Job ID = 6458683 SRX = SRX5379466 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:29 prefetch.2.10.7: 1) Downloading 'SRR8578660'... 2020-06-21T12:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:41 prefetch.2.10.7: 'SRR8578660' is valid 2020-06-21T12:41:41 prefetch.2.10.7: 1) 'SRR8578660' was downloaded successfully 2020-06-21T12:41:41 prefetch.2.10.7: 'SRR8578660' has 0 unresolved dependencies Read 24672355 spots for SRR8578660/SRR8578660.sra Written 24672355 spots for SRR8578660/SRR8578660.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: 00:05:40 24672355 reads; of these: 24672355 (100.00%) were unpaired; of these: 4587270 (18.59%) aligned 0 times 10730366 (43.49%) aligned exactly 1 time 9354719 (37.92%) aligned >1 times 81.41% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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 12 files... [bam_rmdupse_core] 8015232 / 20085085 = 0.3991 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 21:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.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 21:52:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:22: 1000000 INFO @ Sun, 21 Jun 2020 21:52:27: 2000000 INFO @ Sun, 21 Jun 2020 21:52:33: 3000000 INFO @ Sun, 21 Jun 2020 21:52:38: 4000000 INFO @ Sun, 21 Jun 2020 21:52:43: 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 21:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.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 21:52:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:49: 6000000 INFO @ Sun, 21 Jun 2020 21:52:52: 1000000 INFO @ Sun, 21 Jun 2020 21:52:55: 7000000 INFO @ Sun, 21 Jun 2020 21:52:58: 2000000 INFO @ Sun, 21 Jun 2020 21:53:00: 8000000 INFO @ Sun, 21 Jun 2020 21:53:04: 3000000 INFO @ Sun, 21 Jun 2020 21:53:06: 9000000 INFO @ Sun, 21 Jun 2020 21:53:10: 4000000 INFO @ Sun, 21 Jun 2020 21:53:12: 10000000 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 21:53:16: 5000000 INFO @ Sun, 21 Jun 2020 21:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.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 21:53:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:18: 11000000 INFO @ Sun, 21 Jun 2020 21:53:22: 6000000 INFO @ Sun, 21 Jun 2020 21:53:22: 1000000 INFO @ Sun, 21 Jun 2020 21:53:24: 12000000 INFO @ Sun, 21 Jun 2020 21:53:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:25: #1 total tags in treatment: 12069853 INFO @ Sun, 21 Jun 2020 21:53:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:25: #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 21:53:25: #1 tags after filtering in treatment: 12069803 INFO @ Sun, 21 Jun 2020 21:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:26: #2 number of paired peaks: 4455 INFO @ Sun, 21 Jun 2020 21:53:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:27: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 21:53:27: #2 alternative fragment length(s) may be 3,167 bps INFO @ Sun, 21 Jun 2020 21:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05_model.r INFO @ Sun, 21 Jun 2020 21:53:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:28: 7000000 INFO @ Sun, 21 Jun 2020 21:53:28: 2000000 INFO @ Sun, 21 Jun 2020 21:53:33: 8000000 INFO @ Sun, 21 Jun 2020 21:53:34: 3000000 INFO @ Sun, 21 Jun 2020 21:53:39: 9000000 INFO @ Sun, 21 Jun 2020 21:53:40: 4000000 INFO @ Sun, 21 Jun 2020 21:53:46: 10000000 INFO @ Sun, 21 Jun 2020 21:53:46: 5000000 INFO @ Sun, 21 Jun 2020 21:53:52: 11000000 INFO @ Sun, 21 Jun 2020 21:53:52: 6000000 INFO @ Sun, 21 Jun 2020 21:53:58: 12000000 INFO @ Sun, 21 Jun 2020 21:53:58: 7000000 INFO @ Sun, 21 Jun 2020 21:53:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:58: #1 total tags in treatment: 12069853 INFO @ Sun, 21 Jun 2020 21:53:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:58: #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 21:53:59: #1 tags after filtering in treatment: 12069803 INFO @ Sun, 21 Jun 2020 21:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:00: #2 number of paired peaks: 4455 INFO @ Sun, 21 Jun 2020 21:54:00: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:00: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:00: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:00: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:00: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 21:54:00: #2 alternative fragment length(s) may be 3,167 bps INFO @ Sun, 21 Jun 2020 21:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10_model.r INFO @ Sun, 21 Jun 2020 21:54:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:09: 9000000 INFO @ Sun, 21 Jun 2020 21:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:12: Done! pass1 - making usageList (917 chroms): 2 millis pass2 - checking and writing primary data (6812 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:15: 10000000 INFO @ Sun, 21 Jun 2020 21:54:20: 11000000 INFO @ Sun, 21 Jun 2020 21:54:26: 12000000 INFO @ Sun, 21 Jun 2020 21:54:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:54:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:54:26: #1 total tags in treatment: 12069853 INFO @ Sun, 21 Jun 2020 21:54:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:26: #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 21:54:27: #1 tags after filtering in treatment: 12069803 INFO @ Sun, 21 Jun 2020 21:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:28: #2 number of paired peaks: 4455 INFO @ Sun, 21 Jun 2020 21:54:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:28: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 21:54:28: #2 alternative fragment length(s) may be 3,167 bps INFO @ Sun, 21 Jun 2020 21:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20_model.r INFO @ Sun, 21 Jun 2020 21:54:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:54:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:45: Done! pass1 - making usageList (710 chroms): 1 millis pass2 - checking and writing primary data (3456 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379466/SRX5379466.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:13: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (1340 records, 4 fields): 11 millis CompletedMACS2peakCalling