Job ID = 5720748 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,461,881 reads read : 6,923,762 reads written : 3,461,881 reads 0-length : 3,461,881 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: 00:02:05 3461881 reads; of these: 3461881 (100.00%) were unpaired; of these: 573349 (16.56%) aligned 0 times 1514006 (43.73%) aligned exactly 1 time 1374526 (39.70%) aligned >1 times 83.44% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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_rmdupse_core] 485213 / 2888532 = 0.1680 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 01:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.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 01:11:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:11:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:11:41: 1000000 INFO @ Thu, 16 Apr 2020 01:11:47: 2000000 INFO @ Thu, 16 Apr 2020 01:11:49: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:11:49: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:11:49: #1 total tags in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:11:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:49: #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 01:11:49: #1 tags after filtering in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:50: #2 number of paired peaks: 2298 INFO @ Thu, 16 Apr 2020 01:11:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:50: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:11:50: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05_model.r WARNING @ Thu, 16 Apr 2020 01:11:50: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:11:50: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:11:50: #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 01:11:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.05_summits.bed INFO @ Thu, 16 Apr 2020 01:11:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2564 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 01:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.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 01:12:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:12:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:12:11: 1000000 INFO @ Thu, 16 Apr 2020 01:12:17: 2000000 INFO @ Thu, 16 Apr 2020 01:12:20: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:12:20: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:12:20: #1 total tags in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:12:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:12:20: #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 01:12:20: #1 tags after filtering in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:12:20: #1 finished! INFO @ Thu, 16 Apr 2020 01:12:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:12:20: #2 number of paired peaks: 2298 INFO @ Thu, 16 Apr 2020 01:12:20: start model_add_line... INFO @ Thu, 16 Apr 2020 01:12:20: start X-correlation... INFO @ Thu, 16 Apr 2020 01:12:20: end of X-cor INFO @ Thu, 16 Apr 2020 01:12:20: #2 finished! INFO @ Thu, 16 Apr 2020 01:12:20: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:12:20: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10_model.r WARNING @ Thu, 16 Apr 2020 01:12:20: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:12:20: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:12:20: #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 01:12:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.10_summits.bed INFO @ Thu, 16 Apr 2020 01:12:28: Done! 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 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1374 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.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 01:12:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:12:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:12:42: 1000000 INFO @ Thu, 16 Apr 2020 01:12:48: 2000000 INFO @ Thu, 16 Apr 2020 01:12:50: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:12:50: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:12:50: #1 total tags in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:12:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:12:50: #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 01:12:50: #1 tags after filtering in treatment: 2403319 INFO @ Thu, 16 Apr 2020 01:12:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:12:50: #1 finished! INFO @ Thu, 16 Apr 2020 01:12:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:12:51: #2 number of paired peaks: 2298 INFO @ Thu, 16 Apr 2020 01:12:51: start model_add_line... INFO @ Thu, 16 Apr 2020 01:12:51: start X-correlation... INFO @ Thu, 16 Apr 2020 01:12:51: end of X-cor INFO @ Thu, 16 Apr 2020 01:12:51: #2 finished! INFO @ Thu, 16 Apr 2020 01:12:51: #2 predicted fragment length is 84 bps INFO @ Thu, 16 Apr 2020 01:12:51: #2 alternative fragment length(s) may be 84 bps INFO @ Thu, 16 Apr 2020 01:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20_model.r WARNING @ Thu, 16 Apr 2020 01:12:51: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:12:51: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Thu, 16 Apr 2020 01:12:51: #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 01:12:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226986/SRX5226986.20_summits.bed INFO @ Thu, 16 Apr 2020 01:12:58: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。