Job ID = 6454360 SRX = SRX201896 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:16:54 prefetch.2.10.7: 1) Downloading 'SRR609686'... 2020-06-21T09:16:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:31:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:31:05 prefetch.2.10.7: 1) 'SRR609686' was downloaded successfully Read 40933550 spots for SRR609686/SRR609686.sra Written 40933550 spots for SRR609686/SRR609686.sra 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: 00:19:19 40933550 reads; of these: 40933550 (100.00%) were unpaired; of these: 1206828 (2.95%) aligned 0 times 31806274 (77.70%) aligned exactly 1 time 7920448 (19.35%) aligned >1 times 97.05% overall alignment rate Time searching: 00:19:19 Overall time: 00:19:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 31294456 / 39726722 = 0.7877 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 @ Sun, 21 Jun 2020 19:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.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 @ Sun, 21 Jun 2020 19:04:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:06: 1000000 INFO @ Sun, 21 Jun 2020 19:04:12: 2000000 INFO @ Sun, 21 Jun 2020 19:04:17: 3000000 INFO @ Sun, 21 Jun 2020 19:04:23: 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 @ Sun, 21 Jun 2020 19:04:29: 5000000 INFO @ Sun, 21 Jun 2020 19:04:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.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 @ Sun, 21 Jun 2020 19:04:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:35: 6000000 INFO @ Sun, 21 Jun 2020 19:04:36: 1000000 INFO @ Sun, 21 Jun 2020 19:04:41: 7000000 INFO @ Sun, 21 Jun 2020 19:04:42: 2000000 INFO @ Sun, 21 Jun 2020 19:04:48: 8000000 INFO @ Sun, 21 Jun 2020 19:04:48: 3000000 INFO @ Sun, 21 Jun 2020 19:04:51: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:04:51: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:04:51: #1 total tags in treatment: 8432266 INFO @ Sun, 21 Jun 2020 19:04:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:04:51: #1 tags after filtering in treatment: 8432082 INFO @ Sun, 21 Jun 2020 19:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:52: #2 number of paired peaks: 7469 INFO @ Sun, 21 Jun 2020 19:04:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:52: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 19:04:52: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 19:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05_model.r INFO @ Sun, 21 Jun 2020 19:04:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:54: 4000000 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 @ Sun, 21 Jun 2020 19:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.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 @ Sun, 21 Jun 2020 19:05:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:00: 5000000 INFO @ Sun, 21 Jun 2020 19:05:07: 6000000 INFO @ Sun, 21 Jun 2020 19:05:07: 1000000 INFO @ Sun, 21 Jun 2020 19:05:13: 7000000 INFO @ Sun, 21 Jun 2020 19:05:15: 2000000 INFO @ Sun, 21 Jun 2020 19:05:19: 8000000 INFO @ Sun, 21 Jun 2020 19:05:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:23: 3000000 INFO @ Sun, 21 Jun 2020 19:05:23: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:05:23: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:05:23: #1 total tags in treatment: 8432266 INFO @ Sun, 21 Jun 2020 19:05:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:05:23: #1 tags after filtering in treatment: 8432082 INFO @ Sun, 21 Jun 2020 19:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:24: #2 number of paired peaks: 7469 INFO @ Sun, 21 Jun 2020 19:05:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:24: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 19:05:24: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 19:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10_model.r INFO @ Sun, 21 Jun 2020 19:05:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:30: 4000000 INFO @ Sun, 21 Jun 2020 19:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:35: Done! pass1 - making usageList (230 chroms): 2 millis pass2 - checking and writing primary data (9421 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:37: 5000000 INFO @ Sun, 21 Jun 2020 19:05:44: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:51: 7000000 INFO @ Sun, 21 Jun 2020 19:05:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:58: 8000000 INFO @ Sun, 21 Jun 2020 19:06:02: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:06:02: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:06:02: #1 total tags in treatment: 8432266 INFO @ Sun, 21 Jun 2020 19:06:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:06:02: #1 tags after filtering in treatment: 8432082 INFO @ Sun, 21 Jun 2020 19:06:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:03: #2 number of paired peaks: 7469 INFO @ Sun, 21 Jun 2020 19:06:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:04: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 19:06:04: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 19:06:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20_model.r INFO @ Sun, 21 Jun 2020 19:06:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.10_summits.bed INFO @ Sun, 21 Jun 2020 19:06:05: Done! pass1 - making usageList (168 chroms): 2 millis pass2 - checking and writing primary data (7696 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201896/SRX201896.20_summits.bed INFO @ Sun, 21 Jun 2020 19:06:46: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (6029 records, 4 fields): 11 millis CompletedMACS2peakCalling