Job ID = 6453247 SRX = SRX110766 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:12:48 prefetch.2.10.7: 1) Downloading 'SRR388348'... 2020-06-21T08:12:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:30 prefetch.2.10.7: 1) 'SRR388348' was downloaded successfully Read 39116584 spots for SRR388348/SRR388348.sra Written 39116584 spots for SRR388348/SRR388348.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: 00:06:21 39116584 reads; of these: 39116584 (100.00%) were unpaired; of these: 5197511 (13.29%) aligned 0 times 31704556 (81.05%) aligned exactly 1 time 2214517 (5.66%) aligned >1 times 86.71% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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 12 files... [bam_rmdupse_core] 12040154 / 33919073 = 0.3550 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 17:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.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 17:36:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:36:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:36:41: 1000000 INFO @ Sun, 21 Jun 2020 17:36:48: 2000000 INFO @ Sun, 21 Jun 2020 17:36:55: 3000000 INFO @ Sun, 21 Jun 2020 17:37:02: 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 17:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.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 17:37:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:09: 5000000 INFO @ Sun, 21 Jun 2020 17:37:12: 1000000 INFO @ Sun, 21 Jun 2020 17:37:16: 6000000 INFO @ Sun, 21 Jun 2020 17:37:18: 2000000 INFO @ Sun, 21 Jun 2020 17:37:24: 7000000 INFO @ Sun, 21 Jun 2020 17:37:25: 3000000 INFO @ Sun, 21 Jun 2020 17:37:31: 8000000 INFO @ Sun, 21 Jun 2020 17:37:32: 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 17:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.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 17:37:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:37:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:37:38: 9000000 INFO @ Sun, 21 Jun 2020 17:37:39: 5000000 INFO @ Sun, 21 Jun 2020 17:37:42: 1000000 INFO @ Sun, 21 Jun 2020 17:37:46: 10000000 INFO @ Sun, 21 Jun 2020 17:37:46: 6000000 INFO @ Sun, 21 Jun 2020 17:37:50: 2000000 INFO @ Sun, 21 Jun 2020 17:37:53: 7000000 INFO @ Sun, 21 Jun 2020 17:37:53: 11000000 INFO @ Sun, 21 Jun 2020 17:37:57: 3000000 INFO @ Sun, 21 Jun 2020 17:38:00: 8000000 INFO @ Sun, 21 Jun 2020 17:38:01: 12000000 INFO @ Sun, 21 Jun 2020 17:38:05: 4000000 INFO @ Sun, 21 Jun 2020 17:38:07: 9000000 INFO @ Sun, 21 Jun 2020 17:38:08: 13000000 INFO @ Sun, 21 Jun 2020 17:38:12: 5000000 INFO @ Sun, 21 Jun 2020 17:38:15: 10000000 INFO @ Sun, 21 Jun 2020 17:38:16: 14000000 INFO @ Sun, 21 Jun 2020 17:38:20: 6000000 INFO @ Sun, 21 Jun 2020 17:38:22: 11000000 INFO @ Sun, 21 Jun 2020 17:38:24: 15000000 INFO @ Sun, 21 Jun 2020 17:38:27: 7000000 INFO @ Sun, 21 Jun 2020 17:38:29: 12000000 INFO @ Sun, 21 Jun 2020 17:38:31: 16000000 INFO @ Sun, 21 Jun 2020 17:38:35: 8000000 INFO @ Sun, 21 Jun 2020 17:38:36: 13000000 INFO @ Sun, 21 Jun 2020 17:38:39: 17000000 INFO @ Sun, 21 Jun 2020 17:38:42: 9000000 INFO @ Sun, 21 Jun 2020 17:38:43: 14000000 INFO @ Sun, 21 Jun 2020 17:38:46: 18000000 INFO @ Sun, 21 Jun 2020 17:38:50: 10000000 INFO @ Sun, 21 Jun 2020 17:38:50: 15000000 INFO @ Sun, 21 Jun 2020 17:38:54: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:38:57: 11000000 INFO @ Sun, 21 Jun 2020 17:38:57: 16000000 INFO @ Sun, 21 Jun 2020 17:39:02: 20000000 INFO @ Sun, 21 Jun 2020 17:39:05: 17000000 INFO @ Sun, 21 Jun 2020 17:39:05: 12000000 INFO @ Sun, 21 Jun 2020 17:39:09: 21000000 INFO @ Sun, 21 Jun 2020 17:39:12: 18000000 INFO @ Sun, 21 Jun 2020 17:39:12: 13000000 INFO @ Sun, 21 Jun 2020 17:39:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:39:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:39:16: #1 total tags in treatment: 21878919 INFO @ Sun, 21 Jun 2020 17:39:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:16: #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 17:39:16: #1 tags after filtering in treatment: 21878799 INFO @ Sun, 21 Jun 2020 17:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:18: #2 number of paired peaks: 3671 INFO @ Sun, 21 Jun 2020 17:39:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:18: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:39:18: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 17:39:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05_model.r INFO @ Sun, 21 Jun 2020 17:39:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:19: 19000000 INFO @ Sun, 21 Jun 2020 17:39:20: 14000000 INFO @ Sun, 21 Jun 2020 17:39:26: 20000000 INFO @ Sun, 21 Jun 2020 17:39:27: 15000000 INFO @ Sun, 21 Jun 2020 17:39:33: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:39:35: 16000000 INFO @ Sun, 21 Jun 2020 17:39:39: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:39:39: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:39:39: #1 total tags in treatment: 21878919 INFO @ Sun, 21 Jun 2020 17:39:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:39: #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 17:39:40: #1 tags after filtering in treatment: 21878799 INFO @ Sun, 21 Jun 2020 17:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:41: #2 number of paired peaks: 3671 INFO @ Sun, 21 Jun 2020 17:39:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:42: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:39:42: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 17:39:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10_model.r INFO @ Sun, 21 Jun 2020 17:39:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:42: 17000000 INFO @ Sun, 21 Jun 2020 17:39:49: 18000000 INFO @ Sun, 21 Jun 2020 17:39:56: 19000000 INFO @ Sun, 21 Jun 2020 17:40:02: 20000000 INFO @ Sun, 21 Jun 2020 17:40:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:09: 21000000 INFO @ Sun, 21 Jun 2020 17:40:15: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:40:15: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:40:15: #1 total tags in treatment: 21878919 INFO @ Sun, 21 Jun 2020 17:40:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:15: #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 17:40:15: #1 tags after filtering in treatment: 21878799 INFO @ Sun, 21 Jun 2020 17:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:17: #2 number of paired peaks: 3671 INFO @ Sun, 21 Jun 2020 17:40:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:18: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:40:18: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 17:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20_model.r INFO @ Sun, 21 Jun 2020 17:40:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.05_summits.bed INFO @ Sun, 21 Jun 2020 17:40:27: Done! pass1 - making usageList (97 chroms): 3 millis pass2 - checking and writing primary data (22736 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.10_summits.bed INFO @ Sun, 21 Jun 2020 17:40:54: Done! pass1 - making usageList (74 chroms): 3 millis pass2 - checking and writing primary data (15782 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:41:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110766/SRX110766.20_summits.bed INFO @ Sun, 21 Jun 2020 17:41:30: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (9571 records, 4 fields): 13 millis CompletedMACS2peakCalling