Job ID = 6508758 SRX = SRX467114 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:27:10 prefetch.2.10.7: 1) Downloading 'SRR1164538'... 2020-06-26T14:27:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:28:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:28:28 prefetch.2.10.7: 'SRR1164538' is valid 2020-06-26T14:28:28 prefetch.2.10.7: 1) 'SRR1164538' was downloaded successfully Read 14415791 spots for SRR1164538/SRR1164538.sra Written 14415791 spots for SRR1164538/SRR1164538.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:19 14415791 reads; of these: 14415791 (100.00%) were unpaired; of these: 1025343 (7.11%) aligned 0 times 10401798 (72.16%) aligned exactly 1 time 2988650 (20.73%) aligned >1 times 92.89% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 1321310 / 13390448 = 0.0987 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 23:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.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 23:36:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:36:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:36:25: 1000000 INFO @ Fri, 26 Jun 2020 23:36:30: 2000000 INFO @ Fri, 26 Jun 2020 23:36:35: 3000000 INFO @ Fri, 26 Jun 2020 23:36:40: 4000000 INFO @ Fri, 26 Jun 2020 23:36:44: 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 @ Fri, 26 Jun 2020 23:36:49: 6000000 INFO @ Fri, 26 Jun 2020 23:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.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 23:36:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:36:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:36:54: 7000000 INFO @ Fri, 26 Jun 2020 23:36:55: 1000000 INFO @ Fri, 26 Jun 2020 23:36:59: 8000000 INFO @ Fri, 26 Jun 2020 23:37:00: 2000000 INFO @ Fri, 26 Jun 2020 23:37:04: 9000000 INFO @ Fri, 26 Jun 2020 23:37:05: 3000000 INFO @ Fri, 26 Jun 2020 23:37:09: 10000000 INFO @ Fri, 26 Jun 2020 23:37:10: 4000000 INFO @ Fri, 26 Jun 2020 23:37:14: 11000000 INFO @ Fri, 26 Jun 2020 23:37:15: 5000000 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 23:37:19: 12000000 INFO @ Fri, 26 Jun 2020 23:37:20: 6000000 INFO @ Fri, 26 Jun 2020 23:37:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:37:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:37:20: #1 total tags in treatment: 12069138 INFO @ Fri, 26 Jun 2020 23:37:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:20: #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 23:37:20: #1 tags after filtering in treatment: 12069034 INFO @ Fri, 26 Jun 2020 23:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:37:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.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 23:37:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:37:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:37:21: #2 number of paired peaks: 2550 INFO @ Fri, 26 Jun 2020 23:37:21: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:21: #2 predicted fragment length is 195 bps INFO @ Fri, 26 Jun 2020 23:37:21: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 26 Jun 2020 23:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05_model.r INFO @ Fri, 26 Jun 2020 23:37:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:25: 7000000 INFO @ Fri, 26 Jun 2020 23:37:26: 1000000 INFO @ Fri, 26 Jun 2020 23:37:30: 8000000 INFO @ Fri, 26 Jun 2020 23:37:31: 2000000 INFO @ Fri, 26 Jun 2020 23:37:35: 9000000 INFO @ Fri, 26 Jun 2020 23:37:36: 3000000 INFO @ Fri, 26 Jun 2020 23:37:40: 10000000 INFO @ Fri, 26 Jun 2020 23:37:41: 4000000 INFO @ Fri, 26 Jun 2020 23:37:45: 11000000 INFO @ Fri, 26 Jun 2020 23:37:46: 5000000 INFO @ Fri, 26 Jun 2020 23:37:51: 12000000 INFO @ Fri, 26 Jun 2020 23:37:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:37:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:37:51: #1 total tags in treatment: 12069138 INFO @ Fri, 26 Jun 2020 23:37:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:51: #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 23:37:51: 6000000 INFO @ Fri, 26 Jun 2020 23:37:52: #1 tags after filtering in treatment: 12069034 INFO @ Fri, 26 Jun 2020 23:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:37:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:53: #2 number of paired peaks: 2550 INFO @ Fri, 26 Jun 2020 23:37:53: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:53: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:53: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:53: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:53: #2 predicted fragment length is 195 bps INFO @ Fri, 26 Jun 2020 23:37:53: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 26 Jun 2020 23:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10_model.r INFO @ Fri, 26 Jun 2020 23:37:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:37:57: 7000000 INFO @ Fri, 26 Jun 2020 23:38:02: 8000000 INFO @ Fri, 26 Jun 2020 23:38:07: 9000000 INFO @ Fri, 26 Jun 2020 23:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.05_summits.bed INFO @ Fri, 26 Jun 2020 23:38:11: Done! pass1 - making usageList (196 chroms): 2 millis pass2 - checking and writing primary data (7928 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:38:12: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:38:18: 11000000 INFO @ Fri, 26 Jun 2020 23:38:23: 12000000 INFO @ Fri, 26 Jun 2020 23:38:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:38:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:38:24: #1 total tags in treatment: 12069138 INFO @ Fri, 26 Jun 2020 23:38:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:38:24: #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 23:38:24: #1 tags after filtering in treatment: 12069034 INFO @ Fri, 26 Jun 2020 23:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:38:24: #1 finished! INFO @ Fri, 26 Jun 2020 23:38:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:38:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:25: #2 number of paired peaks: 2550 INFO @ Fri, 26 Jun 2020 23:38:25: start model_add_line... INFO @ Fri, 26 Jun 2020 23:38:25: start X-correlation... INFO @ Fri, 26 Jun 2020 23:38:25: end of X-cor INFO @ Fri, 26 Jun 2020 23:38:25: #2 finished! INFO @ Fri, 26 Jun 2020 23:38:25: #2 predicted fragment length is 195 bps INFO @ Fri, 26 Jun 2020 23:38:25: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 26 Jun 2020 23:38:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20_model.r INFO @ Fri, 26 Jun 2020 23:38:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.10_summits.bed INFO @ Fri, 26 Jun 2020 23:38:39: Done! pass1 - making usageList (150 chroms): 2 millis pass2 - checking and writing primary data (5120 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:38:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467114/SRX467114.20_summits.bed INFO @ Fri, 26 Jun 2020 23:39:11: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (2285 records, 4 fields): 6 millis CompletedMACS2peakCalling