Job ID = 14167977 SRX = ERX3978927 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33642530 spots for ERR3975997/ERR3975997.sra Written 33642530 spots for ERR3975997/ERR3975997.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168896 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:25:17 33642530 reads; of these: 33642530 (100.00%) were paired; of these: 3892784 (11.57%) aligned concordantly 0 times 23861756 (70.93%) aligned concordantly exactly 1 time 5887990 (17.50%) aligned concordantly >1 times ---- 3892784 pairs aligned concordantly 0 times; of these: 679398 (17.45%) aligned discordantly 1 time ---- 3213386 pairs aligned 0 times concordantly or discordantly; of these: 6426772 mates make up the pairs; of these: 3405569 (52.99%) aligned 0 times 1460796 (22.73%) aligned exactly 1 time 1560407 (24.28%) aligned >1 times 94.94% overall alignment rate Time searching: 01:25:17 Overall time: 01:25:17 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 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 24382599 / 30297647 = 0.8048 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 15:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.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, 10 Dec 2021 15:45:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:45:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:46:05: 1000000 INFO @ Fri, 10 Dec 2021 15:46:12: 2000000 INFO @ Fri, 10 Dec 2021 15:46:19: 3000000 INFO @ Fri, 10 Dec 2021 15:46:26: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 15:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.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, 10 Dec 2021 15:46:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:46:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:46:33: 5000000 INFO @ Fri, 10 Dec 2021 15:46:34: 1000000 INFO @ Fri, 10 Dec 2021 15:46:39: 2000000 INFO @ Fri, 10 Dec 2021 15:46:41: 6000000 INFO @ Fri, 10 Dec 2021 15:46:45: 3000000 INFO @ Fri, 10 Dec 2021 15:46:48: 7000000 INFO @ Fri, 10 Dec 2021 15:46:51: 4000000 INFO @ Fri, 10 Dec 2021 15:46:55: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 15:46:56: 5000000 INFO @ Fri, 10 Dec 2021 15:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.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, 10 Dec 2021 15:46:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:46:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:47:02: 6000000 INFO @ Fri, 10 Dec 2021 15:47:03: 9000000 INFO @ Fri, 10 Dec 2021 15:47:04: 1000000 INFO @ Fri, 10 Dec 2021 15:47:08: 7000000 INFO @ Fri, 10 Dec 2021 15:47:10: 2000000 INFO @ Fri, 10 Dec 2021 15:47:11: 10000000 INFO @ Fri, 10 Dec 2021 15:47:14: 8000000 INFO @ Fri, 10 Dec 2021 15:47:15: 3000000 INFO @ Fri, 10 Dec 2021 15:47:19: 11000000 INFO @ Fri, 10 Dec 2021 15:47:20: 9000000 INFO @ Fri, 10 Dec 2021 15:47:21: 4000000 INFO @ Fri, 10 Dec 2021 15:47:26: 10000000 INFO @ Fri, 10 Dec 2021 15:47:26: 12000000 INFO @ Fri, 10 Dec 2021 15:47:27: 5000000 INFO @ Fri, 10 Dec 2021 15:47:32: 11000000 INFO @ Fri, 10 Dec 2021 15:47:33: 6000000 INFO @ Fri, 10 Dec 2021 15:47:34: 13000000 INFO @ Fri, 10 Dec 2021 15:47:38: 12000000 INFO @ Fri, 10 Dec 2021 15:47:39: 7000000 INFO @ Fri, 10 Dec 2021 15:47:42: 14000000 INFO @ Fri, 10 Dec 2021 15:47:44: 13000000 INFO @ Fri, 10 Dec 2021 15:47:44: 8000000 INFO @ Fri, 10 Dec 2021 15:47:49: 15000000 INFO @ Fri, 10 Dec 2021 15:47:50: 14000000 INFO @ Fri, 10 Dec 2021 15:47:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:47:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:47:50: #1 total tags in treatment: 5873196 INFO @ Fri, 10 Dec 2021 15:47:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:47:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:47:50: 9000000 INFO @ Fri, 10 Dec 2021 15:47:50: #1 tags after filtering in treatment: 5231475 INFO @ Fri, 10 Dec 2021 15:47:50: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:47:50: #1 finished! INFO @ Fri, 10 Dec 2021 15:47:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:47:51: #2 number of paired peaks: 4548 INFO @ Fri, 10 Dec 2021 15:47:51: start model_add_line... INFO @ Fri, 10 Dec 2021 15:47:51: start X-correlation... INFO @ Fri, 10 Dec 2021 15:47:51: end of X-cor INFO @ Fri, 10 Dec 2021 15:47:51: #2 finished! INFO @ Fri, 10 Dec 2021 15:47:51: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 15:47:51: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 15:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05_model.r INFO @ Fri, 10 Dec 2021 15:47:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:47:56: 15000000 INFO @ Fri, 10 Dec 2021 15:47:56: 10000000 INFO @ Fri, 10 Dec 2021 15:47:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:47:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:47:56: #1 total tags in treatment: 5873196 INFO @ Fri, 10 Dec 2021 15:47:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:47:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:47:56: #1 tags after filtering in treatment: 5231475 INFO @ Fri, 10 Dec 2021 15:47:56: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:47:56: #1 finished! INFO @ Fri, 10 Dec 2021 15:47:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:47:57: #2 number of paired peaks: 4548 INFO @ Fri, 10 Dec 2021 15:47:57: start model_add_line... INFO @ Fri, 10 Dec 2021 15:47:57: start X-correlation... INFO @ Fri, 10 Dec 2021 15:47:57: end of X-cor INFO @ Fri, 10 Dec 2021 15:47:57: #2 finished! INFO @ Fri, 10 Dec 2021 15:47:57: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 15:47:57: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 15:47:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10_model.r INFO @ Fri, 10 Dec 2021 15:47:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:48:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:48:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:48:07: 12000000 INFO @ Fri, 10 Dec 2021 15:48:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:48:12: 13000000 INFO @ Fri, 10 Dec 2021 15:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.05_summits.bed INFO @ Fri, 10 Dec 2021 15:48:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10527 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:48:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:48:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:48:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.10_summits.bed INFO @ Fri, 10 Dec 2021 15:48:15: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7034 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:48:17: 14000000 INFO @ Fri, 10 Dec 2021 15:48:22: 15000000 INFO @ Fri, 10 Dec 2021 15:48:23: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:48:23: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:48:23: #1 total tags in treatment: 5873196 INFO @ Fri, 10 Dec 2021 15:48:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:48:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:48:23: #1 tags after filtering in treatment: 5231475 INFO @ Fri, 10 Dec 2021 15:48:23: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:48:23: #1 finished! INFO @ Fri, 10 Dec 2021 15:48:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:48:24: #2 number of paired peaks: 4548 INFO @ Fri, 10 Dec 2021 15:48:24: start model_add_line... INFO @ Fri, 10 Dec 2021 15:48:24: start X-correlation... INFO @ Fri, 10 Dec 2021 15:48:24: end of X-cor INFO @ Fri, 10 Dec 2021 15:48:24: #2 finished! INFO @ Fri, 10 Dec 2021 15:48:24: #2 predicted fragment length is 180 bps INFO @ Fri, 10 Dec 2021 15:48:24: #2 alternative fragment length(s) may be 180 bps INFO @ Fri, 10 Dec 2021 15:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20_model.r INFO @ Fri, 10 Dec 2021 15:48:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:48:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:48:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978927/ERX3978927.20_summits.bed INFO @ Fri, 10 Dec 2021 15:48:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4041 records, 4 fields): 6 millis CompletedMACS2peakCalling