Job ID = 5721200 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,777,452 reads read : 26,777,452 reads written : 26,777,452 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: 00:09:56 26777452 reads; of these: 26777452 (100.00%) were unpaired; of these: 791474 (2.96%) aligned 0 times 17613247 (65.78%) aligned exactly 1 time 8372731 (31.27%) aligned >1 times 97.04% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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] 3756641 / 25985978 = 0.1446 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 06:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.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 06:07:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:13: 1000000 INFO @ Thu, 16 Apr 2020 06:07:19: 2000000 INFO @ Thu, 16 Apr 2020 06:07:26: 3000000 INFO @ Thu, 16 Apr 2020 06:07:32: 4000000 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 06:07:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.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 06:07:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:38: 5000000 INFO @ Thu, 16 Apr 2020 06:07:43: 1000000 INFO @ Thu, 16 Apr 2020 06:07:45: 6000000 INFO @ Thu, 16 Apr 2020 06:07:50: 2000000 INFO @ Thu, 16 Apr 2020 06:07:52: 7000000 INFO @ Thu, 16 Apr 2020 06:07:57: 3000000 INFO @ Thu, 16 Apr 2020 06:07:58: 8000000 INFO @ Thu, 16 Apr 2020 06:08:04: 4000000 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 06:08:05: 9000000 INFO @ Thu, 16 Apr 2020 06:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.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 06:08:06: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:08:06: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:08:11: 5000000 INFO @ Thu, 16 Apr 2020 06:08:12: 10000000 INFO @ Thu, 16 Apr 2020 06:08:13: 1000000 INFO @ Thu, 16 Apr 2020 06:08:18: 6000000 INFO @ Thu, 16 Apr 2020 06:08:19: 11000000 INFO @ Thu, 16 Apr 2020 06:08:19: 2000000 INFO @ Thu, 16 Apr 2020 06:08:25: 7000000 INFO @ Thu, 16 Apr 2020 06:08:25: 12000000 INFO @ Thu, 16 Apr 2020 06:08:25: 3000000 INFO @ Thu, 16 Apr 2020 06:08:31: 8000000 INFO @ Thu, 16 Apr 2020 06:08:32: 4000000 INFO @ Thu, 16 Apr 2020 06:08:32: 13000000 INFO @ Thu, 16 Apr 2020 06:08:38: 5000000 INFO @ Thu, 16 Apr 2020 06:08:38: 9000000 INFO @ Thu, 16 Apr 2020 06:08:39: 14000000 INFO @ Thu, 16 Apr 2020 06:08:44: 6000000 INFO @ Thu, 16 Apr 2020 06:08:45: 10000000 INFO @ Thu, 16 Apr 2020 06:08:46: 15000000 INFO @ Thu, 16 Apr 2020 06:08:50: 7000000 INFO @ Thu, 16 Apr 2020 06:08:52: 11000000 INFO @ Thu, 16 Apr 2020 06:08:52: 16000000 INFO @ Thu, 16 Apr 2020 06:08:57: 8000000 INFO @ Thu, 16 Apr 2020 06:08:59: 12000000 INFO @ Thu, 16 Apr 2020 06:08:59: 17000000 INFO @ Thu, 16 Apr 2020 06:09:03: 9000000 INFO @ Thu, 16 Apr 2020 06:09:06: 13000000 INFO @ Thu, 16 Apr 2020 06:09:06: 18000000 INFO @ Thu, 16 Apr 2020 06:09:09: 10000000 INFO @ Thu, 16 Apr 2020 06:09:13: 14000000 INFO @ Thu, 16 Apr 2020 06:09:13: 19000000 INFO @ Thu, 16 Apr 2020 06:09:15: 11000000 INFO @ Thu, 16 Apr 2020 06:09:19: 15000000 INFO @ Thu, 16 Apr 2020 06:09:19: 20000000 INFO @ Thu, 16 Apr 2020 06:09:22: 12000000 INFO @ Thu, 16 Apr 2020 06:09:26: 21000000 INFO @ Thu, 16 Apr 2020 06:09:26: 16000000 INFO @ Thu, 16 Apr 2020 06:09:28: 13000000 INFO @ Thu, 16 Apr 2020 06:09:33: 22000000 INFO @ Thu, 16 Apr 2020 06:09:33: 17000000 INFO @ Thu, 16 Apr 2020 06:09:34: 14000000 INFO @ Thu, 16 Apr 2020 06:09:34: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:09:34: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:09:34: #1 total tags in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:09:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:09:34: #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 06:09:35: #1 tags after filtering in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:09:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:09:35: #1 finished! INFO @ Thu, 16 Apr 2020 06:09:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:09:36: #2 number of paired peaks: 323 WARNING @ Thu, 16 Apr 2020 06:09:36: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Thu, 16 Apr 2020 06:09:36: start model_add_line... INFO @ Thu, 16 Apr 2020 06:09:36: start X-correlation... INFO @ Thu, 16 Apr 2020 06:09:36: end of X-cor INFO @ Thu, 16 Apr 2020 06:09:36: #2 finished! INFO @ Thu, 16 Apr 2020 