Job ID = 5721215 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,713,990 reads read : 23,713,990 reads written : 23,713,990 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: 00:08:35 23713990 reads; of these: 23713990 (100.00%) were unpaired; of these: 1051634 (4.43%) aligned 0 times 15314140 (64.58%) aligned exactly 1 time 7348216 (30.99%) aligned >1 times 95.57% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 4007719 / 22662356 = 0.1768 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 06:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.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 06:09:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:09:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:09:47: 1000000 INFO @ Thu, 16 Apr 2020 06:09:52: 2000000 INFO @ Thu, 16 Apr 2020 06:09:57: 3000000 INFO @ Thu, 16 Apr 2020 06:10:02: 4000000 INFO @ Thu, 16 Apr 2020 06:10:07: 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 06:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.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 06:10:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:12: 6000000 INFO @ Thu, 16 Apr 2020 06:10:18: 7000000 INFO @ Thu, 16 Apr 2020 06:10:19: 1000000 INFO @ Thu, 16 Apr 2020 06:10:23: 8000000 INFO @ Thu, 16 Apr 2020 06:10:26: 2000000 INFO @ Thu, 16 Apr 2020 06:10:29: 9000000 INFO @ Thu, 16 Apr 2020 06:10:33: 3000000 INFO @ Thu, 16 Apr 2020 06:10:34: 10000000 INFO @ Thu, 16 Apr 2020 06:10:40: 11000000 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 06:10:41: 4000000 INFO @ Thu, 16 Apr 2020 06:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.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 06:10:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:45: 12000000 INFO @ Thu, 16 Apr 2020 06:10:47: 1000000 INFO @ Thu, 16 Apr 2020 06:10:48: 5000000 INFO @ Thu, 16 Apr 2020 06:10:51: 13000000 INFO @ Thu, 16 Apr 2020 06:10:53: 2000000 INFO @ Thu, 16 Apr 2020 06:10:55: 6000000 INFO @ Thu, 16 Apr 2020 06:10:56: 14000000 INFO @ Thu, 16 Apr 2020 06:10:59: 3000000 INFO @ Thu, 16 Apr 2020 06:11:02: 7000000 INFO @ Thu, 16 Apr 2020 06:11:02: 15000000 INFO @ Thu, 16 Apr 2020 06:11:04: 4000000 INFO @ Thu, 16 Apr 2020 06:11:08: 16000000 INFO @ Thu, 16 Apr 2020 06:11:09: 8000000 INFO @ Thu, 16 Apr 2020 06:11:10: 5000000 INFO @ Thu, 16 Apr 2020 06:11:14: 17000000 INFO @ Thu, 16 Apr 2020 06:11:15: 6000000 INFO @ Thu, 16 Apr 2020 06:11:16: 9000000 INFO @ Thu, 16 Apr 2020 06:11:19: 18000000 INFO @ Thu, 16 Apr 2020 06:11:21: 7000000 INFO @ Thu, 16 Apr 2020 06:11:23: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:11:23: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:11:23: #1 total tags in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:11:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:11:23: #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 06:11:23: #1 tags after filtering in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:11:23: #1 finished! INFO @ Thu, 16 Apr 2020 06:11:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:11:24: 10000000 INFO @ Thu, 16 Apr 2020 06:11:25: #2 number of paired peaks: 533 WARNING @ Thu, 16 Apr 2020 06:11:25: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Thu, 16 Apr 2020 06:11:25: start model_add_line... INFO @ Thu, 16 Apr 2020 06:11:25: start X-correlation... INFO @ Thu, 16 Apr 2020 06:11:25: end of X-cor INFO @ Thu, 16 Apr 2020 06:11:25: #2 finished! INFO @ Thu, 16 Apr 2020 06:11:25: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 06:11:25: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 06:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05_model.r WARNING @ Thu, 16 Apr 2020 06:11:25: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:11:25: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 06:11:25: #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 06:11:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:11:26: 8000000 INFO @ Thu, 16 Apr 2020 06:11:31: 11000000 INFO @ Thu, 16 Apr 2020 06:11:32: 9000000 INFO @ Thu, 16 Apr 2020 06:11:37: 10000000 INFO @ Thu, 16 Apr 2020 06:11:38: 12000000 INFO @ Thu, 16 Apr 2020 06:11:43: 11000000 INFO @ Thu, 16 Apr 2020 06:11:45: 13000000 INFO @ Thu, 16 Apr 2020 06:11:48: 12000000 INFO @ Thu, 16 Apr 2020 06:11:53: 14000000 INFO @ Thu, 16 Apr 2020 06:11:54: 13000000 INFO @ Thu, 16 Apr 2020 06:11:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:00: 14000000 INFO @ Thu, 16 Apr 2020 06:12:00: 15000000 INFO @ Thu, 16 Apr 2020 06:12:05: 15000000 INFO @ Thu, 16 Apr 2020 06:12:08: 16000000 INFO @ Thu, 16 Apr 2020 06:12:11: 16000000 INFO @ Thu, 16 Apr 2020 06:12:16: 17000000 INFO @ Thu, 16 Apr 2020 06:12:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.05_summits.bed INFO @ Thu, 16 Apr 2020 06:12:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3972 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:12:17: 17000000 INFO @ Thu, 16 Apr 2020 06:12:23: 18000000 INFO @ Thu, 16 Apr 2020 06:12:23: 18000000 INFO @ Thu, 16 Apr 2020 06:12:27: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:27: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:27: #1 total tags in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:12:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:27: #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 06:12:27: #1 tags after filtering in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:27: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:28: #2 number of paired peaks: 533 WARNING @ Thu, 16 Apr 2020 06:12:28: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:28: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:28: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:28: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:28: #1 total tags in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:12:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:28: #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 06:12:28: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:28: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:28: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:28: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 06:12:28: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 06:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20_model.r WARNING @ Thu, 16 Apr 2020 06:12:29: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:29: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 06:12:29: #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 06:12:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:29: #1 tags after filtering in treatment: 18654637 INFO @ Thu, 16 Apr 2020 06:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:29: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:30: #2 number of paired peaks: 533 WARNING @ Thu, 16 Apr 2020 06:12:30: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:30: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:30: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:30: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:30: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:30: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 06:12:30: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 06:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10_model.r WARNING @ Thu, 16 Apr 2020 06:12:30: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:30: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 06:12:30: #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 06:12:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:13:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:13:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.20_summits.bed INFO @ Thu, 16 Apr 2020 06:13:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827675/SRX6827675.10_summits.bed INFO @ Thu, 16 Apr 2020 06:13:26: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2592 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。