Job ID = 5790676 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,812,925 reads read : 20,812,925 reads written : 20,812,925 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:16 20812925 reads; of these: 20812925 (100.00%) were unpaired; of these: 3603232 (17.31%) aligned 0 times 10381744 (49.88%) aligned exactly 1 time 6827949 (32.81%) aligned >1 times 82.69% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 1275143 / 17209693 = 0.0741 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 06:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.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 06:12:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:12:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:12:24: 1000000 INFO @ Wed, 22 Apr 2020 06:12:29: 2000000 INFO @ Wed, 22 Apr 2020 06:12:34: 3000000 INFO @ Wed, 22 Apr 2020 06:12:38: 4000000 INFO @ Wed, 22 Apr 2020 06:12:43: 5000000 INFO @ Wed, 22 Apr 2020 06:12:47: 6000000 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 06:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.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 06:12:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:12:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:12:52: 7000000 INFO @ Wed, 22 Apr 2020 06:12:55: 1000000 INFO @ Wed, 22 Apr 2020 06:12:56: 8000000 INFO @ Wed, 22 Apr 2020 06:12:59: 2000000 INFO @ Wed, 22 Apr 2020 06:13:01: 9000000 INFO @ Wed, 22 Apr 2020 06:13:04: 3000000 INFO @ Wed, 22 Apr 2020 06:13:06: 10000000 INFO @ Wed, 22 Apr 2020 06:13:08: 4000000 INFO @ Wed, 22 Apr 2020 06:13:10: 11000000 INFO @ Wed, 22 Apr 2020 06:13:13: 5000000 INFO @ Wed, 22 Apr 2020 06:13:15: 12000000 INFO @ Wed, 22 Apr 2020 06:13:18: 6000000 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 06:13:20: 13000000 INFO @ Wed, 22 Apr 2020 06:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.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 06:13:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:13:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:13:22: 7000000 INFO @ Wed, 22 Apr 2020 06:13:24: 14000000 INFO @ Wed, 22 Apr 2020 06:13:25: 1000000 INFO @ Wed, 22 Apr 2020 06:13:27: 8000000 INFO @ Wed, 22 Apr 2020 06:13:29: 15000000 INFO @ Wed, 22 Apr 2020 06:13:31: 2000000 INFO @ Wed, 22 Apr 2020 06:13:32: 9000000 INFO @ Wed, 22 Apr 2020 06:13:34: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:13:34: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:13:34: #1 total tags in treatment: 15934550 INFO @ Wed, 22 Apr 2020 06:13:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:13:34: #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 06:13:34: #1 tags after filtering in treatment: 15934417 INFO @ Wed, 22 Apr 2020 06:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:13:34: #1 finished! INFO @ Wed, 22 Apr 2020 06:13:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:13:36: #2 number of paired peaks: 12351 INFO @ Wed, 22 Apr 2020 06:13:36: start model_add_line... INFO @ Wed, 22 Apr 2020 06:13:36: start X-correlation... INFO @ Wed, 22 Apr 2020 06:13:36: end of X-cor INFO @ Wed, 22 Apr 2020 06:13:36: #2 finished! INFO @ Wed, 22 Apr 2020 06:13:36: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:13:36: #2 alternative fragment length(s) may be 40,143 bps INFO @ Wed, 22 Apr 2020 06:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05_model.r INFO @ Wed, 22 Apr 2020 06:13:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:13:36: 3000000 INFO @ Wed, 22 Apr 2020 06:13:37: 10000000 INFO @ Wed, 22 Apr 2020 06:13:42: 11000000 INFO @ Wed, 22 Apr 2020 06:13:42: 4000000 INFO @ Wed, 22 Apr 2020 06:13:46: 12000000 INFO @ Wed, 22 Apr 2020 06:13:48: 5000000 INFO @ Wed, 22 Apr 2020 06:13:51: 13000000 INFO @ Wed, 22 Apr 2020 06:13:54: 6000000 INFO @ Wed, 22 Apr 2020 06:13:56: 14000000 INFO @ Wed, 22 Apr 2020 06:14:00: 7000000 INFO @ Wed, 22 Apr 2020 06:14:00: 15000000 INFO @ Wed, 22 Apr 2020 06:14:05: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:14:05: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:14:05: #1 total tags in treatment: 15934550 INFO @ Wed, 22 Apr 2020 06:14:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:14:05: #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 06:14:05: #1 tags after filtering in treatment: 15934417 INFO @ Wed, 22 Apr 2020 06:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:14:05: #1 finished! INFO @ Wed, 22 Apr 2020 06:14:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:14:06: 8000000 INFO @ Wed, 22 Apr 2020 06:14:07: #2 number of paired peaks: 12351 INFO @ Wed, 22 Apr 2020 06:14:07: start model_add_line... INFO @ Wed, 22 Apr 2020 06:14:07: start X-correlation... INFO @ Wed, 22 Apr 2020 06:14:07: end of X-cor INFO @ Wed, 22 Apr 2020 06:14:07: #2 finished! INFO @ Wed, 22 Apr 2020 06:14:07: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:14:07: #2 alternative fragment length(s) may be 40,143 bps INFO @ Wed, 22 Apr 2020 06:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10_model.r INFO @ Wed, 22 Apr 2020 06:14:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:14:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:14:12: 9000000 INFO @ Wed, 22 Apr 2020 06:14:18: 10000000 INFO @ Wed, 22 Apr 2020 06:14:24: 11000000 INFO @ Wed, 22 Apr 2020 06:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.05_summits.bed INFO @ Wed, 22 Apr 2020 06:14:30: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (3508 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:14:30: 12000000 INFO @ Wed, 22 Apr 2020 06:14:36: 13000000 INFO @ Wed, 22 Apr 2020 06:14:42: 14000000 INFO @ Wed, 22 Apr 2020 06:14:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:14:47: 15000000 INFO @ Wed, 22 Apr 2020 06:14:53: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:14:53: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:14:53: #1 total tags in treatment: 15934550 INFO @ Wed, 22 Apr 2020 06:14:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:14:53: #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 06:14:53: #1 tags after filtering in treatment: 15934417 INFO @ Wed, 22 Apr 2020 06:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:14:53: #1 finished! INFO @ Wed, 22 Apr 2020 06:14:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:14:55: #2 number of paired peaks: 12351 INFO @ Wed, 22 Apr 2020 06:14:55: start model_add_line... INFO @ Wed, 22 Apr 2020 06:14:55: start X-correlation... INFO @ Wed, 22 Apr 2020 06:14:55: end of X-cor INFO @ Wed, 22 Apr 2020 06:14:55: #2 finished! INFO @ Wed, 22 Apr 2020 06:14:55: #2 predicted fragment length is 143 bps INFO @ Wed, 22 Apr 2020 06:14:55: #2 alternative fragment length(s) may be 40,143 bps INFO @ Wed, 22 Apr 2020 06:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20_model.r INFO @ Wed, 22 Apr 2020 06:14:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:15:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:15:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:15:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.10_summits.bed INFO @ Wed, 22 Apr 2020 06:15:04: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:15:32: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:15:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:15:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:15:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761711/SRX5761711.20_summits.bed INFO @ Wed, 22 Apr 2020 06:15:52: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (342 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。