Job ID = 6454212 SRX = SRX191908 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:35 prefetch.2.10.7: 1) Downloading 'SRR580338'... 2020-06-21T09:02:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:28 prefetch.2.10.7: 1) 'SRR580338' was downloaded successfully Read 30269050 spots for SRR580338/SRR580338.sra Written 30269050 spots for SRR580338/SRR580338.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: 00:05:30 30269050 reads; of these: 30269050 (100.00%) were unpaired; of these: 1702686 (5.63%) aligned 0 times 23617881 (78.03%) aligned exactly 1 time 4948483 (16.35%) aligned >1 times 94.37% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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] 18491979 / 28566364 = 0.6473 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 18:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.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 18:19:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:08: 1000000 INFO @ Sun, 21 Jun 2020 18:19:13: 2000000 INFO @ Sun, 21 Jun 2020 18:19:18: 3000000 INFO @ Sun, 21 Jun 2020 18:19:24: 4000000 INFO @ Sun, 21 Jun 2020 18:19:29: 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 18:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.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 18:19:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:34: 6000000 INFO @ Sun, 21 Jun 2020 18:19:40: 1000000 INFO @ Sun, 21 Jun 2020 18:19:40: 7000000 INFO @ Sun, 21 Jun 2020 18:19:46: 2000000 INFO @ Sun, 21 Jun 2020 18:19:46: 8000000 INFO @ Sun, 21 Jun 2020 18:19:52: 3000000 INFO @ Sun, 21 Jun 2020 18:19:52: 9000000 INFO @ Sun, 21 Jun 2020 18:19:59: 4000000 INFO @ Sun, 21 Jun 2020 18:19:59: 10000000 INFO @ Sun, 21 Jun 2020 18:19:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:19:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:19:59: #1 total tags in treatment: 10074385 INFO @ Sun, 21 Jun 2020 18:19:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:59: #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 18:19:59: #1 tags after filtering in treatment: 10074269 INFO @ Sun, 21 Jun 2020 18:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:00: #2 number of paired peaks: 2974 INFO @ Sun, 21 Jun 2020 18:20:00: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:01: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05_model.r INFO @ Sun, 21 Jun 2020 18:20:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:01: #3 Pre-compute pvalue-qvalue table... 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 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.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 18:20:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:04: 5000000 INFO @ Sun, 21 Jun 2020 18:20:09: 1000000 INFO @ Sun, 21 Jun 2020 18:20:11: 6000000 INFO @ Sun, 21 Jun 2020 18:20:16: 2000000 INFO @ Sun, 21 Jun 2020 18:20:18: 7000000 INFO @ Sun, 21 Jun 2020 18:20:22: 3000000 INFO @ Sun, 21 Jun 2020 18:20:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:25: 8000000 INFO @ Sun, 21 Jun 2020 18:20:29: 4000000 INFO @ Sun, 21 Jun 2020 18:20:32: 9000000 INFO @ Sun, 21 Jun 2020 18:20:35: 5000000 INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:37: Done! pass1 - making usageList (465 chroms): 2 millis pass2 - checking and writing primary data (12838 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:39: 10000000 INFO @ Sun, 21 Jun 2020 18:20:39: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:20:39: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:20:39: #1 total tags in treatment: 10074385 INFO @ Sun, 21 Jun 2020 18:20:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:39: #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 18:20:39: #1 tags after filtering in treatment: 10074269 INFO @ Sun, 21 Jun 2020 18:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:40: #2 number of paired peaks: 2974 INFO @ Sun, 21 Jun 2020 18:20:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:41: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 18:20:41: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 18:20:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10_model.r INFO @ Sun, 21 Jun 2020 18:20:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:42: 6000000 INFO @ Sun, 21 Jun 2020 18:20:48: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:54: 8000000 INFO @ Sun, 21 Jun 2020 18:21:00: 9000000 INFO @ Sun, 21 Jun 2020 18:21:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:06: 10000000 INFO @ Sun, 21 Jun 2020 18:21:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:21:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:21:07: #1 total tags in treatment: 10074385 INFO @ Sun, 21 Jun 2020 18:21:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:07: #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 18:21:07: #1 tags after filtering in treatment: 10074269 INFO @ Sun, 21 Jun 2020 18:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #2 number of paired peaks: 2974 INFO @ Sun, 21 Jun 2020 18:21:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:08: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 18:21:08: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 18:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20_model.r INFO @ Sun, 21 Jun 2020 18:21:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:16: Done! pass1 - making usageList (371 chroms): 3 millis pass2 - checking and writing primary data (9490 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX191908/SRX191908.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:44: Done! pass1 - making usageList (261 chroms): 2 millis pass2 - checking and writing primary data (6589 records, 4 fields): 13 millis CompletedMACS2peakCalling