Job ID = 6454507 SRX = SRX2172425 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:14 prefetch.2.10.7: 1) Downloading 'SRR4252436'... 2020-06-21T09:28:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:53 prefetch.2.10.7: 1) 'SRR4252436' was downloaded successfully Read 34113877 spots for SRR4252436/SRR4252436.sra Written 34113877 spots for SRR4252436/SRR4252436.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: 00:07:50 34113877 reads; of these: 34113877 (100.00%) were unpaired; of these: 3134032 (9.19%) aligned 0 times 23717168 (69.52%) aligned exactly 1 time 7262677 (21.29%) aligned >1 times 90.81% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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] 11734679 / 30979845 = 0.3788 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 18:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.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 18:50:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:46: 1000000 INFO @ Sun, 21 Jun 2020 18:50:52: 2000000 INFO @ Sun, 21 Jun 2020 18:50:58: 3000000 INFO @ Sun, 21 Jun 2020 18:51:04: 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 18:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.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 18:51:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:11: 5000000 INFO @ Sun, 21 Jun 2020 18:51:16: 1000000 INFO @ Sun, 21 Jun 2020 18:51:18: 6000000 INFO @ Sun, 21 Jun 2020 18:51:23: 2000000 INFO @ Sun, 21 Jun 2020 18:51:25: 7000000 INFO @ Sun, 21 Jun 2020 18:51:30: 3000000 INFO @ Sun, 21 Jun 2020 18:51:31: 8000000 INFO @ Sun, 21 Jun 2020 18:51:37: 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 18:51:38: 9000000 INFO @ Sun, 21 Jun 2020 18:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.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 18:51:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:44: 5000000 INFO @ Sun, 21 Jun 2020 18:51:46: 10000000 INFO @ Sun, 21 Jun 2020 18:51:47: 1000000 INFO @ Sun, 21 Jun 2020 18:51:51: 6000000 INFO @ Sun, 21 Jun 2020 18:51:53: 11000000 INFO @ Sun, 21 Jun 2020 18:51:54: 2000000 INFO @ Sun, 21 Jun 2020 18:51:58: 7000000 INFO @ Sun, 21 Jun 2020 18:52:00: 12000000 INFO @ Sun, 21 Jun 2020 18:52:01: 3000000 INFO @ Sun, 21 Jun 2020 18:52:05: 8000000 INFO @ Sun, 21 Jun 2020 18:52:07: 13000000 INFO @ Sun, 21 Jun 2020 18:52:09: 4000000 INFO @ Sun, 21 Jun 2020 18:52:12: 9000000 INFO @ Sun, 21 Jun 2020 18:52:15: 14000000 INFO @ Sun, 21 Jun 2020 18:52:16: 5000000 INFO @ Sun, 21 Jun 2020 18:52:20: 10000000 INFO @ Sun, 21 Jun 2020 18:52:22: 15000000 INFO @ Sun, 21 Jun 2020 18:52:23: 6000000 INFO @ Sun, 21 Jun 2020 18:52:27: 11000000 INFO @ Sun, 21 Jun 2020 18:52:29: 16000000 INFO @ Sun, 21 Jun 2020 18:52:31: 7000000 INFO @ Sun, 21 Jun 2020 18:52:34: 12000000 INFO @ Sun, 21 Jun 2020 18:52:37: 17000000 INFO @ Sun, 21 Jun 2020 18:52:38: 8000000 INFO @ Sun, 21 Jun 2020 18:52:41: 13000000 INFO @ Sun, 21 Jun 2020 18:52:44: 18000000 INFO @ Sun, 21 Jun 2020 18:52:45: 9000000 INFO @ Sun, 21 Jun 2020 18:52:48: 14000000 INFO @ Sun, 21 Jun 2020 18:52:52: 19000000 INFO @ Sun, 21 Jun 2020 18:52:52: 10000000 INFO @ Sun, 21 Jun 2020 18:52:54: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:52:54: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:52:54: #1 total tags in treatment: 19245166 INFO @ Sun, 21 Jun 2020 18:52:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:54: #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 18:52:54: #1 tags after filtering in treatment: 19245095 INFO @ Sun, 21 Jun 2020 18:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:55: 15000000 INFO @ Sun, 21 Jun 2020 18:52:56: #2 number of paired peaks: 1626 INFO @ Sun, 21 Jun 2020 18:52:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:56: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:52:56: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05_model.r INFO @ Sun, 21 Jun 2020 18:52:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:59: 11000000 INFO @ Sun, 21 Jun 2020 18:53:02: 16000000 INFO @ Sun, 21 Jun 2020 18:53:06: 12000000 INFO @ Sun, 21 Jun 2020 18:53:09: 17000000 INFO @ Sun, 21 Jun 2020 18:53:13: 13000000 INFO @ Sun, 21 Jun 2020 18:53:16: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:20: 14000000 INFO @ Sun, 21 Jun 2020 18:53:23: 19000000 INFO @ Sun, 21 Jun 2020 18:53:25: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:53:25: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:53:25: #1 total tags in treatment: 19245166 INFO @ Sun, 21 Jun 2020 18:53:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:25: #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 18:53:26: #1 tags after filtering in treatment: 19245095 INFO @ Sun, 21 Jun 2020 18:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:27: 15000000 INFO @ Sun, 21 Jun 2020 18:53:27: #2 number of paired peaks: 1626 INFO @ Sun, 21 Jun 2020 18:53:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:28: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:53:28: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10_model.r INFO @ Sun, 21 Jun 2020 18:53:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:33: 16000000 INFO @ Sun, 21 Jun 2020 18:53:40: 17000000 INFO @ Sun, 21 Jun 2020 18:53:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:47: 18000000 INFO @ Sun, 21 Jun 2020 18:53:53: 19000000 INFO @ Sun, 21 Jun 2020 18:53:55: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:53:55: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:53:55: #1 total tags in treatment: 19245166 INFO @ Sun, 21 Jun 2020 18:53:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:55: #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 18:53:56: #1 tags after filtering in treatment: 19245095 INFO @ Sun, 21 Jun 2020 18:53:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:57: #2 number of paired peaks: 1626 INFO @ Sun, 21 Jun 2020 18:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:58: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:53:58: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20_model.r INFO @ Sun, 21 Jun 2020 18:53:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:02: Done! pass1 - making usageList (687 chroms): 3 millis pass2 - checking and writing primary data (12813 records, 4 fields): 53 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:33: Done! pass1 - making usageList (553 chroms): 3 millis pass2 - checking and writing primary data (9907 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172425/SRX2172425.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:03: Done! pass1 - making usageList (403 chroms): 2 millis pass2 - checking and writing primary data (6577 records, 4 fields): 31 millis CompletedMACS2peakCalling