Job ID = 5720916 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,021,442 reads read : 26,042,884 reads written : 13,021,442 reads 0-length : 13,021,442 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: 00:05:40 13021442 reads; of these: 13021442 (100.00%) were unpaired; of these: 404613 (3.11%) aligned 0 times 8089992 (62.13%) aligned exactly 1 time 4526837 (34.76%) aligned >1 times 96.89% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 1604684 / 12616829 = 0.1272 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 03:21:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.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 03:21:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:21:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:21:39: 1000000 INFO @ Thu, 16 Apr 2020 03:21:45: 2000000 INFO @ Thu, 16 Apr 2020 03:21:50: 3000000 INFO @ Thu, 16 Apr 2020 03:21:55: 4000000 INFO @ Thu, 16 Apr 2020 03:22:00: 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 03:22:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.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 03:22:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:06: 6000000 INFO @ Thu, 16 Apr 2020 03:22:10: 1000000 INFO @ Thu, 16 Apr 2020 03:22:11: 7000000 INFO @ Thu, 16 Apr 2020 03:22:15: 2000000 INFO @ Thu, 16 Apr 2020 03:22:16: 8000000 INFO @ Thu, 16 Apr 2020 03:22:21: 3000000 INFO @ Thu, 16 Apr 2020 03:22:22: 9000000 INFO @ Thu, 16 Apr 2020 03:22:26: 4000000 INFO @ Thu, 16 Apr 2020 03:22:27: 10000000 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 03:22:32: 5000000 INFO @ Thu, 16 Apr 2020 03:22:33: 11000000 INFO @ Thu, 16 Apr 2020 03:22:33: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:22:33: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:22:33: #1 total tags in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:22:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:22:33: #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 03:22:33: #1 tags after filtering in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:22:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:22:33: #1 finished! INFO @ Thu, 16 Apr 2020 03:22:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:22:34: #2 number of paired peaks: 153 WARNING @ Thu, 16 Apr 2020 03:22:34: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Thu, 16 Apr 2020 03:22:34: start model_add_line... INFO @ Thu, 16 Apr 2020 03:22:34: start X-correlation... INFO @ Thu, 16 Apr 2020 03:22:34: end of X-cor INFO @ Thu, 16 Apr 2020 03:22:34: #2 finished! INFO @ Thu, 16 Apr 2020 03:22:34: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:22:34: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05_model.r WARNING @ Thu, 16 Apr 2020 03:22:34: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:22:34: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:22:34: #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 03:22:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.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 03:22:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:37: 6000000 INFO @ Thu, 16 Apr 2020 03:22:40: 1000000 INFO @ Thu, 16 Apr 2020 03:22:43: 7000000 INFO @ Thu, 16 Apr 2020 03:22:46: 2000000 INFO @ Thu, 16 Apr 2020 03:22:48: 8000000 INFO @ Thu, 16 Apr 2020 03:22:51: 3000000 INFO @ Thu, 16 Apr 2020 03:22:53: 9000000 INFO @ Thu, 16 Apr 2020 03:22:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:22:57: 4000000 INFO @ Thu, 16 Apr 2020 03:22:59: 10000000 INFO @ Thu, 16 Apr 2020 03:23:02: 5000000 INFO @ Thu, 16 Apr 2020 03:23:04: 11000000 INFO @ Thu, 16 Apr 2020 03:23:04: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:23:04: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:23:04: #1 total tags in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:23:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:04: #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 03:23:04: #1 tags after filtering in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:04: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:05: #2 number of paired peaks: 153 WARNING @ Thu, 16 Apr 2020 03:23:05: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:05: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:05: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:05: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:05: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:05: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:23:05: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10_model.r WARNING @ Thu, 16 Apr 2020 03:23:05: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:05: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:23:05: #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 03:23:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.05_summits.bed INFO @ Thu, 16 Apr 2020 03:23:06: Done! INFO @ Thu, 16 Apr 2020 03:23:07: 6000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:23:13: 7000000 INFO @ Thu, 16 Apr 2020 03:23:18: 8000000 INFO @ Thu, 16 Apr 2020 03:23:23: 9000000 INFO @ Thu, 16 Apr 2020 03:23:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:23:28: 10000000 INFO @ Thu, 16 Apr 2020 03:23:34: 11000000 INFO @ Thu, 16 Apr 2020 03:23:34: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:23:34: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:23:34: #1 total tags in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:23:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:34: #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 03:23:34: #1 tags after filtering in treatment: 11012145 INFO @ Thu, 16 Apr 2020 03:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:34: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:35: #2 number of paired peaks: 153 WARNING @ Thu, 16 Apr 2020 03:23:35: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:35: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:35: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:35: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:35: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:35: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:23:35: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20_model.r WARNING @ Thu, 16 Apr 2020 03:23:35: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:35: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:23:35: #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 03:23:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.10_summits.bed INFO @ Thu, 16 Apr 2020 03:23:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:23:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775943/SRX5775943.20_summits.bed INFO @ Thu, 16 Apr 2020 03:24:07: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。