Job ID = 5790654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,346,548 reads read : 70,693,096 reads written : 35,346,548 reads 0-length : 35,346,548 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:16:41 35346548 reads; of these: 35346548 (100.00%) were unpaired; of these: 6154413 (17.41%) aligned 0 times 22582012 (63.89%) aligned exactly 1 time 6610123 (18.70%) aligned >1 times 82.59% overall alignment rate Time searching: 01:16:43 Overall time: 01:16:43 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 12 files... [bam_rmdupse_core] 3103376 / 29192135 = 0.1063 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 06:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.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 06:45:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:45:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:45:15: 1000000 INFO @ Wed, 22 Apr 2020 06:45:23: 2000000 INFO @ Wed, 22 Apr 2020 06:45:31: 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 06:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.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 06:45:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:45:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:45:38: 4000000 INFO @ Wed, 22 Apr 2020 06:45:45: 1000000 INFO @ Wed, 22 Apr 2020 06:45:46: 5000000 INFO @ Wed, 22 Apr 2020 06:45:53: 2000000 INFO @ Wed, 22 Apr 2020 06:45:53: 6000000 INFO @ Wed, 22 Apr 2020 06:46:00: 3000000 INFO @ Wed, 22 Apr 2020 06:46:00: 7000000 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 06:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.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 06:46:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:46:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:46:08: 8000000 INFO @ Wed, 22 Apr 2020 06:46:08: 4000000 INFO @ Wed, 22 Apr 2020 06:46:16: 1000000 INFO @ Wed, 22 Apr 2020 06:46:16: 9000000 INFO @ Wed, 22 Apr 2020 06:46:16: 5000000 INFO @ Wed, 22 Apr 2020 06:46:24: 10000000 INFO @ Wed, 22 Apr 2020 06:46:25: 6000000 INFO @ Wed, 22 Apr 2020 06:46:25: 2000000 INFO @ Wed, 22 Apr 2020 06:46:33: 11000000 INFO @ Wed, 22 Apr 2020 06:46:33: 7000000 INFO @ Wed, 22 Apr 2020 06:46:34: 3000000 INFO @ Wed, 22 Apr 2020 06:46:41: 8000000 INFO @ Wed, 22 Apr 2020 06:46:41: 12000000 INFO @ Wed, 22 Apr 2020 06:46:42: 4000000 INFO @ Wed, 22 Apr 2020 06:46:50: 9000000 INFO @ Wed, 22 Apr 2020 06:46:50: 13000000 INFO @ Wed, 22 Apr 2020 06:46:51: 5000000 INFO @ Wed, 22 Apr 2020 06:46:58: 14000000 INFO @ Wed, 22 Apr 2020 06:46:58: 10000000 INFO @ Wed, 22 Apr 2020 06:46:59: 6000000 INFO @ Wed, 22 Apr 2020 06:47:06: 15000000 INFO @ Wed, 22 Apr 2020 06:47:06: 11000000 INFO @ Wed, 22 Apr 2020 06:47:08: 7000000 INFO @ Wed, 22 Apr 2020 06:47:14: 16000000 INFO @ Wed, 22 Apr 2020 06:47:15: 12000000 INFO @ Wed, 22 Apr 2020 06:47:16: 8000000 INFO @ Wed, 22 Apr 2020 06:47:21: 17000000 INFO @ Wed, 22 Apr 2020 06:47:23: 13000000 INFO @ Wed, 22 Apr 2020 06:47:25: 9000000 INFO @ Wed, 22 Apr 2020 06:47:29: 18000000 INFO @ Wed, 22 Apr 2020 06:47:31: 14000000 INFO @ Wed, 22 Apr 2020 06:47:33: 10000000 INFO @ Wed, 22 Apr 2020 06:47:38: 19000000 INFO @ Wed, 22 Apr 2020 06:47:39: 15000000 INFO @ Wed, 22 Apr 2020 06:47:41: 11000000 INFO @ Wed, 22 Apr 2020 06:47:46: 20000000 INFO @ Wed, 22 Apr 2020 06:47:46: 16000000 INFO @ Wed, 22 Apr 2020 06:47:49: 12000000 INFO @ Wed, 22 Apr 2020 06:47:54: 17000000 INFO @ Wed, 22 Apr 2020 06:47:54: 21000000 INFO @ Wed, 22 Apr 2020 06:47:58: 13000000 INFO @ Wed, 22 Apr 2020 06:48:02: 18000000 INFO @ Wed, 22 Apr 2020 06:48:03: 22000000 INFO @ Wed, 22 Apr 2020 06:48:06: 14000000 INFO @ Wed, 22 Apr 2020 06:48:11: 19000000 INFO @ Wed, 22 Apr 2020 06:48:12: 23000000 INFO @ Wed, 22 Apr 2020 06:48:15: 15000000 INFO @ Wed, 22 Apr 2020 06:48:20: 20000000 INFO @ Wed, 22 Apr 2020 06:48:21: 24000000 INFO @ Wed, 22 Apr 2020 06:48:24: 16000000 INFO @ Wed, 22 Apr 2020 06:48:28: 21000000 INFO @ Wed, 22 Apr 2020 06:48:29: 25000000 INFO @ Wed, 22 Apr 2020 06:48:31: 17000000 INFO @ Wed, 22 Apr 2020 06:48:37: 22000000 INFO @ Wed, 22 Apr 2020 06:48:38: 26000000 INFO @ Wed, 22 Apr 2020 06:48:39: 18000000 INFO @ Wed, 22 Apr 2020 06:48:39: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:48:39: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:48:39: #1 total tags in treatment: 26088759 INFO @ Wed, 22 Apr 2020 06:48:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:48:39: #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 06:48:39: #1 tags after filtering in treatment: 26088645 INFO @ Wed, 22 Apr 2020 06:48:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:48:39: #1 finished! INFO @ Wed, 22 Apr 2020 