Job ID = 5721280 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,887,584 reads read : 37,775,168 reads written : 18,887,584 reads 0-length : 18,887,584 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: 00:06:15 18887584 reads; of these: 18887584 (100.00%) were unpaired; of these: 795248 (4.21%) aligned 0 times 13286489 (70.35%) aligned exactly 1 time 4805847 (25.44%) aligned >1 times 95.79% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 3548142 / 18092336 = 0.1961 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 06:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.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 06:25:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:25:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:25:07: 1000000 INFO @ Thu, 16 Apr 2020 06:25:12: 2000000 INFO @ Thu, 16 Apr 2020 06:25:16: 3000000 INFO @ Thu, 16 Apr 2020 06:25:21: 4000000 INFO @ Thu, 16 Apr 2020 06:25:25: 5000000 INFO @ Thu, 16 Apr 2020 06:25:29: 6000000 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 06:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.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 06:25:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:25:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:25:34: 7000000 INFO @ Thu, 16 Apr 2020 06:25:37: 1000000 INFO @ Thu, 16 Apr 2020 06:25:38: 8000000 INFO @ Thu, 16 Apr 2020 06:25:42: 2000000 INFO @ Thu, 16 Apr 2020 06:25:42: 9000000 INFO @ Thu, 16 Apr 2020 06:25:46: 3000000 INFO @ Thu, 16 Apr 2020 06:25:47: 10000000 INFO @ Thu, 16 Apr 2020 06:25:51: 4000000 INFO @ Thu, 16 Apr 2020 06:25:51: 11000000 INFO @ Thu, 16 Apr 2020 06:25:55: 5000000 INFO @ Thu, 16 Apr 2020 06:25:56: 12000000 INFO @ Thu, 16 Apr 2020 06:26:00: 6000000 INFO @ Thu, 16 Apr 2020 06:26:01: 13000000 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 06:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.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 06:26:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:26:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:26:04: 7000000 INFO @ Thu, 16 Apr 2020 06:26:05: 14000000 INFO @ Thu, 16 Apr 2020 06:26:07: 1000000 INFO @ Thu, 16 Apr 2020 06:26:08: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:26:08: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:26:08: #1 total tags in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:26:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:08: #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 06:26:08: #1 tags after filtering in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:26:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:26:08: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:08: 8000000 INFO @ Thu, 16 Apr 2020 06:26:09: #2 number of paired peaks: 115 WARNING @ Thu, 16 Apr 2020 06:26:09: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:09: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:09: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:09: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:09: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:09: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 06:26:09: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 06:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05_model.r WARNING @ Thu, 16 Apr 2020 06:26:09: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:26:09: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 06:26:09: #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 06:26:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:12: 2000000 INFO @ Thu, 16 Apr 2020 06:26:13: 9000000 INFO @ Thu, 16 Apr 2020 06:26:17: 3000000 INFO @ Thu, 16 Apr 2020 06:26:17: 10000000 INFO @ Thu, 16 Apr 2020 06:26:21: 4000000 INFO @ Thu, 16 Apr 2020 06:26:22: 11000000 INFO @ Thu, 16 Apr 2020 06:26:26: 5000000 INFO @ Thu, 16 Apr 2020 06:26:26: 12000000 INFO @ Thu, 16 Apr 2020 06:26:30: 6000000 INFO @ Thu, 16 Apr 2020 06:26:31: 13000000 INFO @ Thu, 16 Apr 2020 06:26:35: 7000000 INFO @ Thu, 16 Apr 2020 06:26:36: 14000000 INFO @ Thu, 16 Apr 2020 06:26:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:38: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:26:38: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:26:38: #1 total tags in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:26:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:38: #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 06:26:38: #1 tags after filtering in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:26:38: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:39: #2 number of paired peaks: 115 WARNING @ Thu, 16 Apr 2020 06:26:39: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:39: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:39: 8000000 INFO @ Thu, 16 Apr 2020 06:26:39: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:39: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:39: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:39: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 06:26:39: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 06:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10_model.r WARNING @ Thu, 16 Apr 2020 06:26:39: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:26:39: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 06:26:39: #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 06:26:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:44: 9000000 INFO @ Thu, 16 Apr 2020 06:26:49: 10000000 INFO @ Thu, 16 Apr 2020 06:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.05_summits.bed INFO @ Thu, 16 Apr 2020 06:26:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3278 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:26:53: 11000000 INFO @ Thu, 16 Apr 2020 06:26:58: 12000000 INFO @ Thu, 16 Apr 2020 06:27:03: 13000000 INFO @ Thu, 16 Apr 2020 06:27:07: 14000000 INFO @ Thu, 16 Apr 2020 06:27:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:10: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:27:10: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:27:10: #1 total tags in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:27:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:27:10: #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 06:27:10: #1 tags after filtering in treatment: 14544194 INFO @ Thu, 16 Apr 2020 06:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:27:10: #1 finished! INFO @ Thu, 16 Apr 2020 06:27:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:27:11: #2 number of paired peaks: 115 WARNING @ Thu, 16 Apr 2020 06:27:11: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Thu, 16 Apr 2020 06:27:11: start model_add_line... INFO @ Thu, 16 Apr 2020 06:27:11: start X-correlation... INFO @ Thu, 16 Apr 2020 06:27:11: end of X-cor INFO @ Thu, 16 Apr 2020 06:27:11: #2 finished! INFO @ Thu, 16 Apr 2020 06:27:11: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 06:27:11: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 06:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20_model.r WARNING @ Thu, 16 Apr 2020 06:27:11: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:27:11: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 06:27:11: #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 06:27:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.10_summits.bed INFO @ Thu, 16 Apr 2020 06:27:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1878 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:27:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7299238/SRX7299238.20_summits.bed INFO @ Thu, 16 Apr 2020 06:27:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (947 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。