Job ID = 6458585 SRX = SRX5343121 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:40:11 prefetch.2.10.7: 1) Downloading 'SRR8540821'... 2020-06-21T12:40:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:42:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:42:47 prefetch.2.10.7: 1) 'SRR8540821' was downloaded successfully 2020-06-21T12:42:47 prefetch.2.10.7: 'SRR8540821' has 0 unresolved dependencies Read 21106797 spots for SRR8540821/SRR8540821.sra Written 21106797 spots for SRR8540821/SRR8540821.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:57 21106797 reads; of these: 21106797 (100.00%) were unpaired; of these: 2099375 (9.95%) aligned 0 times 16395224 (77.68%) aligned exactly 1 time 2612198 (12.38%) aligned >1 times 90.05% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 7582387 / 19007422 = 0.3989 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 21:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.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 21:54:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:55: 1000000 INFO @ Sun, 21 Jun 2020 21:55:01: 2000000 INFO @ Sun, 21 Jun 2020 21:55:06: 3000000 INFO @ Sun, 21 Jun 2020 21:55:12: 4000000 INFO @ Sun, 21 Jun 2020 21:55:18: 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 21:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.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 21:55:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:23: 6000000 INFO @ Sun, 21 Jun 2020 21:55:24: 1000000 INFO @ Sun, 21 Jun 2020 21:55:29: 7000000 INFO @ Sun, 21 Jun 2020 21:55:29: 2000000 INFO @ Sun, 21 Jun 2020 21:55:34: 8000000 INFO @ Sun, 21 Jun 2020 21:55:35: 3000000 INFO @ Sun, 21 Jun 2020 21:55:40: 4000000 INFO @ Sun, 21 Jun 2020 21:55:40: 9000000 INFO @ Sun, 21 Jun 2020 21:55:44: 5000000 INFO @ Sun, 21 Jun 2020 21:55:46: 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 21:55:49: 6000000 INFO @ Sun, 21 Jun 2020 21:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.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 21:55:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:52: 11000000 INFO @ Sun, 21 Jun 2020 21:55:54: 7000000 INFO @ Sun, 21 Jun 2020 21:55:54: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:54: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:54: #1 total tags in treatment: 11425035 INFO @ Sun, 21 Jun 2020 21:55:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:54: #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 21:55:55: #1 tags after filtering in treatment: 11425033 INFO @ Sun, 21 Jun 2020 21:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:55: 1000000 INFO @ Sun, 21 Jun 2020 21:55:56: #2 number of paired peaks: 8550 INFO @ Sun, 21 Jun 2020 21:55:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:56: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:55:56: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 21:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05_model.r INFO @ Sun, 21 Jun 2020 21:55:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:59: 8000000 INFO @ Sun, 21 Jun 2020 21:56:01: 2000000 INFO @ Sun, 21 Jun 2020 21:56:04: 9000000 INFO @ Sun, 21 Jun 2020 21:56:08: 3000000 INFO @ Sun, 21 Jun 2020 21:56:10: 10000000 INFO @ Sun, 21 Jun 2020 21:56:13: 4000000 INFO @ Sun, 21 Jun 2020 21:56:14: 11000000 INFO @ Sun, 21 Jun 2020 21:56:17: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:56:17: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:56:17: #1 total tags in treatment: 11425035 INFO @ Sun, 21 Jun 2020 21:56:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:17: #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 21:56:17: #1 tags after filtering in treatment: 11425033 INFO @ Sun, 21 Jun 2020 21:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:19: #2 number of paired peaks: 8550 INFO @ Sun, 21 Jun 2020 21:56:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:19: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:56:19: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 21:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10_model.r INFO @ Sun, 21 Jun 2020 21:56:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:19: 5000000 INFO @ Sun, 21 Jun 2020 21:56:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:25: 6000000 INFO @ Sun, 21 Jun 2020 21:56:31: 7000000 INFO @ Sun, 21 Jun 2020 21:56:36: 8000000 INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:37: Done! pass1 - making usageList (364 chroms): 2 millis pass2 - checking and writing primary data (8122 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:42: 9000000 INFO @ Sun, 21 Jun 2020 21:56:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:48: 10000000 INFO @ Sun, 21 Jun 2020 21:56:53: 11000000 INFO @ Sun, 21 Jun 2020 21:56:56: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:56:56: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:56:56: #1 total tags in treatment: 11425035 INFO @ Sun, 21 Jun 2020 21:56:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:56: #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 21:56:57: #1 tags after filtering in treatment: 11425033 INFO @ Sun, 21 Jun 2020 21:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:58: #2 number of paired peaks: 8550 INFO @ Sun, 21 Jun 2020 21:56:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:58: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 21:56:58: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 21:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20_model.r INFO @ Sun, 21 Jun 2020 21:56:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:00: Done! pass1 - making usageList (192 chroms): 2 millis pass2 - checking and writing primary data (7118 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343121/SRX5343121.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:38: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (6116 records, 4 fields): 10 millis CompletedMACS2peakCalling