Job ID = 5720714 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,469,311 reads read : 8,469,311 reads written : 8,469,311 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: 00:00:00 Multiseed full-index search: 00:01:50 8469311 reads; of these: 8469311 (100.00%) were unpaired; of these: 304270 (3.59%) aligned 0 times 7380364 (87.14%) aligned exactly 1 time 784677 (9.26%) aligned >1 times 96.41% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1543215 / 8165041 = 0.1890 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 @ Thu, 16 Apr 2020 01:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:09:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:28: 1000000 INFO @ Thu, 16 Apr 2020 01:09:34: 2000000 INFO @ Thu, 16 Apr 2020 01:09:39: 3000000 INFO @ Thu, 16 Apr 2020 01:09:45: 4000000 INFO @ Thu, 16 Apr 2020 01:09:51: 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 @ Thu, 16 Apr 2020 01:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:09:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:57: 6000000 INFO @ Thu, 16 Apr 2020 01:10:00: 1000000 INFO @ Thu, 16 Apr 2020 01:10:01: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:10:01: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:10:01: #1 total tags in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:10:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:10:01: #1 tags after filtering in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:01: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:02: #2 number of paired peaks: 8104 INFO @ Thu, 16 Apr 2020 01:10:02: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:02: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:02: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:02: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:02: #2 predicted fragment length is 158 bps INFO @ Thu, 16 Apr 2020 01:10:02: #2 alternative fragment length(s) may be 158 bps INFO @ Thu, 16 Apr 2020 01:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05_model.r INFO @ Thu, 16 Apr 2020 01:10:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:10:08: 2000000 INFO @ Thu, 16 Apr 2020 01:10:15: 3000000 INFO @ Thu, 16 Apr 2020 01:10:20: #3 Call peaks for each chromosome... 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 @ Thu, 16 Apr 2020 01:10:22: 4000000 INFO @ Thu, 16 Apr 2020 01:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:10:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.05_summits.bed INFO @ Thu, 16 Apr 2020 01:10:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6901 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:10:30: 5000000 INFO @ Thu, 16 Apr 2020 01:10:30: 1000000 INFO @ Thu, 16 Apr 2020 01:10:37: 2000000 INFO @ Thu, 16 Apr 2020 01:10:37: 6000000 INFO @ Thu, 16 Apr 2020 01:10:42: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:10:42: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:10:42: #1 total tags in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:10:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:10:42: #1 tags after filtering in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:10:42: #1 finished! INFO @ Thu, 16 Apr 2020 01:10:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:10:43: #2 number of paired peaks: 8104 INFO @ Thu, 16 Apr 2020 01:10:43: start model_add_line... INFO @ Thu, 16 Apr 2020 01:10:43: start X-correlation... INFO @ Thu, 16 Apr 2020 01:10:43: end of X-cor INFO @ Thu, 16 Apr 2020 01:10:43: #2 finished! INFO @ Thu, 16 Apr 2020 01:10:43: #2 predicted fragment length is 158 bps INFO @ Thu, 16 Apr 2020 01:10:43: #2 alternative fragment length(s) may be 158 bps INFO @ Thu, 16 Apr 2020 01:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10_model.r INFO @ Thu, 16 Apr 2020 01:10:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:10:44: 3000000 INFO @ Thu, 16 Apr 2020 01:10:50: 4000000 INFO @ Thu, 16 Apr 2020 01:10:56: 5000000 INFO @ Thu, 16 Apr 2020 01:11:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:03: 6000000 INFO @ Thu, 16 Apr 2020 01:11:06: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:11:06: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:11:06: #1 total tags in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:11:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:11:06: #1 tags after filtering in treatment: 6621826 INFO @ Thu, 16 Apr 2020 01:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:06: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.10_summits.bed INFO @ Thu, 16 Apr 2020 01:11:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6302 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:07: #2 number of paired peaks: 8104 INFO @ Thu, 16 Apr 2020 01:11:07: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:07: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:07: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:07: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:07: #2 predicted fragment length is 158 bps INFO @ Thu, 16 Apr 2020 01:11:07: #2 alternative fragment length(s) may be 158 bps INFO @ Thu, 16 Apr 2020 01:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20_model.r INFO @ Thu, 16 Apr 2020 01:11:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:11:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158178/SRX4158178.20_summits.bed INFO @ Thu, 16 Apr 2020 01:11:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5446 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。