Job ID = 6455747 SRX = SRX288041 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:10 prefetch.2.10.7: 1) Downloading 'SRR870230'... 2020-06-21T10:23:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:22 prefetch.2.10.7: 1) 'SRR870230' was downloaded successfully Read 16285409 spots for SRR870230/SRR870230.sra Written 16285409 spots for SRR870230/SRR870230.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: 00:03:53 16285409 reads; of these: 16285409 (100.00%) were unpaired; of these: 1036083 (6.36%) aligned 0 times 13080473 (80.32%) aligned exactly 1 time 2168853 (13.32%) aligned >1 times 93.64% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 2566716 / 15249326 = 0.1683 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 19:35:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.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 19:35:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:24: 1000000 INFO @ Sun, 21 Jun 2020 19:35:29: 2000000 INFO @ Sun, 21 Jun 2020 19:35:34: 3000000 INFO @ Sun, 21 Jun 2020 19:35:40: 4000000 INFO @ Sun, 21 Jun 2020 19:35:45: 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 19:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.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 19:35:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:51: 6000000 INFO @ Sun, 21 Jun 2020 19:35:53: 1000000 INFO @ Sun, 21 Jun 2020 19:35:56: 7000000 INFO @ Sun, 21 Jun 2020 19:36:00: 2000000 INFO @ Sun, 21 Jun 2020 19:36:02: 8000000 INFO @ Sun, 21 Jun 2020 19:36:06: 3000000 INFO @ Sun, 21 Jun 2020 19:36:07: 9000000 INFO @ Sun, 21 Jun 2020 19:36:12: 4000000 INFO @ Sun, 21 Jun 2020 19:36:13: 10000000 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 19:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.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 19:36:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:19: 5000000 INFO @ Sun, 21 Jun 2020 19:36:19: 11000000 INFO @ Sun, 21 Jun 2020 19:36:23: 1000000 INFO @ Sun, 21 Jun 2020 19:36:25: 12000000 INFO @ Sun, 21 Jun 2020 19:36:25: 6000000 INFO @ Sun, 21 Jun 2020 19:36:28: 2000000 INFO @ Sun, 21 Jun 2020 19:36:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:29: #1 total tags in treatment: 12682610 INFO @ Sun, 21 Jun 2020 19:36:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:29: #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 19:36:29: #1 tags after filtering in treatment: 12682606 INFO @ Sun, 21 Jun 2020 19:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:31: #2 number of paired peaks: 3870 INFO @ Sun, 21 Jun 2020 19:36:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:31: #2 predicted fragment length is 242 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2 alternative fragment length(s) may be 3,224,232,242 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05_model.r INFO @ Sun, 21 Jun 2020 19:36:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:32: 7000000 INFO @ Sun, 21 Jun 2020 19:36:34: 3000000 INFO @ Sun, 21 Jun 2020 19:36:38: 8000000 INFO @ Sun, 21 Jun 2020 19:36:39: 4000000 INFO @ Sun, 21 Jun 2020 19:36:44: 9000000 INFO @ Sun, 21 Jun 2020 19:36:45: 5000000 INFO @ Sun, 21 Jun 2020 19:36:50: 6000000 INFO @ Sun, 21 Jun 2020 19:36:51: 10000000 INFO @ Sun, 21 Jun 2020 19:36:56: 7000000 INFO @ Sun, 21 Jun 2020 19:36:58: 11000000 INFO @ Sun, 21 Jun 2020 19:37:01: 8000000 INFO @ Sun, 21 Jun 2020 19:37:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:04: 12000000 INFO @ Sun, 21 Jun 2020 19:37:07: 9000000 INFO @ Sun, 21 Jun 2020 19:37:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:09: #1 total tags in treatment: 12682610 INFO @ Sun, 21 Jun 2020 19:37:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:09: #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 19:37:09: #1 tags after filtering in treatment: 12682606 INFO @ Sun, 21 Jun 2020 19:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:11: #2 number of paired peaks: 3870 INFO @ Sun, 21 Jun 2020 19:37:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:11: #2 predicted fragment length is 242 bps INFO @ Sun, 21 Jun 2020 19:37:11: #2 alternative fragment length(s) may be 3,224,232,242 bps INFO @ Sun, 21 Jun 2020 19:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10_model.r INFO @ Sun, 21 Jun 2020 19:37:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:12: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:37:18: 11000000 INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:21: Done! pass1 - making usageList (391 chroms): 2 millis pass2 - checking and writing primary data (7737 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:23: 12000000 INFO @ Sun, 21 Jun 2020 19:37:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:27: #1 total tags in treatment: 12682610 INFO @ Sun, 21 Jun 2020 19:37:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:27: #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 19:37:27: #1 tags after filtering in treatment: 12682606 INFO @ Sun, 21 Jun 2020 19:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:28: #2 number of paired peaks: 3870 INFO @ Sun, 21 Jun 2020 19:37:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:29: #2 predicted fragment length is 242 bps INFO @ Sun, 21 Jun 2020 19:37:29: #2 alternative fragment length(s) may be 3,224,232,242 bps INFO @ Sun, 21 Jun 2020 19:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20_model.r INFO @ Sun, 21 Jun 2020 19:37:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:03: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (4593 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288041/SRX288041.20_summits.bed INFO @ Sun, 21 Jun 2020 19:38:19: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (1478 records, 4 fields): 6 millis CompletedMACS2peakCalling