Job ID = 6452381 SRX = SRX013021 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:22:47 prefetch.2.10.7: 1) Downloading 'SRR030287'... 2020-06-21T07:22:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:23:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:23:57 prefetch.2.10.7: 'SRR030287' is valid 2020-06-21T07:23:57 prefetch.2.10.7: 1) 'SRR030287' was downloaded successfully Read 7437147 spots for SRR030287/SRR030287.sra Written 7437147 spots for SRR030287/SRR030287.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: 00:00:57 7437147 reads; of these: 7437147 (100.00%) were unpaired; of these: 3119683 (41.95%) aligned 0 times 3907048 (52.53%) aligned exactly 1 time 410416 (5.52%) aligned >1 times 58.05% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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_rmdupse_core] 1005962 / 4317464 = 0.2330 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 16:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.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 16:26:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:26:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:26:41: 1000000 INFO @ Sun, 21 Jun 2020 16:26:45: 2000000 INFO @ Sun, 21 Jun 2020 16:26:50: 3000000 INFO @ Sun, 21 Jun 2020 16:26:51: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:26:51: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:26:51: #1 total tags in treatment: 3311502 INFO @ Sun, 21 Jun 2020 16:26:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:26:51: #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 16:26:51: #1 tags after filtering in treatment: 3311199 INFO @ Sun, 21 Jun 2020 16:26:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:26:51: #1 finished! INFO @ Sun, 21 Jun 2020 16:26:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:26:52: #2 number of paired peaks: 8604 INFO @ Sun, 21 Jun 2020 16:26:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:26:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:26:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:26:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:26:52: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 16:26:52: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 16:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05_model.r INFO @ Sun, 21 Jun 2020 16:26:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:27:02: #3 Call peaks for each chromosome... 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 16:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.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 16:27:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.05_summits.bed INFO @ Sun, 21 Jun 2020 16:27:06: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (6064 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:27:11: 1000000 INFO @ Sun, 21 Jun 2020 16:27:15: 2000000 INFO @ Sun, 21 Jun 2020 16:27:20: 3000000 INFO @ Sun, 21 Jun 2020 16:27:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:27:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:27:21: #1 total tags in treatment: 3311502 INFO @ Sun, 21 Jun 2020 16:27:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:27:21: #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 16:27:22: #1 tags after filtering in treatment: 3311199 INFO @ Sun, 21 Jun 2020 16:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:27:22: #1 finished! INFO @ Sun, 21 Jun 2020 16:27:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:27:22: #2 number of paired peaks: 8604 INFO @ Sun, 21 Jun 2020 16:27:22: start model_add_line... INFO @ Sun, 21 Jun 2020 16:27:22: start X-correlation... INFO @ Sun, 21 Jun 2020 16:27:22: end of X-cor INFO @ Sun, 21 Jun 2020 16:27:22: #2 finished! INFO @ Sun, 21 Jun 2020 16:27:22: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 16:27:22: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 16:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10_model.r INFO @ Sun, 21 Jun 2020 16:27:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:27:32: #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 @ Sun, 21 Jun 2020 16:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.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 16:27:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.10_summits.bed INFO @ Sun, 21 Jun 2020 16:27:37: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (5702 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:27:41: 1000000 INFO @ Sun, 21 Jun 2020 16:27:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:27:50: 3000000 INFO @ Sun, 21 Jun 2020 16:27:52: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:27:52: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:27:52: #1 total tags in treatment: 3311502 INFO @ Sun, 21 Jun 2020 16:27:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:27:52: #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 16:27:52: #1 tags after filtering in treatment: 3311199 INFO @ Sun, 21 Jun 2020 16:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:27:52: #1 finished! INFO @ Sun, 21 Jun 2020 16:27:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:27:53: #2 number of paired peaks: 8604 INFO @ Sun, 21 Jun 2020 16:27:53: start model_add_line... INFO @ Sun, 21 Jun 2020 16:27:53: start X-correlation... INFO @ Sun, 21 Jun 2020 16:27:53: end of X-cor INFO @ Sun, 21 Jun 2020 16:27:53: #2 finished! INFO @ Sun, 21 Jun 2020 16:27:53: #2 predicted fragment length is 177 bps INFO @ Sun, 21 Jun 2020 16:27:53: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 21 Jun 2020 16:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20_model.r INFO @ Sun, 21 Jun 2020 16:27:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:27:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:28:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013021/SRX013021.20_summits.bed INFO @ Sun, 21 Jun 2020 16:28:08: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (4971 records, 4 fields): 7 millis CompletedMACS2peakCalling