Job ID = 6455533 SRX = SRX287863 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:10 prefetch.2.10.7: 1) Downloading 'SRR870052'... 2020-06-21T10:02:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:03:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:03:44 prefetch.2.10.7: 'SRR870052' is valid 2020-06-21T10:03:44 prefetch.2.10.7: 1) 'SRR870052' was downloaded successfully Read 13658367 spots for SRR870052/SRR870052.sra Written 13658367 spots for SRR870052/SRR870052.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: 00:03:31 13658367 reads; of these: 13658367 (100.00%) were unpaired; of these: 618347 (4.53%) aligned 0 times 11163703 (81.74%) aligned exactly 1 time 1876317 (13.74%) aligned >1 times 95.47% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 1690595 / 13040020 = 0.1296 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 19:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.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 19:11:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:41: 1000000 INFO @ Sun, 21 Jun 2020 19:11:47: 2000000 INFO @ Sun, 21 Jun 2020 19:11:54: 3000000 INFO @ Sun, 21 Jun 2020 19:12:00: 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 19:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.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 19:12:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:06: 5000000 INFO @ Sun, 21 Jun 2020 19:12:12: 1000000 INFO @ Sun, 21 Jun 2020 19:12:12: 6000000 INFO @ Sun, 21 Jun 2020 19:12:19: 2000000 INFO @ Sun, 21 Jun 2020 19:12:20: 7000000 INFO @ Sun, 21 Jun 2020 19:12:26: 3000000 INFO @ Sun, 21 Jun 2020 19:12:26: 8000000 INFO @ Sun, 21 Jun 2020 19:12:33: 4000000 INFO @ Sun, 21 Jun 2020 19:12:33: 9000000 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 19:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.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 19:12:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:40: 5000000 INFO @ Sun, 21 Jun 2020 19:12:40: 10000000 INFO @ Sun, 21 Jun 2020 19:12:44: 1000000 INFO @ Sun, 21 Jun 2020 19:12:48: 6000000 INFO @ Sun, 21 Jun 2020 19:12:48: 11000000 INFO @ Sun, 21 Jun 2020 19:12:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:51: #1 total tags in treatment: 11349425 INFO @ Sun, 21 Jun 2020 19:12:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:51: #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 19:12:51: #1 tags after filtering in treatment: 11349422 INFO @ Sun, 21 Jun 2020 19:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:52: #2 number of paired peaks: 3944 INFO @ Sun, 21 Jun 2020 19:12:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:52: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:12:52: #2 alternative fragment length(s) may be 2,198,216 bps INFO @ Sun, 21 Jun 2020 19:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05_model.r INFO @ Sun, 21 Jun 2020 19:12:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:52: 2000000 INFO @ Sun, 21 Jun 2020 19:12:56: 7000000 INFO @ Sun, 21 Jun 2020 19:13:01: 3000000 INFO @ Sun, 21 Jun 2020 19:13:03: 8000000 INFO @ Sun, 21 Jun 2020 19:13:09: 4000000 INFO @ Sun, 21 Jun 2020 19:13:10: 9000000 INFO @ Sun, 21 Jun 2020 19:13:18: 5000000 INFO @ Sun, 21 Jun 2020 19:13:18: 10000000 INFO @ Sun, 21 Jun 2020 19:13:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:25: 11000000 INFO @ Sun, 21 Jun 2020 19:13:26: 6000000 INFO @ Sun, 21 Jun 2020 19:13:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:28: #1 total tags in treatment: 11349425 INFO @ Sun, 21 Jun 2020 19:13:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:28: #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 19:13:28: #1 tags after filtering in treatment: 11349422 INFO @ Sun, 21 Jun 2020 19:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:29: #2 number of paired peaks: 3944 INFO @ Sun, 21 Jun 2020 19:13:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:30: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:13:30: #2 alternative fragment length(s) may be 2,198,216 bps INFO @ Sun, 21 Jun 2020 19:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10_model.r INFO @ Sun, 21 Jun 2020 19:13:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:34: 7000000 INFO @ Sun, 21 Jun 2020 19:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:35: Done! pass1 - making usageList (284 chroms): 2 millis pass2 - checking and writing primary data (5217 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:41: 8000000 INFO @ Sun, 21 Jun 2020 19:13:48: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:56: 10000000 INFO @ Sun, 21 Jun 2020 19:13:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:03: 11000000 INFO @ Sun, 21 Jun 2020 19:14:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:05: #1 total tags in treatment: 11349425 INFO @ Sun, 21 Jun 2020 19:14:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:05: #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 19:14:06: #1 tags after filtering in treatment: 11349422 INFO @ Sun, 21 Jun 2020 19:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:07: #2 number of paired peaks: 3944 INFO @ Sun, 21 Jun 2020 19:14:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:07: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 19:14:07: #2 alternative fragment length(s) may be 2,198,216 bps INFO @ Sun, 21 Jun 2020 19:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20_model.r INFO @ Sun, 21 Jun 2020 19:14:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:10: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (2570 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287863/SRX287863.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:48: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 5 millis CompletedMACS2peakCalling