Job ID = 5790684 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,349,281 reads read : 24,349,281 reads written : 24,349,281 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: 00:00:01 Multiseed full-index search: 00:08:58 24349281 reads; of these: 24349281 (100.00%) were unpaired; of these: 3540762 (14.54%) aligned 0 times 11377653 (46.73%) aligned exactly 1 time 9430866 (38.73%) aligned >1 times 85.46% overall alignment rate Time searching: 00:08:59 Overall time: 00:08:59 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 8 files... [bam_rmdupse_core] 2258045 / 20808519 = 0.1085 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 06:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.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 06:20:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:20:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:20:39: 1000000 INFO @ Wed, 22 Apr 2020 06:20:44: 2000000 INFO @ Wed, 22 Apr 2020 06:20:49: 3000000 INFO @ Wed, 22 Apr 2020 06:20:54: 4000000 INFO @ Wed, 22 Apr 2020 06:20:58: 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 @ Wed, 22 Apr 2020 06:21:03: 6000000 INFO @ Wed, 22 Apr 2020 06:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.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 06:21:03: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:03: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:08: 7000000 INFO @ Wed, 22 Apr 2020 06:21:09: 1000000 INFO @ Wed, 22 Apr 2020 06:21:14: 8000000 INFO @ Wed, 22 Apr 2020 06:21:14: 2000000 INFO @ Wed, 22 Apr 2020 06:21:19: 9000000 INFO @ Wed, 22 Apr 2020 06:21:19: 3000000 INFO @ Wed, 22 Apr 2020 06:21:24: 10000000 INFO @ Wed, 22 Apr 2020 06:21:24: 4000000 INFO @ Wed, 22 Apr 2020 06:21:29: 11000000 INFO @ Wed, 22 Apr 2020 06:21:30: 5000000 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 06:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.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 06:21:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:34: 12000000 INFO @ Wed, 22 Apr 2020 06:21:35: 6000000 INFO @ Wed, 22 Apr 2020 06:21:40: 13000000 INFO @ Wed, 22 Apr 2020 06:21:40: 1000000 INFO @ Wed, 22 Apr 2020 06:21:40: 7000000 INFO @ Wed, 22 Apr 2020 06:21:45: 14000000 INFO @ Wed, 22 Apr 2020 06:21:46: 8000000 INFO @ Wed, 22 Apr 2020 06:21:46: 2000000 INFO @ Wed, 22 Apr 2020 06:21:51: 15000000 INFO @ Wed, 22 Apr 2020 06:21:51: 9000000 INFO @ Wed, 22 Apr 2020 06:21:52: 3000000 INFO @ Wed, 22 Apr 2020 06:21:56: 16000000 INFO @ Wed, 22 Apr 2020 06:21:57: 10000000 INFO @ Wed, 22 Apr 2020 06:21:59: 4000000 INFO @ Wed, 22 Apr 2020 06:22:02: 17000000 INFO @ Wed, 22 Apr 2020 06:22:02: 11000000 INFO @ Wed, 22 Apr 2020 06:22:05: 5000000 INFO @ Wed, 22 Apr 2020 06:22:07: 18000000 INFO @ Wed, 22 Apr 2020 06:22:08: 12000000 INFO @ Wed, 22 Apr 2020 06:22:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:10: #1 total tags in treatment: 18550474 INFO @ Wed, 22 Apr 2020 06:22:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:10: #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 06:22:11: #1 tags after filtering in treatment: 18550361 INFO @ Wed, 22 Apr 2020 06:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:11: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:11: 6000000 INFO @ Wed, 22 Apr 2020 06:22:13: #2 number of paired peaks: 6752 INFO @ Wed, 22 Apr 2020 06:22:13: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:13: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:13: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:13: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:13: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:22:13: #2 alternative fragment length(s) may be 37,125,215,395,551 bps INFO @ Wed, 22 Apr 2020 06:22:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05_model.r WARNING @ Wed, 22 Apr 2020 06:22:13: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:22:13: #2 You may need to consider one of the other alternative d(s): 37,125,215,395,551 WARNING @ Wed, 22 Apr 2020 06:22:13: #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 06:22:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:13: 13000000 INFO @ Wed, 22 Apr 2020 06:22:17: 7000000 INFO @ Wed, 22 Apr 2020 06:22:19: 14000000 INFO @ Wed, 22 Apr 2020 06:22:24: 