Job ID = 5790641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 50,988,265 reads read : 101,976,530 reads written : 50,988,265 reads 0-length : 50,988,265 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: 00:00:05 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:25 50988265 reads; of these: 50988265 (100.00%) were unpaired; of these: 4946314 (9.70%) aligned 0 times 42527559 (83.41%) aligned exactly 1 time 3514392 (6.89%) aligned >1 times 90.30% overall alignment rate Time searching: 00:32:31 Overall time: 00:32:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 28036655 / 46041951 = 0.6089 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 @ Wed, 22 Apr 2020 05:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:52:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:52:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:52:08: 1000000 INFO @ Wed, 22 Apr 2020 05:52:15: 2000000 INFO @ Wed, 22 Apr 2020 05:52:22: 3000000 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 @ Wed, 22 Apr 2020 05:52:28: 4000000 INFO @ Wed, 22 Apr 2020 05:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:52:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:52:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:52:36: 5000000 INFO @ Wed, 22 Apr 2020 05:52:39: 1000000 INFO @ Wed, 22 Apr 2020 05:52:44: 6000000 INFO @ Wed, 22 Apr 2020 05:52:46: 2000000 INFO @ Wed, 22 Apr 2020 05:52:52: 7000000 INFO @ Wed, 22 Apr 2020 05:52:54: 3000000 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 @ Wed, 22 Apr 2020 05:53:00: 8000000 INFO @ Wed, 22 Apr 2020 05:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:53:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:53:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:53:02: 4000000 INFO @ Wed, 22 Apr 2020 05:53:08: 9000000 INFO @ Wed, 22 Apr 2020 05:53:09: 1000000 INFO @ Wed, 22 Apr 2020 05:53:10: 5000000 INFO @ Wed, 22 Apr 2020 05:53:16: 10000000 INFO @ Wed, 22 Apr 2020 05:53:17: 2000000 INFO @ Wed, 22 Apr 2020 05:53:18: 6000000 INFO @ Wed, 22 Apr 2020 05:53:24: 11000000 INFO @ Wed, 22 Apr 2020 05:53:25: 3000000 INFO @ Wed, 22 Apr 2020 05:53:26: 7000000 INFO @ Wed, 22 Apr 2020 05:53:32: 12000000 INFO @ Wed, 22 Apr 2020 05:53:33: 4000000 INFO @ Wed, 22 Apr 2020 05:53:34: 8000000 INFO @ Wed, 22 Apr 2020 05:53:40: 13000000 INFO @ Wed, 22 Apr 2020 05:53:41: 5000000 INFO @ Wed, 22 Apr 2020 05:53:43: 9000000 INFO @ Wed, 22 Apr 2020 05:53:48: 14000000 INFO @ Wed, 22 Apr 2020 05:53:49: 6000000 INFO @ Wed, 22 Apr 2020 05:53:51: 10000000 INFO @ Wed, 22 Apr 2020 05:53:56: 15000000 INFO @ Wed, 22 Apr 2020 05:53:57: 7000000 INFO @ Wed, 22 Apr 2020 05:53:59: 11000000 INFO @ Wed, 22 Apr 2020 05:54:04: 16000000 INFO @ Wed, 22 Apr 2020 05:54:05: 8000000 INFO @ Wed, 22 Apr 2020 05:54:07: 12000000 INFO @ Wed, 22 Apr 2020 05:54:12: 17000000 INFO @ Wed, 22 Apr 2020 05:54:13: 9000000 INFO @ Wed, 22 Apr 2020 05:54:15: 13000000 INFO @ Wed, 22 Apr 2020 05:54:20: 18000000 INFO @ Wed, 22 Apr 2020 05:54:20: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:54:20: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:54:20: #1 total tags in treatment: 18005296 INFO @ Wed, 22 Apr 2020 05:54:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:54:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:54:20: #1 tags after filtering in treatment: 18005012 INFO @ Wed, 22 Apr 2020 05:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:54:20: #1 finished! INFO @ Wed, 22 Apr 2020 05:54:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:54:21: 10000000 INFO @ Wed, 22 Apr 2020 05:54:22: #2 number of paired peaks: 15094 INFO @ Wed, 22 Apr 2020 05:54:22: start model_add_line... INFO @ Wed, 22 Apr 2020 05:54:22: start X-correlation... INFO @ Wed, 22 Apr 2020 05:54:22: end of X-cor INFO @ Wed, 22 Apr 2020 05:54:22: #2 finished! INFO @ Wed, 22 Apr 2020 05:54:22: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 05:54:22: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 05:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05_model.r WARNING @ Wed, 22 Apr 2020 05:54:22: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:54:22: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Wed, 22 Apr 2020 