06:09:36: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:09:36: #2 alternative fragment length(s) may be 4,46 bps INFO @ Thu, 16 Apr 2020 06:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05_model.r WARNING @ Thu, 16 Apr 2020 06:09:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:09:36: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Thu, 16 Apr 2020 06:09:36: #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 06:09:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:09:40: 18000000 INFO @ Thu, 16 Apr 2020 06:09:40: 15000000 INFO @ Thu, 16 Apr 2020 06:09:46: 16000000 INFO @ Thu, 16 Apr 2020 06:09:47: 19000000 INFO @ Thu, 16 Apr 2020 06:09:52: 17000000 INFO @ Thu, 16 Apr 2020 06:09:53: 20000000 INFO @ Thu, 16 Apr 2020 06:09:59: 18000000 INFO @ Thu, 16 Apr 2020 06:10:00: 21000000 INFO @ Thu, 16 Apr 2020 06:10:05: 19000000 INFO @ Thu, 16 Apr 2020 06:10:07: 22000000 INFO @ Thu, 16 Apr 2020 06:10:08: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:10:08: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:10:08: #1 total tags in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:10:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:10:08: #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 06:10:08: #1 tags after filtering in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:10:08: #1 finished! INFO @ Thu, 16 Apr 2020 06:10:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:10:10: #2 number of paired peaks: 323 WARNING @ Thu, 16 Apr 2020 06:10:10: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Thu, 16 Apr 2020 06:10:10: start model_add_line... INFO @ Thu, 16 Apr 2020 06:10:10: start X-correlation... INFO @ Thu, 16 Apr 2020 06:10:10: end of X-cor INFO @ Thu, 16 Apr 2020 06:10:10: #2 finished! INFO @ Thu, 16 Apr 2020 06:10:10: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:10:10: #2 alternative fragment length(s) may be 4,46 bps INFO @ Thu, 16 Apr 2020 06:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10_model.r WARNING @ Thu, 16 Apr 2020 06:10:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:10:10: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Thu, 16 Apr 2020 06:10:10: #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 06:10:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:10:11: 20000000 INFO @ Thu, 16 Apr 2020 06:10:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:10:17: 21000000 INFO @ Thu, 16 Apr 2020 06:10:22: 22000000 INFO @ Thu, 16 Apr 2020 06:10:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:10:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:10:24: #1 total tags in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:10:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:10:24: #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 06:10:24: #1 tags after filtering in treatment: 22229337 INFO @ Thu, 16 Apr 2020 06:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:10:24: #1 finished! INFO @ Thu, 16 Apr 2020 06:10:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:10:25: #2 number of paired peaks: 323 WARNING @ Thu, 16 Apr 2020 06:10:25: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Thu, 16 Apr 2020 06:10:25: start model_add_line... INFO @ Thu, 16 Apr 2020 06:10:26: start X-correlation... INFO @ Thu, 16 Apr 2020 06:10:26: end of X-cor INFO @ Thu, 16 Apr 2020 06:10:26: #2 finished! INFO @ Thu, 16 Apr 2020 06:10:26: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:10:26: #2 alternative fragment length(s) may be 4,46 bps INFO @ Thu, 16 Apr 2020 06:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20_model.r WARNING @ Thu, 16 Apr 2020 06:10:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:10:26: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Thu, 16 Apr 2020 06:10:26: #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 06:10:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.05_summits.bed INFO @ Thu, 16 Apr 2020 06:10:32: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3516 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:10:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.10_summits.bed INFO @ Thu, 16 Apr 2020 06:11:07: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2435 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827668/SRX6827668.20_summits.bed INFO @ Thu, 16 Apr 2020 06:11:23: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1309 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。