 9000000 INFO @ Thu, 16 Apr 2020 05:10:20: 4000000 INFO @ Thu, 16 Apr 2020 05:10:21: 15000000 INFO @ Thu, 16 Apr 2020 05:10:24: 10000000 INFO @ Thu, 16 Apr 2020 05:10:26: 5000000 INFO @ Thu, 16 Apr 2020 05:10:28: 16000000 INFO @ Thu, 16 Apr 2020 05:10:30: 11000000 INFO @ Thu, 16 Apr 2020 05:10:33: 6000000 INFO @ Thu, 16 Apr 2020 05:10:34: 17000000 INFO @ Thu, 16 Apr 2020 05:10:36: 12000000 INFO @ Thu, 16 Apr 2020 05:10:40: 18000000 INFO @ Thu, 16 Apr 2020 05:10:40: 7000000 INFO @ Thu, 16 Apr 2020 05:10:42: 13000000 INFO @ Thu, 16 Apr 2020 05:10:46: 19000000 INFO @ Thu, 16 Apr 2020 05:10:47: 8000000 INFO @ Thu, 16 Apr 2020 05:10:48: 14000000 INFO @ Thu, 16 Apr 2020 05:10:53: 20000000 INFO @ Thu, 16 Apr 2020 05:10:55: 15000000 INFO @ Thu, 16 Apr 2020 05:10:55: 9000000 INFO @ Thu, 16 Apr 2020 05:10:59: 21000000 INFO @ Thu, 16 Apr 2020 05:11:01: 16000000 INFO @ Thu, 16 Apr 2020 05:11:02: 10000000 INFO @ Thu, 16 Apr 2020 05:11:05: 22000000 INFO @ Thu, 16 Apr 2020 05:11:07: 17000000 INFO @ Thu, 16 Apr 2020 05:11:08: 11000000 INFO @ Thu, 16 Apr 2020 05:11:09: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:11:09: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:11:09: #1 total tags in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:11:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:11:10: #1 tags after filtering in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:11:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:11:10: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:12: #2 number of paired peaks: 2277 INFO @ Thu, 16 Apr 2020 05:11:12: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:12: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:12: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:12: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:12: #2 predicted fragment length is 129 bps INFO @ Thu, 16 Apr 2020 05:11:12: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 16 Apr 2020 05:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05_model.r WARNING @ Thu, 16 Apr 2020 05:11:12: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:11:12: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Thu, 16 Apr 2020 05:11:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:11:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:13: 18000000 INFO @ Thu, 16 Apr 2020 05:11:15: 12000000 INFO @ Thu, 16 Apr 2020 05:11:20: 19000000 INFO @ Thu, 16 Apr 2020 05:11:22: 13000000 INFO @ Thu, 16 Apr 2020 05:11:26: 20000000 INFO @ Thu, 16 Apr 2020 05:11:29: 14000000 INFO @ Thu, 16 Apr 2020 05:11:32: 21000000 INFO @ Thu, 16 Apr 2020 05:11:36: 15000000 INFO @ Thu, 16 Apr 2020 05:11:38: 22000000 INFO @ Thu, 16 Apr 2020 05:11:42: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:11:42: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:11:42: #1 total tags in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:11:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:11:43: #1 tags after filtering in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:11:43: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:43: 16000000 INFO @ Thu, 16 Apr 2020 05:11:44: #2 number of paired peaks: 2277 INFO @ Thu, 16 Apr 2020 05:11:44: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:45: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:45: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:45: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:45: #2 predicted fragment length is 129 bps INFO @ Thu, 16 Apr 2020 05:11:45: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 16 Apr 2020 05:11:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10_model.r WARNING @ Thu, 16 Apr 2020 05:11:45: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:11:45: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Thu, 16 Apr 2020 05:11:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:11:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:50: 17000000 INFO @ Thu, 16 Apr 2020 05:11:57: 18000000 INFO @ Thu, 16 Apr 2020 05:11:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:04: 19000000 INFO @ Thu, 16 Apr 2020 05:12:10: 20000000 INFO @ Thu, 16 Apr 2020 05:12:17: 21000000 INFO @ Thu, 16 Apr 2020 05:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.05_summits.bed INFO @ Thu, 16 Apr 2020 05:12:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (20190 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:12:23: 22000000 INFO @ Thu, 16 Apr 2020 05:12:28: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:12:28: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:12:28: #1 total tags in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:12:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:12:28: #1 tags after filtering in treatment: 22745879 INFO @ Thu, 16 Apr 2020 05:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:12:28: #1 finished! INFO @ Thu, 16 Apr 2020 05:12:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:12:30: #2 number of paired peaks: 2277 INFO @ Thu, 16 Apr 2020 05:12:30: start model_add_line... INFO @ Thu, 16 Apr 2020 05:12:30: start X-correlation... INFO @ Thu, 16 Apr 2020 05:12:30: end of X-cor INFO @ Thu, 16 Apr 2020 05:12:30: #2 finished! INFO @ Thu, 16 Apr 2020 05:12:30: #2 predicted fragment length is 129 bps INFO @ Thu, 16 Apr 2020 05:12:30: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 16 Apr 2020 05:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20_model.r WARNING @ Thu, 16 Apr 2020 05:12:30: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:12:30: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Thu, 16 Apr 2020 05:12:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:12:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:12:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.10_summits.bed INFO @ Thu, 16 Apr 2020 05:12:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (15913 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:13:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685743/SRX6685743.20_summits.bed INFO @ Thu, 16 Apr 2020 05:13:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11322 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。