05:54:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:54:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:54:23: 14000000 INFO @ Wed, 22 Apr 2020 05:54:29: 11000000 INFO @ Wed, 22 Apr 2020 05:54:30: 15000000 INFO @ Wed, 22 Apr 2020 05:54:36: 12000000 INFO @ Wed, 22 Apr 2020 05:54:38: 16000000 INFO @ Wed, 22 Apr 2020 05:54:44: 13000000 INFO @ Wed, 22 Apr 2020 05:54:46: 17000000 INFO @ Wed, 22 Apr 2020 05:54:52: 14000000 INFO @ Wed, 22 Apr 2020 05:54:54: 18000000 INFO @ Wed, 22 Apr 2020 05:54:54: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:54:54: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:54:54: #1 total tags in treatment: 18005296 INFO @ Wed, 22 Apr 2020 05:54:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:54:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:54:54: #1 tags after filtering in treatment: 18005012 INFO @ Wed, 22 Apr 2020 05:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:54:54: #1 finished! INFO @ Wed, 22 Apr 2020 05:54:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:54:56: #2 number of paired peaks: 15094 INFO @ Wed, 22 Apr 2020 05:54:56: start model_add_line... INFO @ Wed, 22 Apr 2020 05:54:56: start X-correlation... INFO @ Wed, 22 Apr 2020 05:54:56: end of X-cor INFO @ Wed, 22 Apr 2020 05:54:56: #2 finished! INFO @ Wed, 22 Apr 2020 05:54:56: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 05:54:56: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 05:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10_model.r WARNING @ Wed, 22 Apr 2020 05:54:56: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:54:56: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Wed, 22 Apr 2020 05:54:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:54:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:55:00: 15000000 INFO @ Wed, 22 Apr 2020 05:55:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:55:07: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:55:14: 17000000 INFO @ Wed, 22 Apr 2020 05:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.05_summits.bed INFO @ Wed, 22 Apr 2020 05:55:18: Done! INFO @ Wed, 22 Apr 2020 05:55:21: 18000000 INFO @ Wed, 22 Apr 2020 05:55:21: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:55:21: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:55:21: #1 total tags in treatment: 18005296 INFO @ Wed, 22 Apr 2020 05:55:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:55:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:55:21: #1 tags after filtering in treatment: 18005012 INFO @ Wed, 22 Apr 2020 05:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:55:21: #1 finished! INFO @ Wed, 22 Apr 2020 05:55:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:55:21: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (126 chroms): 3 millis pass2 - checking and writing primary data (21621 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:55:23: #2 number of paired peaks: 15094 INFO @ Wed, 22 Apr 2020 05:55:23: start model_add_line... INFO @ Wed, 22 Apr 2020 05:55:23: start X-correlation... INFO @ Wed, 22 Apr 2020 05:55:23: end of X-cor INFO @ Wed, 22 Apr 2020 05:55:23: #2 finished! INFO @ Wed, 22 Apr 2020 05:55:23: #2 predicted fragment length is 181 bps INFO @ Wed, 22 Apr 2020 05:55:23: #2 alternative fragment length(s) may be 181 bps INFO @ Wed, 22 Apr 2020 05:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20_model.r WARNING @ Wed, 22 Apr 2020 05:55:23: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:55:23: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Wed, 22 Apr 2020 05:55:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:55:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:55:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 05:55:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.10_summits.bed INFO @ Wed, 22 Apr 2020 05:55:51: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (19961 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:56:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299284/SRX5299284.20_summits.bed INFO @ Wed, 22 Apr 2020 05:56:18: Done! pass1 - making usageList (104 chroms): 3 millis pass2 - checking and writing primary data (18400 records, 4 fields): 20 millis CompletedMACS2peakCalling