Job ID = 6498755 SRX = SRX750078 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:17:57 prefetch.2.10.7: 1) Downloading 'SRR1638768'... 2020-06-26T00:17:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:20:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:20:16 prefetch.2.10.7: 1) 'SRR1638768' was downloaded successfully Read 19677191 spots for SRR1638768/SRR1638768.sra Written 19677191 spots for SRR1638768/SRR1638768.sra 2020-06-26T00:21:35 prefetch.2.10.7: 1) Downloading 'SRR1638769'... 2020-06-26T00:21:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:23:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:23:27 prefetch.2.10.7: 1) 'SRR1638769' was downloaded successfully Read 17826106 spots for SRR1638769/SRR1638769.sra Written 17826106 spots for SRR1638769/SRR1638769.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: 00:13:04 37503297 reads; of these: 37503297 (100.00%) were unpaired; of these: 2923743 (7.80%) aligned 0 times 29896724 (79.72%) aligned exactly 1 time 4682830 (12.49%) aligned >1 times 92.20% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 23543430 / 34579554 = 0.6808 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 @ Fri, 26 Jun 2020 09:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.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 @ Fri, 26 Jun 2020 09:45:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:45:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:45:32: 1000000 INFO @ Fri, 26 Jun 2020 09:45:39: 2000000 INFO @ Fri, 26 Jun 2020 09:45:46: 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 @ Fri, 26 Jun 2020 09:45:53: 4000000 INFO @ Fri, 26 Jun 2020 09:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.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 @ Fri, 26 Jun 2020 09:45:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:45:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:46:00: 5000000 INFO @ Fri, 26 Jun 2020 09:46:02: 1000000 INFO @ Fri, 26 Jun 2020 09:46:07: 6000000 INFO @ Fri, 26 Jun 2020 09:46:09: 2000000 INFO @ Fri, 26 Jun 2020 09:46:15: 7000000 INFO @ Fri, 26 Jun 2020 09:46:16: 3000000 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 @ Fri, 26 Jun 2020 09:46:23: 8000000 INFO @ Fri, 26 Jun 2020 09:46:23: 4000000 INFO @ Fri, 26 Jun 2020 09:46:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.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 @ Fri, 26 Jun 2020 09:46:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:46:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:46:31: 9000000 INFO @ Fri, 26 Jun 2020 09:46:31: 5000000 INFO @ Fri, 26 Jun 2020 09:46:33: 1000000 INFO @ Fri, 26 Jun 2020 09:46:38: 6000000 INFO @ Fri, 26 Jun 2020 09:46:39: 10000000 INFO @ Fri, 26 Jun 2020 09:46:41: 2000000 INFO @ Fri, 26 Jun 2020 09:46:46: 7000000 INFO @ Fri, 26 Jun 2020 09:46:47: 11000000 INFO @ Fri, 26 Jun 2020 09:46:48: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:46:48: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:46:48: #1 total tags in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:46:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:46:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:46:48: #1 tags after filtering in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:46:48: #1 finished! INFO @ Fri, 26 Jun 2020 09:46:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:46:49: #2 number of paired peaks: 6741 INFO @ Fri, 26 Jun 2020 09:46:49: start model_add_line... INFO @ Fri, 26 Jun 2020 09:46:49: 3000000 INFO @ Fri, 26 Jun 2020 09:46:49: start X-correlation... INFO @ Fri, 26 Jun 2020 09:46:49: end of X-cor INFO @ Fri, 26 Jun 2020 09:46:49: #2 finished! INFO @ Fri, 26 Jun 2020 09:46:49: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 09:46:49: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 09:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05_model.r INFO @ Fri, 26 Jun 2020 09:46:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:46:53: 8000000 INFO @ Fri, 26 Jun 2020 09:46:58: 4000000 INFO @ Fri, 26 Jun 2020 09:47:00: 9000000 INFO @ Fri, 26 Jun 2020 09:47:06: 5000000 INFO @ Fri, 26 Jun 2020 09:47:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:47:14: 6000000 INFO @ Fri, 26 Jun 2020 09:47:15: 11000000 INFO @ Fri, 26 Jun 2020 09:47:15: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:47:15: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:47:15: #1 total tags in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:47:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:47:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:47:15: #1 tags after filtering in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:47:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:47:15: #1 finished! INFO @ Fri, 26 Jun 2020 09:47:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:47:17: #2 number of paired peaks: 6741 INFO @ Fri, 26 Jun 2020 09:47:17: start model_add_line... INFO @ Fri, 26 Jun 2020 09:47:17: start X-correlation... INFO @ Fri, 26 Jun 2020 09:47:17: end of X-cor INFO @ Fri, 26 Jun 2020 09:47:17: #2 finished! INFO @ Fri, 26 Jun 2020 09:47:17: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 09:47:17: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 09:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10_model.r INFO @ Fri, 26 Jun 2020 09:47:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:47:22: 7000000 INFO @ Fri, 26 Jun 2020 09:47:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:47:29: 8000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:47:37: 9000000 INFO @ Fri, 26 Jun 2020 09:47:44: 10000000 INFO @ Fri, 26 Jun 2020 09:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.05_summits.bed INFO @ Fri, 26 Jun 2020 09:47:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8222 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:47:52: 11000000 INFO @ Fri, 26 Jun 2020 09:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:47:52: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:47:52: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:47:52: #1 total tags in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:47:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:47:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:47:52: #1 tags after filtering in treatment: 11036124 INFO @ Fri, 26 Jun 2020 09:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:47:52: #1 finished! INFO @ Fri, 26 Jun 2020 09:47:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:47:54: #2 number of paired peaks: 6741 INFO @ Fri, 26 Jun 2020 09:47:54: start model_add_line... INFO @ Fri, 26 Jun 2020 09:47:54: start X-correlation... INFO @ Fri, 26 Jun 2020 09:47:54: end of X-cor INFO @ Fri, 26 Jun 2020 09:47:54: #2 finished! INFO @ Fri, 26 Jun 2020 09:47:54: #2 predicted fragment length is 168 bps INFO @ Fri, 26 Jun 2020 09:47:54: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 26 Jun 2020 09:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20_model.r INFO @ Fri, 26 Jun 2020 09:47:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.10_summits.bed INFO @ Fri, 26 Jun 2020 09:48:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6714 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:48:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750078/SRX750078.20_summits.bed INFO @ Fri, 26 Jun 2020 09:48:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4918 records, 4 fields): 7 millis CompletedMACS2peakCalling