Job ID = 5721165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,915,668 reads read : 73,831,336 reads written : 36,915,668 reads 0-length : 36,915,668 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: 00:09:56 36915668 reads; of these: 36915668 (100.00%) were unpaired; of these: 22191654 (60.11%) aligned 0 times 9638069 (26.11%) aligned exactly 1 time 5085945 (13.78%) aligned >1 times 39.89% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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 8 files... [bam_rmdupse_core] 2800069 / 14724014 = 0.1902 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 05:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.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 05:53:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:53:24: 1000000 INFO @ Thu, 16 Apr 2020 05:53:31: 2000000 INFO @ Thu, 16 Apr 2020 05:53:37: 3000000 INFO @ Thu, 16 Apr 2020 05:53:43: 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 @ Thu, 16 Apr 2020 05:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.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 05:53:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:53:50: 5000000 INFO @ Thu, 16 Apr 2020 05:53:54: 1000000 INFO @ Thu, 16 Apr 2020 05:53:57: 6000000 INFO @ Thu, 16 Apr 2020 05:54:01: 2000000 INFO @ Thu, 16 Apr 2020 05:54:04: 7000000 INFO @ Thu, 16 Apr 2020 05:54:08: 3000000 INFO @ Thu, 16 Apr 2020 05:54:11: 8000000 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 05:54:15: 4000000 INFO @ Thu, 16 Apr 2020 05:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.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 05:54:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:54:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:54:18: 9000000 INFO @ Thu, 16 Apr 2020 05:54:23: 5000000 INFO @ Thu, 16 Apr 2020 05:54:25: 1000000 INFO @ Thu, 16 Apr 2020 05:54:25: 10000000 INFO @ Thu, 16 Apr 2020 05:54:30: 6000000 INFO @ Thu, 16 Apr 2020 05:54:32: 2000000 INFO @ Thu, 16 Apr 2020 05:54:32: 11000000 INFO @ Thu, 16 Apr 2020 05:54:37: 7000000 INFO @ Thu, 16 Apr 2020 05:54:39: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:54:39: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:54:39: #1 total tags in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:54:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:54:39: #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 05:54:39: 3000000 INFO @ Thu, 16 Apr 2020 05:54:39: #1 tags after filtering in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:54:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:54:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:54:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:54:40: #2 number of paired peaks: 1064 INFO @ Thu, 16 Apr 2020 05:54:40: start model_add_line... INFO @ Thu, 16 Apr 2020 05:54:40: start X-correlation... INFO @ Thu, 16 Apr 2020 05:54:40: end of X-cor INFO @ Thu, 16 Apr 2020 05:54:40: #2 finished! INFO @ Thu, 16 Apr 2020 05:54:40: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:54:40: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05_model.r WARNING @ Thu, 16 Apr 2020 05:54:40: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:54:40: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:54:40: #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 05:54:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:54:44: 8000000 INFO @ Thu, 16 Apr 2020 05:54:46: 4000000 INFO @ Thu, 16 Apr 2020 05:54:51: 9000000 INFO @ Thu, 16 Apr 2020 05:54:53: 5000000 INFO @ Thu, 16 Apr 2020 05:54:59: 10000000 INFO @ Thu, 16 Apr 2020 05:55:01: 6000000 INFO @ Thu, 16 Apr 2020 05:55:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:55:06: 11000000 INFO @ Thu, 16 Apr 2020 05:55:08: 7000000 INFO @ Thu, 16 Apr 2020 05:55:12: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:55:12: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:55:12: #1 total tags in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:55:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:55:12: #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 05:55:13: #1 tags after filtering in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:55:13: #1 finished! INFO @ Thu, 16 Apr 2020 05:55:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:55:13: #2 number of paired peaks: 1064 INFO @ Thu, 16 Apr 2020 05:55:13: start model_add_line... INFO @ Thu, 16 Apr 2020 05:55:14: start X-correlation... INFO @ Thu, 16 Apr 2020 05:55:14: end of X-cor INFO @ Thu, 16 Apr 2020 05:55:14: #2 finished! INFO @ Thu, 16 Apr 2020 05:55:14: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:55:14: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10_model.r WARNING @ Thu, 16 Apr 2020 05:55:14: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:55:14: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:55:14: #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 05:55:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:55:15: 8000000 INFO @ Thu, 16 Apr 2020 05:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:55:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.05_summits.bed INFO @ Thu, 16 Apr 2020 05:55:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2947 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:55:21: 9000000 INFO @ Thu, 16 Apr 2020 05:55:28: 10000000 INFO @ Thu, 16 Apr 2020 05:55:34: 11000000 INFO @ Thu, 16 Apr 2020 05:55:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:55:40: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:55:40: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:55:40: #1 total tags in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:55:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:55:40: #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 05:55:40: #1 tags after filtering in treatment: 11923945 INFO @ Thu, 16 Apr 2020 05:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:55:40: #1 finished! INFO @ Thu, 16 Apr 2020 05:55:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:55:41: #2 number of paired peaks: 1064 INFO @ Thu, 16 Apr 2020 05:55:41: start model_add_line... INFO @ Thu, 16 Apr 2020 05:55:41: start X-correlation... INFO @ Thu, 16 Apr 2020 05:55:41: end of X-cor INFO @ Thu, 16 Apr 2020 05:55:41: #2 finished! INFO @ Thu, 16 Apr 2020 05:55:41: #2 predicted fragment length is 76 bps INFO @ Thu, 16 Apr 2020 05:55:41: #2 alternative fragment length(s) may be 3,76 bps INFO @ Thu, 16 Apr 2020 05:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20_model.r WARNING @ Thu, 16 Apr 2020 05:55:41: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:55:41: #2 You may need to consider one of the other alternative d(s): 3,76 WARNING @ Thu, 16 Apr 2020 05:55:41: #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 05:55:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:55:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:55:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:55:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.10_summits.bed INFO @ Thu, 16 Apr 2020 05:55:50: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1749 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:56:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747983/SRX6747983.20_summits.bed INFO @ Thu, 16 Apr 2020 05:56:18: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (861 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。