06:48:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:48:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:48:42: #2 number of paired peaks: 7126 INFO @ Wed, 22 Apr 2020 06:48:42: start model_add_line... INFO @ Wed, 22 Apr 2020 06:48:42: start X-correlation... INFO @ Wed, 22 Apr 2020 06:48:42: end of X-cor INFO @ Wed, 22 Apr 2020 06:48:42: #2 finished! INFO @ Wed, 22 Apr 2020 06:48:42: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 06:48:42: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 06:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05_model.r WARNING @ Wed, 22 Apr 2020 06:48:42: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:48:42: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 06:48:42: #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 06:48:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:48:45: 23000000 INFO @ Wed, 22 Apr 2020 06:48:47: 19000000 INFO @ Wed, 22 Apr 2020 06:48:54: 24000000 INFO @ Wed, 22 Apr 2020 06:48:55: 20000000 INFO @ Wed, 22 Apr 2020 06:49:02: 25000000 INFO @ Wed, 22 Apr 2020 06:49:04: 21000000 INFO @ Wed, 22 Apr 2020 06:49:10: 26000000 INFO @ Wed, 22 Apr 2020 06:49:11: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:49:11: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:49:11: #1 total tags in treatment: 26088759 INFO @ Wed, 22 Apr 2020 06:49:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:49:11: #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 06:49:11: #1 tags after filtering in treatment: 26088645 INFO @ Wed, 22 Apr 2020 06:49:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:49:11: #1 finished! INFO @ Wed, 22 Apr 2020 06:49:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:49:12: 22000000 INFO @ Wed, 22 Apr 2020 06:49:14: #2 number of paired peaks: 7126 INFO @ Wed, 22 Apr 2020 06:49:14: start model_add_line... INFO @ Wed, 22 Apr 2020 06:49:14: start X-correlation... INFO @ Wed, 22 Apr 2020 06:49:14: end of X-cor INFO @ Wed, 22 Apr 2020 06:49:14: #2 finished! INFO @ Wed, 22 Apr 2020 06:49:14: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 06:49:14: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 06:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10_model.r WARNING @ Wed, 22 Apr 2020 06:49:14: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:49:14: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 06:49:14: #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 06:49:14: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:49:20: 23000000 INFO @ Wed, 22 Apr 2020 06:49:27: 24000000 INFO @ Wed, 22 Apr 2020 06:49:35: 25000000 INFO @ Wed, 22 Apr 2020 06:49:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:49:43: 26000000 INFO @ Wed, 22 Apr 2020 06:49:43: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:49:43: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:49:43: #1 total tags in treatment: 26088759 INFO @ Wed, 22 Apr 2020 06:49:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:49:43: #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 06:49:44: #1 tags after filtering in treatment: 26088645 INFO @ Wed, 22 Apr 2020 06:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:49:44: #1 finished! INFO @ Wed, 22 Apr 2020 06:49:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:49:46: #2 number of paired peaks: 7126 INFO @ Wed, 22 Apr 2020 06:49:46: start model_add_line... INFO @ Wed, 22 Apr 2020 06:49:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:49:47: end of X-cor INFO @ Wed, 22 Apr 2020 06:49:47: #2 finished! INFO @ Wed, 22 Apr 2020 06:49:47: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 06:49:47: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 06:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20_model.r WARNING @ Wed, 22 Apr 2020 06:49:47: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:49:47: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 06:49:47: #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 06:49:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.05_summits.bed INFO @ Wed, 22 Apr 2020 06:50:09: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (3257 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:50:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.10_summits.bed INFO @ Wed, 22 Apr 2020 06:50:41: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1270 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:50:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299296/SRX5299296.20_summits.bed INFO @ Wed, 22 Apr 2020 06:51:12: Done! pass1 - making usageList (37 chroms): 0 millis pass2 - checking and writing primary data (542 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。