Job ID = 5721206 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,277,298 reads read : 24,277,298 reads written : 24,277,298 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: 00:08:15 24277298 reads; of these: 24277298 (100.00%) were unpaired; of these: 915629 (3.77%) aligned 0 times 16115523 (66.38%) aligned exactly 1 time 7246146 (29.85%) aligned >1 times 96.23% overall alignment rate Time searching: 00:08:15 Overall time: 00:08:15 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 12 files... [bam_rmdupse_core] 3383651 / 23361669 = 0.1448 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 06:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.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 06:07:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:07: 1000000 INFO @ Thu, 16 Apr 2020 06:07:13: 2000000 INFO @ Thu, 16 Apr 2020 06:07:18: 3000000 INFO @ Thu, 16 Apr 2020 06:07:24: 4000000 INFO @ Thu, 16 Apr 2020 06:07:29: 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 06:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.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 06:07:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:35: 6000000 INFO @ Thu, 16 Apr 2020 06:07:38: 1000000 INFO @ Thu, 16 Apr 2020 06:07:40: 7000000 INFO @ Thu, 16 Apr 2020 06:07:43: 2000000 INFO @ Thu, 16 Apr 2020 06:07:46: 8000000 INFO @ Thu, 16 Apr 2020 06:07:49: 3000000 INFO @ Thu, 16 Apr 2020 06:07:52: 9000000 INFO @ Thu, 16 Apr 2020 06:07:55: 4000000 INFO @ Thu, 16 Apr 2020 06:07:57: 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 06:08:01: 5000000 INFO @ Thu, 16 Apr 2020 06:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.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 06:08:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:08:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:08:03: 11000000 INFO @ Thu, 16 Apr 2020 06:08:07: 6000000 INFO @ Thu, 16 Apr 2020 06:08:09: 1000000 INFO @ Thu, 16 Apr 2020 06:08:09: 12000000 INFO @ Thu, 16 Apr 2020 06:08:13: 7000000 INFO @ Thu, 16 Apr 2020 06:08:15: 13000000 INFO @ Thu, 16 Apr 2020 06:08:16: 2000000 INFO @ Thu, 16 Apr 2020 06:08:19: 8000000 INFO @ Thu, 16 Apr 2020 06:08:21: 14000000 INFO @ Thu, 16 Apr 2020 06:08:23: 3000000 INFO @ Thu, 16 Apr 2020 06:08:25: 9000000 INFO @ Thu, 16 Apr 2020 06:08:28: 15000000 INFO @ Thu, 16 Apr 2020 06:08:29: 4000000 INFO @ Thu, 16 Apr 2020 06:08:32: 10000000 INFO @ Thu, 16 Apr 2020 06:08:34: 16000000 INFO @ Thu, 16 Apr 2020 06:08:36: 5000000 INFO @ Thu, 16 Apr 2020 06:08:38: 11000000 INFO @ Thu, 16 Apr 2020 06:08:40: 17000000 INFO @ Thu, 16 Apr 2020 06:08:43: 6000000 INFO @ Thu, 16 Apr 2020 06:08:44: 12000000 INFO @ Thu, 16 Apr 2020 06:08:46: 18000000 INFO @ Thu, 16 Apr 2020 06:08:50: 13000000 INFO @ Thu, 16 Apr 2020 06:08:50: 7000000 INFO @ Thu, 16 Apr 2020 06:08:52: 19000000 INFO @ Thu, 16 Apr 2020 06:08:56: 14000000 INFO @ Thu, 16 Apr 2020 06:08:57: 8000000 INFO @ Thu, 16 Apr 2020 06:08:58: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:08:58: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:08:58: #1 total tags in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:08:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:08:58: #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 06:08:59: #1 tags after filtering in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:08:59: #1 finished! INFO @ Thu, 16 Apr 2020 06:08:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:00: #2 number of paired peaks: 359 WARNING @ Thu, 16 Apr 2020 06:09:00: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:00: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:00: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:00: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:00: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:00: #2 predicted fragment length is 44 bps INFO @ Thu, 16 Apr 2020 06:09:00: #2 alternative fragment length(s) may be 44 bps INFO @ Thu, 16 Apr 2020 06:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05_model.r WARNING @ Thu, 16 Apr 2020 06:09:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:09:00: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Thu, 16 Apr 2020 06:09:00: #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 06:09:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:02: 15000000 INFO @ Thu, 16 Apr 2020 06:09:04: 9000000 INFO @ Thu, 16 Apr 2020 06:09:09: 16000000 INFO @ Thu, 16 Apr 2020 06:09:10: 10000000 INFO @ Thu, 16 Apr 2020 06:09:15: 17000000 INFO @ Thu, 16 Apr 2020 06:09:17: 11000000 INFO @ Thu, 16 Apr 2020 06:09:21: 18000000 INFO @ Thu, 16 Apr 2020 06:09:24: 12000000 INFO @ Thu, 16 Apr 2020 06:09:27: 19000000 INFO @ Thu, 16 Apr 2020 06:09:30: 13000000 INFO @ Thu, 16 Apr 2020 06:09:33: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:09:33: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:09:33: #1 total tags in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:09:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:09:33: #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 06:09:33: #1 tags after filtering in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:09:33: #1 finished! INFO @ Thu, 16 Apr 2020 06:09:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:35: #2 number of paired peaks: 359 WARNING @ Thu, 16 Apr 2020 06:09:35: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:35: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:35: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:35: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:35: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:35: #2 predicted fragment length is 44 bps INFO @ Thu, 16 Apr 2020 06:09:35: #2 alternative fragment length(s) may be 44 bps INFO @ Thu, 16 Apr 2020 06:09:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10_model.r WARNING @ Thu, 16 Apr 2020 06:09:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:09:35: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Thu, 16 Apr 2020 06:09:35: #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 06:09:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:09:37: 14000000 INFO @ Thu, 16 Apr 2020 06:09:44: 15000000 INFO @ Thu, 16 Apr 2020 06:09:50: 16000000 INFO @ Thu, 16 Apr 2020 06:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.05_summits.bed INFO @ Thu, 16 Apr 2020 06:09:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3468 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:09:56: 17000000 INFO @ Thu, 16 Apr 2020 06:10:03: 18000000 INFO @ Thu, 16 Apr 2020 06:10:09: 19000000 INFO @ Thu, 16 Apr 2020 06:10:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:10:15: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:10:15: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:10:15: #1 total tags in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:10:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:10:15: #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 06:10:16: #1 tags after filtering in treatment: 19978018 INFO @ Thu, 16 Apr 2020 06:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:10:16: #1 finished! INFO @ Thu, 16 Apr 2020 06:10:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:10:17: #2 number of paired peaks: 359 WARNING @ Thu, 16 Apr 2020 06:10:17: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 16 Apr 2020 06:10:17: start model_add_line... INFO @ Thu, 16 Apr 2020 06:10:17: start X-correlation... INFO @ Thu, 16 Apr 2020 06:10:17: end of X-cor INFO @ Thu, 16 Apr 2020 06:10:17: #2 finished! INFO @ Thu, 16 Apr 2020 06:10:17: #2 predicted fragment length is 44 bps INFO @ Thu, 16 Apr 2020 06:10:17: #2 alternative fragment length(s) may be 44 bps INFO @ Thu, 16 Apr 2020 06:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20_model.r WARNING @ Thu, 16 Apr 2020 06:10:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:10:17: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Thu, 16 Apr 2020 06:10:17: #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 06:10:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.10_summits.bed INFO @ Thu, 16 Apr 2020 06:10:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2295 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:10:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827672/SRX6827672.20_summits.bed INFO @ Thu, 16 Apr 2020 06:11:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1228 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。