Job ID = 6454916 SRX = SRX2592498 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:55 prefetch.2.10.7: 1) Downloading 'SRR5289775'... 2020-06-21T09:38:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:42:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:42:01 prefetch.2.10.7: 1) 'SRR5289775' was downloaded successfully Read 17469483 spots for SRR5289775/SRR5289775.sra Written 17469483 spots for SRR5289775/SRR5289775.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: 00:03:21 17469483 reads; of these: 17469483 (100.00%) were unpaired; of these: 4706699 (26.94%) aligned 0 times 11244956 (64.37%) aligned exactly 1 time 1517828 (8.69%) aligned >1 times 73.06% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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 8 files... [bam_rmdupse_core] 2785347 / 12762784 = 0.2182 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 18:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.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 18:49:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:56: 1000000 INFO @ Sun, 21 Jun 2020 18:50:02: 2000000 INFO @ Sun, 21 Jun 2020 18:50:09: 3000000 INFO @ Sun, 21 Jun 2020 18:50:15: 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 18:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.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 18:50:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:22: 5000000 INFO @ Sun, 21 Jun 2020 18:50:25: 1000000 INFO @ Sun, 21 Jun 2020 18:50:29: 6000000 INFO @ Sun, 21 Jun 2020 18:50:31: 2000000 INFO @ Sun, 21 Jun 2020 18:50:35: 7000000 INFO @ Sun, 21 Jun 2020 18:50:38: 3000000 INFO @ Sun, 21 Jun 2020 18:50:42: 8000000 INFO @ Sun, 21 Jun 2020 18:50:44: 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 18:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.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 18:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:49: 9000000 INFO @ Sun, 21 Jun 2020 18:50:50: 5000000 INFO @ Sun, 21 Jun 2020 18:50:56: 6000000 INFO @ Sun, 21 Jun 2020 18:50:56: 1000000 INFO @ Sun, 21 Jun 2020 18:50:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:57: #1 total tags in treatment: 9977437 INFO @ Sun, 21 Jun 2020 18:50:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:57: #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 18:50:57: #1 tags after filtering in treatment: 9977238 INFO @ Sun, 21 Jun 2020 18:50:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:58: #2 number of paired peaks: 8828 INFO @ Sun, 21 Jun 2020 18:50:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:58: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:50:58: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05_model.r INFO @ Sun, 21 Jun 2020 18:50:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:02: 7000000 INFO @ Sun, 21 Jun 2020 18:51:03: 2000000 INFO @ Sun, 21 Jun 2020 18:51:08: 8000000 INFO @ Sun, 21 Jun 2020 18:51:10: 3000000 INFO @ Sun, 21 Jun 2020 18:51:15: 9000000 INFO @ Sun, 21 Jun 2020 18:51:17: 4000000 INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:21: #1 total tags in treatment: 9977437 INFO @ Sun, 21 Jun 2020 18:51:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:21: #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 18:51:21: #1 tags after filtering in treatment: 9977238 INFO @ Sun, 21 Jun 2020 18:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:22: #2 number of paired peaks: 8828 INFO @ Sun, 21 Jun 2020 18:51:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:22: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:51:22: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10_model.r INFO @ Sun, 21 Jun 2020 18:51:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:23: 5000000 INFO @ Sun, 21 Jun 2020 18:51:30: 6000000 INFO @ Sun, 21 Jun 2020 18:51:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:51:36: 7000000 INFO @ Sun, 21 Jun 2020 18:51:43: 8000000 INFO @ Sun, 21 Jun 2020 18:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.05_summits.bed INFO @ Sun, 21 Jun 2020 18:51:44: Done! pass1 - making usageList (98 chroms): 2 millis pass2 - checking and writing primary data (10973 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:49: 9000000 INFO @ Sun, 21 Jun 2020 18:51:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:51:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:51:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:51:55: #1 total tags in treatment: 9977437 INFO @ Sun, 21 Jun 2020 18:51:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:55: #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 18:51:56: #1 tags after filtering in treatment: 9977238 INFO @ Sun, 21 Jun 2020 18:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:57: #2 number of paired peaks: 8828 INFO @ Sun, 21 Jun 2020 18:51:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:57: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 18:51:57: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 18:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20_model.r INFO @ Sun, 21 Jun 2020 18:51:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:06: Done! pass1 - making usageList (73 chroms): 2 millis pass2 - checking and writing primary data (8749 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592498/SRX2592498.20_summits.bed INFO @ Sun, 21 Jun 2020 18:52:44: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (6498 records, 4 fields): 9 millis CompletedMACS2peakCalling