Job ID = 5790669 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,236,756 reads read : 25,236,756 reads written : 25,236,756 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:36 25236756 reads; of these: 25236756 (100.00%) were unpaired; of these: 5806525 (23.01%) aligned 0 times 11522164 (45.66%) aligned exactly 1 time 7908067 (31.34%) aligned >1 times 76.99% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 904416 / 19430231 = 0.0465 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 06:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.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 06:13:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:13:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:14:04: 1000000 INFO @ Wed, 22 Apr 2020 06:14:09: 2000000 INFO @ Wed, 22 Apr 2020 06:14:14: 3000000 INFO @ Wed, 22 Apr 2020 06:14:19: 4000000 INFO @ Wed, 22 Apr 2020 06:14:24: 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 06:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.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 06:14:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:14:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:14:29: 6000000 INFO @ Wed, 22 Apr 2020 06:14:34: 1000000 INFO @ Wed, 22 Apr 2020 06:14:35: 7000000 INFO @ Wed, 22 Apr 2020 06:14:39: 2000000 INFO @ Wed, 22 Apr 2020 06:14:40: 8000000 INFO @ Wed, 22 Apr 2020 06:14:44: 3000000 INFO @ Wed, 22 Apr 2020 06:14:45: 9000000 INFO @ Wed, 22 Apr 2020 06:14:49: 4000000 INFO @ Wed, 22 Apr 2020 06:14:50: 10000000 INFO @ Wed, 22 Apr 2020 06:14:55: 5000000 INFO @ Wed, 22 Apr 2020 06:14:56: 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 @ Wed, 22 Apr 2020 06:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.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 06:14:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:14:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:15:00: 6000000 INFO @ Wed, 22 Apr 2020 06:15:01: 12000000 INFO @ Wed, 22 Apr 2020 06:15:04: 1000000 INFO @ Wed, 22 Apr 2020 06:15:05: 7000000 INFO @ Wed, 22 Apr 2020 06:15:06: 13000000 INFO @ Wed, 22 Apr 2020 06:15:09: 2000000 INFO @ Wed, 22 Apr 2020 06:15:10: 8000000 INFO @ Wed, 22 Apr 2020 06:15:11: 14000000 INFO @ Wed, 22 Apr 2020 06:15:15: 3000000 INFO @ Wed, 22 Apr 2020 06:15:16: 9000000 INFO @ Wed, 22 Apr 2020 06:15:17: 15000000 INFO @ Wed, 22 Apr 2020 06:15:20: 4000000 INFO @ Wed, 22 Apr 2020 06:15:21: 10000000 INFO @ Wed, 22 Apr 2020 06:15:22: 16000000 INFO @ Wed, 22 Apr 2020 06:15:25: 5000000 INFO @ Wed, 22 Apr 2020 06:15:26: 11000000 INFO @ Wed, 22 Apr 2020 06:15:27: 17000000 INFO @ Wed, 22 Apr 2020 06:15:30: 6000000 INFO @ Wed, 22 Apr 2020 06:15:31: 12000000 INFO @ Wed, 22 Apr 2020 06:15:33: 18000000 INFO @ Wed, 22 Apr 2020 06:15:36: 7000000 INFO @ Wed, 22 Apr 2020 06:15:36: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:15:36: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:15:36: #1 total tags in treatment: 18525815 INFO @ Wed, 22 Apr 2020 06:15:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:15:36: #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 06:15:36: #1 tags after filtering in treatment: 18525691 INFO @ Wed, 22 Apr 2020 06:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:15:36: #1 finished! INFO @ Wed, 22 Apr 2020 06:15:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:15:36: 13000000 INFO @ Wed, 22 Apr 2020 06:15:38: #2 number of paired peaks: 5908 INFO @ Wed, 22 Apr 2020 06:15:38: start model_add_line... INFO @ Wed, 22 Apr 2020 06:15:38: start X-correlation... INFO @ Wed, 22 Apr 2020 06:15:38: end of X-cor INFO @ Wed, 22 Apr 2020 06:15:38: #2 finished! INFO @ Wed, 22 Apr 2020 06:15:38: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:15:38: #2 alternative fragment length(s) may be 37,129,217,366,396 bps INFO @ Wed, 22 Apr 2020 06:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05_model.r WARNING @ Wed, 22 Apr 2020 06:15:38: #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 06:15:38: #2 You may need to consider one of the other alternative d(s): 37,129,217,366,396 WARNING @ Wed, 22 Apr 2020 06:15:38: #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 06:15:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:15:41: 8000000 INFO @ Wed, 22 Apr 2020 06:15:42: 14000000 INFO @ Wed, 22 Apr 2020 06:15:46: 9000000 INFO @ Wed, 22 Apr 2020 06:15:47: 15000000 INFO @ Wed, 22 Apr 2020 06:15:51: 10000000 INFO @ Wed, 22 Apr 2020 06:15:52: 16000000 INFO @ Wed, 22 Apr 2020 06:15:56: 11000000 INFO @ Wed, 22 Apr 2020 06:15:57: 17000000 INFO @ Wed, 22 Apr 2020 06:16:02: 12000000 INFO @ Wed, 22 Apr 2020 06:16:03: 18000000 INFO @ Wed, 22 Apr 2020 06:16:06: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:16:06: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:16:06: #1 total tags in treatment: 18525815 INFO @ Wed, 22 Apr 2020 06:16:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:16:06: #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 06:16:06: #1 tags after filtering in treatment: 18525691 INFO @ Wed, 22 Apr 2020 06:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:16:06: #1 finished! INFO @ Wed, 22 Apr 2020 06:16:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:16:07: 13000000 INFO @ Wed, 22 Apr 2020 06:16:08: #2 number of paired peaks: 5908 INFO @ Wed, 22 Apr 2020 06:16:08: start model_add_line... INFO @ Wed, 22 Apr 2020 06:16:08: start X-correlation... INFO @ Wed, 22 Apr 2020 06:16:08: end of X-cor INFO @ Wed, 22 Apr 2020 06:16:08: #2 finished! INFO @ Wed, 22 Apr 2020 06:16:08: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:16:08: #2 alternative fragment length(s) may be 37,129,217,366,396 bps INFO @ Wed, 22 Apr 2020 06:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10_model.r WARNING @ Wed, 22 Apr 2020 06:16:08: #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 06:16:08: #2 You may need to consider one of the other alternative d(s): 37,129,217,366,396 WARNING @ Wed, 22 Apr 2020 06:16:08: #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 06:16:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:16:12: 14000000 INFO @ Wed, 22 Apr 2020 06:16:17: 15000000 INFO @ Wed, 22 Apr 2020 06:16:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:16:22: 16000000 INFO @ Wed, 22 Apr 2020 06:16:27: 17000000 INFO @ Wed, 22 Apr 2020 06:16:33: 18000000 INFO @ Wed, 22 Apr 2020 06:16:36: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:16:36: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:16:36: #1 total tags in treatment: 18525815 INFO @ Wed, 22 Apr 2020 06:16:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:16:36: #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 06:16:36: #1 tags after filtering in treatment: 18525691 INFO @ Wed, 22 Apr 2020 06:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:16:36: #1 finished! INFO @ Wed, 22 Apr 2020 06:16:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:16:38: #2 number of paired peaks: 5908 INFO @ Wed, 22 Apr 2020 06:16:38: start model_add_line... INFO @ Wed, 22 Apr 2020 06:16:38: start X-correlation... INFO @ Wed, 22 Apr 2020 06:16:38: end of X-cor INFO @ Wed, 22 Apr 2020 06:16:38: #2 finished! INFO @ Wed, 22 Apr 2020 06:16:38: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:16:38: #2 alternative fragment length(s) may be 37,129,217,366,396 bps INFO @ Wed, 22 Apr 2020 06:16:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20_model.r WARNING @ Wed, 22 Apr 2020 06:16:38: #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 06:16:38: #2 You may need to consider one of the other alternative d(s): 37,129,217,366,396 WARNING @ Wed, 22 Apr 2020 06:16:38: #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 06:16:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:16:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.05_summits.bed INFO @ Wed, 22 Apr 2020 06:16:40: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2045 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:16:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.10_summits.bed INFO @ Wed, 22 Apr 2020 06:17:10: Done! pass1 - making usageList (39 chroms): 0 millis pass2 - checking and writing primary data (1168 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:17:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:17:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761704/SRX5761704.20_summits.bed INFO @ Wed, 22 Apr 2020 06:17:40: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (553 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。