Job ID = 5790642 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,730,440 reads read : 81,460,880 reads written : 40,730,440 reads 0-length : 40,730,440 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:41 40730440 reads; of these: 40730440 (100.00%) were unpaired; of these: 4192718 (10.29%) aligned 0 times 33525045 (82.31%) aligned exactly 1 time 3012677 (7.40%) aligned >1 times 89.71% overall alignment rate Time searching: 00:30:43 Overall time: 00:30:43 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 16 files... [bam_rmdupse_core] 18082908 / 36537722 = 0.4949 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 05:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.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 05:46:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:47:04: 1000000 INFO @ Wed, 22 Apr 2020 05:47:10: 2000000 INFO @ Wed, 22 Apr 2020 05:47:17: 3000000 INFO @ Wed, 22 Apr 2020 05:47:23: 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 @ Wed, 22 Apr 2020 05:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.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 05:47:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:47:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:47:29: 5000000 INFO @ Wed, 22 Apr 2020 05:47:35: 1000000 INFO @ Wed, 22 Apr 2020 05:47:36: 6000000 INFO @ Wed, 22 Apr 2020 05:47:42: 2000000 INFO @ Wed, 22 Apr 2020 05:47:43: 7000000 INFO @ Wed, 22 Apr 2020 05:47:50: 3000000 INFO @ Wed, 22 Apr 2020 05:47:50: 8000000 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 05:47:56: 9000000 INFO @ Wed, 22 Apr 2020 05:47:57: 4000000 INFO @ Wed, 22 Apr 2020 05:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.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 05:47:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:47:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:48:04: 10000000 INFO @ Wed, 22 Apr 2020 05:48:05: 1000000 INFO @ Wed, 22 Apr 2020 05:48:05: 5000000 INFO @ Wed, 22 Apr 2020 05:48:11: 11000000 INFO @ Wed, 22 Apr 2020 05:48:11: 2000000 INFO @ Wed, 22 Apr 2020 05:48:13: 6000000 INFO @ Wed, 22 Apr 2020 05:48:17: 12000000 INFO @ Wed, 22 Apr 2020 05:48:18: 3000000 INFO @ Wed, 22 Apr 2020 05:48:20: 7000000 INFO @ Wed, 22 Apr 2020 05:48:24: 13000000 INFO @ Wed, 22 Apr 2020 05:48:24: 4000000 INFO @ Wed, 22 Apr 2020 05:48:28: 8000000 INFO @ Wed, 22 Apr 2020 05:48:31: 14000000 INFO @ Wed, 22 Apr 2020 05:48:31: 5000000 INFO @ Wed, 22 Apr 2020 05:48:36: 9000000 INFO @ Wed, 22 Apr 2020 05:48:38: 6000000 INFO @ Wed, 22 Apr 2020 05:48:38: 15000000 INFO @ Wed, 22 Apr 2020 05:48:43: 10000000 INFO @ Wed, 22 Apr 2020 05:48:44: 7000000 INFO @ Wed, 22 Apr 2020 05:48:45: 16000000 INFO @ Wed, 22 Apr 2020 05:48:50: 11000000 INFO @ Wed, 22 Apr 2020 05:48:51: 8000000 INFO @ Wed, 22 Apr 2020 05:48:51: 17000000 INFO @ Wed, 22 Apr 2020 05:48:58: 9000000 INFO @ Wed, 22 Apr 2020 05:48:58: 12000000 INFO @ Wed, 22 Apr 2020 05:48:58: 18000000 INFO @ Wed, 22 Apr 2020 05:49:01: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:49:01: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:49:01: #1 total tags in treatment: 18454814 INFO @ Wed, 22 Apr 2020 05:49:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:49:01: #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 05:49:02: #1 tags after filtering in treatment: 18454557 INFO @ Wed, 22 Apr 2020 05:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:49:02: #1 finished! INFO @ Wed, 22 Apr 2020 05:49:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:49:04: #2 number of paired peaks: 19062 INFO @ Wed, 22 Apr 2020 05:49:04: start model_add_line... INFO @ Wed, 22 Apr 2020 05:49:04: start X-correlation... INFO @ Wed, 22 Apr 2020 05:49:04: end of X-cor INFO @ Wed, 22 Apr 2020 05:49:04: #2 finished! INFO @ Wed, 22 Apr 2020 05:49:04: #2 predicted fragment length is 178 bps INFO @ Wed, 22 Apr 2020 05:49:04: #2 alternative fragment length(s) may be 178 bps INFO @ Wed, 22 Apr 2020 05:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05_model.r WARNING @ Wed, 22 Apr 2020 05:49:04: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:49:04: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Wed, 22 Apr 2020 05:49:04: #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 05:49:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:49:04: 10000000 INFO @ Wed, 22 Apr 2020 05:49:05: 13000000 INFO @ Wed, 22 Apr 2020 05:49:11: 11000000 INFO @ Wed, 22 Apr 2020 05:49:12: 14000000 INFO @ Wed, 22 Apr 2020 05:49:17: 12000000 INFO @ Wed, 22 Apr 2020 05:49:20: 15000000 INFO @ Wed, 22 Apr 2020 05:49:24: 13000000 INFO @ Wed, 22 Apr 2020 05:49:27: 16000000 INFO @ Wed, 22 Apr 2020 05:49:30: 14000000 INFO @ Wed, 22 Apr 2020 05:49:34: 17000000 INFO @ Wed, 22 Apr 2020 05:49:36: 15000000 INFO @ Wed, 22 Apr 2020 05:49:41: 18000000 INFO @ Wed, 22 Apr 2020 05:49:43: 16000000 INFO @ Wed, 22 Apr 2020 05:49:45: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:49:45: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:49:45: #1 total tags in treatment: 18454814 INFO @ Wed, 22 Apr 2020 05:49:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:49:45: #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 05:49:45: #1 tags after filtering in treatment: 18454557 INFO @ Wed, 22 Apr 2020 05:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:49:45: #1 finished! INFO @ Wed, 22 Apr 2020 05:49:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:49:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:47: #2 number of paired peaks: 19062 INFO @ Wed, 22 Apr 2020 05:49:47: start model_add_line... INFO @ Wed, 22 Apr 2020 05:49:47: start X-correlation... INFO @ Wed, 22 Apr 2020 05:49:47: end of X-cor INFO @ Wed, 22 Apr 2020 05:49:47: #2 finished! INFO @ Wed, 22 Apr 2020 05:49:47: #2 predicted fragment length is 178 bps INFO @ Wed, 22 Apr 2020 05:49:47: #2 alternative fragment length(s) may be 178 bps INFO @ Wed, 22 Apr 2020 05:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10_model.r WARNING @ Wed, 22 Apr 2020 05:49:47: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:49:47: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Wed, 22 Apr 2020 05:49:47: #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 05:49:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:49:49: 17000000 INFO @ Wed, 22 Apr 2020 05:49:55: 18000000 INFO @ Wed, 22 Apr 2020 05:49:58: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:49:58: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:49:58: #1 total tags in treatment: 18454814 INFO @ Wed, 22 Apr 2020 05:49:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:49:58: #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 05:49:59: #1 tags after filtering in treatment: 18454557 INFO @ Wed, 22 Apr 2020 05:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:49:59: #1 finished! INFO @ Wed, 22 Apr 2020 05:49:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:50:00: #2 number of paired peaks: 19062 INFO @ Wed, 22 Apr 2020 05:50:00: start model_add_line... INFO @ Wed, 22 Apr 2020 05:50:01: start X-correlation... INFO @ Wed, 22 Apr 2020 05:50:01: end of X-cor INFO @ Wed, 22 Apr 2020 05:50:01: #2 finished! INFO @ Wed, 22 Apr 2020 05:50:01: #2 predicted fragment length is 178 bps INFO @ Wed, 22 Apr 2020 05:50:01: #2 alternative fragment length(s) may be 178 bps INFO @ Wed, 22 Apr 2020 05:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20_model.r WARNING @ Wed, 22 Apr 2020 05:50:01: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:50:01: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Wed, 22 Apr 2020 05:50:01: #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 05:50:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.05_summits.bed INFO @ Wed, 22 Apr 2020 05:50:08: Done! pass1 - making usageList (125 chroms): 4 millis pass2 - checking and writing primary data (23263 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:50:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:50:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.10_summits.bed INFO @ Wed, 22 Apr 2020 05:50:46: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (21183 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 05:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299285/SRX5299285.20_summits.bed INFO @ Wed, 22 Apr 2020 05:50:59: Done! pass1 - making usageList (102 chroms): 3 millis pass2 - checking and writing primary data (19188 records, 4 fields): 21 millis CompletedMACS2peakCalling