Job ID = 6459889 SRX = SRX969921 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:38:28 prefetch.2.10.7: 1) Downloading 'SRR1931637'... 2020-06-21T13:38:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:40:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:40:25 prefetch.2.10.7: 'SRR1931637' is valid 2020-06-21T13:40:25 prefetch.2.10.7: 1) 'SRR1931637' was downloaded successfully Read 17332179 spots for SRR1931637/SRR1931637.sra Written 17332179 spots for SRR1931637/SRR1931637.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: 00:05:01 17332179 reads; of these: 17332179 (100.00%) were unpaired; of these: 674744 (3.89%) aligned 0 times 12777866 (73.72%) aligned exactly 1 time 3879569 (22.38%) aligned >1 times 96.11% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 3606834 / 16657435 = 0.2165 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 22:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.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 22:50:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:50:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:50:15: 1000000 INFO @ Sun, 21 Jun 2020 22:50:22: 2000000 INFO @ Sun, 21 Jun 2020 22:50:30: 3000000 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 22:50:37: 4000000 INFO @ Sun, 21 Jun 2020 22:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.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 22:50:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:50:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:50:45: 5000000 INFO @ Sun, 21 Jun 2020 22:50:45: 1000000 INFO @ Sun, 21 Jun 2020 22:50:53: 2000000 INFO @ Sun, 21 Jun 2020 22:50:53: 6000000 INFO @ Sun, 21 Jun 2020 22:51:00: 3000000 INFO @ Sun, 21 Jun 2020 22:51:01: 7000000 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 22:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.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 22:51:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:51:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:51:08: 4000000 INFO @ Sun, 21 Jun 2020 22:51:09: 8000000 INFO @ Sun, 21 Jun 2020 22:51:16: 1000000 INFO @ Sun, 21 Jun 2020 22:51:16: 5000000 INFO @ Sun, 21 Jun 2020 22:51:18: 9000000 INFO @ Sun, 21 Jun 2020 22:51:24: 6000000 INFO @ Sun, 21 Jun 2020 22:51:25: 2000000 INFO @ Sun, 21 Jun 2020 22:51:26: 10000000 INFO @ Sun, 21 Jun 2020 22:51:32: 7000000 INFO @ Sun, 21 Jun 2020 22:51:34: 3000000 INFO @ Sun, 21 Jun 2020 22:51:35: 11000000 INFO @ Sun, 21 Jun 2020 22:51:40: 8000000 INFO @ Sun, 21 Jun 2020 22:51:43: 4000000 INFO @ Sun, 21 Jun 2020 22:51:43: 12000000 INFO @ Sun, 21 Jun 2020 22:51:48: 9000000 INFO @ Sun, 21 Jun 2020 22:51:51: 13000000 INFO @ Sun, 21 Jun 2020 22:51:52: 5000000 INFO @ Sun, 21 Jun 2020 22:51:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:51:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:51:52: #1 total tags in treatment: 13050601 INFO @ Sun, 21 Jun 2020 22:51:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:51:52: #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 22:51:52: #1 tags after filtering in treatment: 13050599 INFO @ Sun, 21 Jun 2020 22:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:51:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:51:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:51:54: #2 number of paired peaks: 2748 INFO @ Sun, 21 Jun 2020 22:51:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:51:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:51:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:51:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:51:54: #2 predicted fragment length is 292 bps INFO @ Sun, 21 Jun 2020 22:51:54: #2 alternative fragment length(s) may be 292 bps INFO @ Sun, 21 Jun 2020 22:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05_model.r INFO @ Sun, 21 Jun 2020 22:51:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:51:55: 10000000 INFO @ Sun, 21 Jun 2020 22:52:00: 6000000 INFO @ Sun, 21 Jun 2020 22:52:03: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:52:09: 7000000 INFO @ Sun, 21 Jun 2020 22:52:11: 12000000 INFO @ Sun, 21 Jun 2020 22:52:17: 8000000 INFO @ Sun, 21 Jun 2020 22:52:18: 13000000 INFO @ Sun, 21 Jun 2020 22:52:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:52:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:52:19: #1 total tags in treatment: 13050601 INFO @ Sun, 21 Jun 2020 22:52:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:52:19: #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 22:52:19: #1 tags after filtering in treatment: 13050599 INFO @ Sun, 21 Jun 2020 22:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:52:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:52:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:52:21: #2 number of paired peaks: 2748 INFO @ Sun, 21 Jun 2020 22:52:21: start model_add_line... INFO @ Sun, 21 Jun 2020 22:52:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:52:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:52:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:52:21: #2 predicted fragment length is 292 bps INFO @ Sun, 21 Jun 2020 22:52:21: #2 alternative fragment length(s) may be 292 bps INFO @ Sun, 21 Jun 2020 22:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10_model.r INFO @ Sun, 21 Jun 2020 22:52:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:52:25: 9000000 INFO @ Sun, 21 Jun 2020 22:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:52:32: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:52:40: 11000000 INFO @ Sun, 21 Jun 2020 22:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.05_summits.bed INFO @ Sun, 21 Jun 2020 22:52:46: Done! pass1 - making usageList (493 chroms): 2 millis pass2 - checking and writing primary data (6430 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:52:47: 12000000 INFO @ Sun, 21 Jun 2020 22:52:55: 13000000 INFO @ Sun, 21 Jun 2020 22:52:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:52:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:52:55: #1 total tags in treatment: 13050601 INFO @ Sun, 21 Jun 2020 22:52:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:52:55: #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 22:52:56: #1 tags after filtering in treatment: 13050599 INFO @ Sun, 21 Jun 2020 22:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:52:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:52:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:52:57: #2 number of paired peaks: 2748 INFO @ Sun, 21 Jun 2020 22:52:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:52:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:52:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:52:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:52:57: #2 predicted fragment length is 292 bps INFO @ Sun, 21 Jun 2020 22:52:57: #2 alternative fragment length(s) may be 292 bps INFO @ Sun, 21 Jun 2020 22:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20_model.r INFO @ Sun, 21 Jun 2020 22:52:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:52:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:53:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:53:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:53:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.10_summits.bed INFO @ Sun, 21 Jun 2020 22:53:14: Done! pass1 - making usageList (448 chroms): 2 millis pass2 - checking and writing primary data (5526 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:53:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969921/SRX969921.20_summits.bed INFO @ Sun, 21 Jun 2020 22:53:49: Done! pass1 - making usageList (399 chroms): 1 millis pass2 - checking and writing primary data (4552 records, 4 fields): 18 millis CompletedMACS2peakCalling