Job ID = 5720749 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,389,430 reads read : 8,778,860 reads written : 4,389,430 reads 0-length : 4,389,430 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: 00:04:14 4389430 reads; of these: 4389430 (100.00%) were unpaired; of these: 628804 (14.33%) aligned 0 times 928119 (21.14%) aligned exactly 1 time 2832507 (64.53%) aligned >1 times 85.67% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 1537320 / 3760626 = 0.4088 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 01:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.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 01:14:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:14:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:14:44: 1000000 INFO @ Thu, 16 Apr 2020 01:14:50: 2000000 INFO @ Thu, 16 Apr 2020 01:14:52: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:14:52: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:14:52: #1 total tags in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:14:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:14:52: #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 01:14:52: #1 tags after filtering in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:14:52: #1 finished! INFO @ Thu, 16 Apr 2020 01:14:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:14:52: #2 number of paired peaks: 3646 INFO @ Thu, 16 Apr 2020 01:14:52: start model_add_line... INFO @ Thu, 16 Apr 2020 01:14:52: start X-correlation... INFO @ Thu, 16 Apr 2020 01:14:52: end of X-cor INFO @ Thu, 16 Apr 2020 01:14:52: #2 finished! INFO @ Thu, 16 Apr 2020 01:14:52: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 01:14:52: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 01:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05_model.r WARNING @ Thu, 16 Apr 2020 01:14:52: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:14:52: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 16 Apr 2020 01:14:52: #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 01:14:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:14:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:15:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.05_summits.bed INFO @ Thu, 16 Apr 2020 01:15:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3587 records, 4 fields): 5 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 01:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.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 01:15:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:14: 1000000 INFO @ Thu, 16 Apr 2020 01:15:20: 2000000 INFO @ Thu, 16 Apr 2020 01:15:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:15:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:15:22: #1 total tags in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:15:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:15:22: #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 01:15:22: #1 tags after filtering in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:15:22: #1 finished! INFO @ Thu, 16 Apr 2020 01:15:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:15:22: #2 number of paired peaks: 3646 INFO @ Thu, 16 Apr 2020 01:15:22: start model_add_line... INFO @ Thu, 16 Apr 2020 01:15:22: start X-correlation... INFO @ Thu, 16 Apr 2020 01:15:22: end of X-cor INFO @ Thu, 16 Apr 2020 01:15:22: #2 finished! INFO @ Thu, 16 Apr 2020 01:15:22: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 01:15:22: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 01:15:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10_model.r WARNING @ Thu, 16 Apr 2020 01:15:22: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:15:22: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 16 Apr 2020 01:15:22: #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 01:15:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:15:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:15:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.10_summits.bed INFO @ Thu, 16 Apr 2020 01:15:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2185 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 01:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.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 01:15:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:15:46: 1000000 INFO @ Thu, 16 Apr 2020 01:15:53: 2000000 INFO @ Thu, 16 Apr 2020 01:15:55: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:15:55: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:15:55: #1 total tags in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:15:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:15:55: #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 01:15:55: #1 tags after filtering in treatment: 2223306 INFO @ Thu, 16 Apr 2020 01:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:15:55: #1 finished! INFO @ Thu, 16 Apr 2020 01:15:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:15:55: #2 number of paired peaks: 3646 INFO @ Thu, 16 Apr 2020 01:15:55: start model_add_line... INFO @ Thu, 16 Apr 2020 01:15:55: start X-correlation... INFO @ Thu, 16 Apr 2020 01:15:55: end of X-cor INFO @ Thu, 16 Apr 2020 01:15:55: #2 finished! INFO @ Thu, 16 Apr 2020 01:15:55: #2 predicted fragment length is 89 bps INFO @ Thu, 16 Apr 2020 01:15:55: #2 alternative fragment length(s) may be 89 bps INFO @ Thu, 16 Apr 2020 01:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20_model.r WARNING @ Thu, 16 Apr 2020 01:15:55: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:15:55: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Thu, 16 Apr 2020 01:15:55: #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 01:15:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:16:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226987/SRX5226987.20_summits.bed INFO @ Thu, 16 Apr 2020 01:16:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。