8000000 INFO @ Wed, 22 Apr 2020 06:22:24: 15000000 INFO @ Wed, 22 Apr 2020 06:22:30: 16000000 INFO @ Wed, 22 Apr 2020 06:22:30: 9000000 INFO @ Wed, 22 Apr 2020 06:22:35: 17000000 INFO @ Wed, 22 Apr 2020 06:22:36: 10000000 INFO @ Wed, 22 Apr 2020 06:22:41: 18000000 INFO @ Wed, 22 Apr 2020 06:22:42: 11000000 INFO @ Wed, 22 Apr 2020 06:22:44: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:22:44: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:22:44: #1 total tags in treatment: 18550474 INFO @ Wed, 22 Apr 2020 06:22:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:22:44: #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 06:22:45: #1 tags after filtering in treatment: 18550361 INFO @ Wed, 22 Apr 2020 06:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:22:45: #1 finished! INFO @ Wed, 22 Apr 2020 06:22:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:22:46: #2 number of paired peaks: 6752 INFO @ Wed, 22 Apr 2020 06:22:46: start model_add_line... INFO @ Wed, 22 Apr 2020 06:22:47: start X-correlation... INFO @ Wed, 22 Apr 2020 06:22:47: end of X-cor INFO @ Wed, 22 Apr 2020 06:22:47: #2 finished! INFO @ Wed, 22 Apr 2020 06:22:47: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:22:47: #2 alternative fragment length(s) may be 37,125,215,395,551 bps INFO @ Wed, 22 Apr 2020 06:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10_model.r WARNING @ Wed, 22 Apr 2020 06:22:47: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:22:47: #2 You may need to consider one of the other alternative d(s): 37,125,215,395,551 WARNING @ Wed, 22 Apr 2020 06:22:47: #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 06:22:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:22:48: 12000000 INFO @ Wed, 22 Apr 2020 06:22:54: 13000000 INFO @ Wed, 22 Apr 2020 06:22:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:00: 14000000 INFO @ Wed, 22 Apr 2020 06:23:06: 15000000 INFO @ Wed, 22 Apr 2020 06:23:11: 16000000 INFO @ Wed, 22 Apr 2020 06:23:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.05_summits.bed INFO @ Wed, 22 Apr 2020 06:23:15: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (2342 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:23:17: 17000000 INFO @ Wed, 22 Apr 2020 06:23:23: 18000000 INFO @ Wed, 22 Apr 2020 06:23:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:23:26: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:23:26: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:23:26: #1 total tags in treatment: 18550474 INFO @ Wed, 22 Apr 2020 06:23:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:23:26: #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 06:23:27: #1 tags after filtering in treatment: 18550361 INFO @ Wed, 22 Apr 2020 06:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:23:27: #1 finished! INFO @ Wed, 22 Apr 2020 06:23:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:23:29: #2 number of paired peaks: 6752 INFO @ Wed, 22 Apr 2020 06:23:29: start model_add_line... INFO @ Wed, 22 Apr 2020 06:23:29: start X-correlation... INFO @ Wed, 22 Apr 2020 06:23:29: end of X-cor INFO @ Wed, 22 Apr 2020 06:23:29: #2 finished! INFO @ Wed, 22 Apr 2020 06:23:29: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:23:29: #2 alternative fragment length(s) may be 37,125,215,395,551 bps INFO @ Wed, 22 Apr 2020 06:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20_model.r WARNING @ Wed, 22 Apr 2020 06:23:29: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:23:29: #2 You may need to consider one of the other alternative d(s): 37,125,215,395,551 WARNING @ Wed, 22 Apr 2020 06:23:29: #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 06:23:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.10_summits.bed INFO @ Wed, 22 Apr 2020 06:23:47: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1233 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:24:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:24:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:24:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:24:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761716/SRX5761716.20_summits.bed INFO @ Wed, 22 Apr 2020 06:24:30: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (559 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。