Job ID = 6453585 SRX = SRX128300 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:26 prefetch.2.10.7: 1) Downloading 'SRR442239'... 2020-06-21T08:30:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:29 prefetch.2.10.7: 1) 'SRR442239' was downloaded successfully Read 29363939 spots for SRR442239/SRR442239.sra Written 29363939 spots for SRR442239/SRR442239.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: 00:06:12 29363939 reads; of these: 29363939 (100.00%) were unpaired; of these: 5611560 (19.11%) aligned 0 times 16998521 (57.89%) aligned exactly 1 time 6753858 (23.00%) aligned >1 times 80.89% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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] 11131949 / 23752379 = 0.4687 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 17:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.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 17:45:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:42: 1000000 INFO @ Sun, 21 Jun 2020 17:45:47: 2000000 INFO @ Sun, 21 Jun 2020 17:45:52: 3000000 INFO @ Sun, 21 Jun 2020 17:45:57: 4000000 INFO @ Sun, 21 Jun 2020 17:46:01: 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 @ Sun, 21 Jun 2020 17:46:06: 6000000 INFO @ Sun, 21 Jun 2020 17:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.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 17:46:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:11: 7000000 INFO @ Sun, 21 Jun 2020 17:46:13: 1000000 INFO @ Sun, 21 Jun 2020 17:46:15: 8000000 INFO @ Sun, 21 Jun 2020 17:46:17: 2000000 INFO @ Sun, 21 Jun 2020 17:46:20: 9000000 INFO @ Sun, 21 Jun 2020 17:46:22: 3000000 INFO @ Sun, 21 Jun 2020 17:46:25: 10000000 INFO @ Sun, 21 Jun 2020 17:46:27: 4000000 INFO @ Sun, 21 Jun 2020 17:46:30: 11000000 INFO @ Sun, 21 Jun 2020 17:46:32: 5000000 INFO @ Sun, 21 Jun 2020 17:46:35: 12000000 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 17:46:37: 6000000 INFO @ Sun, 21 Jun 2020 17:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.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 17:46:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:46:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:46:38: #1 total tags in treatment: 12620430 INFO @ Sun, 21 Jun 2020 17:46:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:38: #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 17:46:39: #1 tags after filtering in treatment: 12620366 INFO @ Sun, 21 Jun 2020 17:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:40: #2 number of paired peaks: 3563 INFO @ Sun, 21 Jun 2020 17:46:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:40: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:46:40: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05_model.r INFO @ Sun, 21 Jun 2020 17:46:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:42: 7000000 INFO @ Sun, 21 Jun 2020 17:46:44: 1000000 INFO @ Sun, 21 Jun 2020 17:46:47: 8000000 INFO @ Sun, 21 Jun 2020 17:46:49: 2000000 INFO @ Sun, 21 Jun 2020 17:46:52: 9000000 INFO @ Sun, 21 Jun 2020 17:46:55: 3000000 INFO @ Sun, 21 Jun 2020 17:46:56: 10000000 INFO @ Sun, 21 Jun 2020 17:47:01: 4000000 INFO @ Sun, 21 Jun 2020 17:47:02: 11000000 INFO @ Sun, 21 Jun 2020 17:47:07: 5000000 INFO @ Sun, 21 Jun 2020 17:47:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:07: 12000000 INFO @ Sun, 21 Jun 2020 17:47:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:47:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:47:10: #1 total tags in treatment: 12620430 INFO @ Sun, 21 Jun 2020 17:47:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:10: #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 17:47:10: #1 tags after filtering in treatment: 12620366 INFO @ Sun, 21 Jun 2020 17:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:12: #2 number of paired peaks: 3563 INFO @ Sun, 21 Jun 2020 17:47:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:12: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:47:12: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10_model.r INFO @ Sun, 21 Jun 2020 17:47:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:12: 6000000 INFO @ Sun, 21 Jun 2020 17:47:18: 7000000 INFO @ Sun, 21 Jun 2020 17:47:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:21: Done! pass1 - making usageList (681 chroms): 3 millis pass2 - checking and writing primary data (12656 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:23: 8000000 INFO @ Sun, 21 Jun 2020 17:47:29: 9000000 INFO @ Sun, 21 Jun 2020 17:47:34: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:47:40: 11000000 INFO @ Sun, 21 Jun 2020 17:47:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:45: 12000000 INFO @ Sun, 21 Jun 2020 17:47:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:47:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:47:49: #1 total tags in treatment: 12620430 INFO @ Sun, 21 Jun 2020 17:47:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:49: #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 17:47:49: #1 tags after filtering in treatment: 12620366 INFO @ Sun, 21 Jun 2020 17:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:50: #2 number of paired peaks: 3563 INFO @ Sun, 21 Jun 2020 17:47:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:50: #2 predicted fragment length is 85 bps INFO @ Sun, 21 Jun 2020 17:47:50: #2 alternative fragment length(s) may be 85 bps INFO @ Sun, 21 Jun 2020 17:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20_model.r INFO @ Sun, 21 Jun 2020 17:47:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:54: Done! pass1 - making usageList (569 chroms): 2 millis pass2 - checking and writing primary data (7318 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128300/SRX128300.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:34: Done! pass1 - making usageList (481 chroms): 1 millis pass2 - checking and writing primary data (3449 records, 4 fields): 18 millis CompletedMACS2peakCalling