Job ID = 14167457 SRX = ERX3978912 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25288761 spots for ERR3975981/ERR3975981.sra Written 25288761 spots for ERR3975981/ERR3975981.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168365 ("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: 01:15:40 25288761 reads; of these: 25288761 (100.00%) were paired; of these: 3041554 (12.03%) aligned concordantly 0 times 16926867 (66.93%) aligned concordantly exactly 1 time 5320340 (21.04%) aligned concordantly >1 times ---- 3041554 pairs aligned concordantly 0 times; of these: 405914 (13.35%) aligned discordantly 1 time ---- 2635640 pairs aligned 0 times concordantly or discordantly; of these: 5271280 mates make up the pairs; of these: 2579406 (48.93%) aligned 0 times 1185460 (22.49%) aligned exactly 1 time 1506414 (28.58%) aligned >1 times 94.90% overall alignment rate Time searching: 01:15:40 Overall time: 01:15:40 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 20 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] 15270754 / 22522197 = 0.6780 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 13:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.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 13:51:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:51:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:51:06: 1000000 INFO @ Fri, 10 Dec 2021 13:51:12: 2000000 INFO @ Fri, 10 Dec 2021 13:51:18: 3000000 INFO @ Fri, 10 Dec 2021 13:51:24: 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 13:51:30: 5000000 INFO @ Fri, 10 Dec 2021 13:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.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 13:51:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:51:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:51:37: 6000000 INFO @ Fri, 10 Dec 2021 13:51:37: 1000000 INFO @ Fri, 10 Dec 2021 13:51:44: 7000000 INFO @ Fri, 10 Dec 2021 13:51:44: 2000000 INFO @ Fri, 10 Dec 2021 13:51:51: 8000000 INFO @ Fri, 10 Dec 2021 13:51:51: 3000000 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 13:51:58: 9000000 INFO @ Fri, 10 Dec 2021 13:51:58: 4000000 INFO @ Fri, 10 Dec 2021 13:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.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 13:52:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:52:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:52:06: 10000000 INFO @ Fri, 10 Dec 2021 13:52:06: 5000000 INFO @ Fri, 10 Dec 2021 13:52:09: 1000000 INFO @ Fri, 10 Dec 2021 13:52:14: 11000000 INFO @ Fri, 10 Dec 2021 13:52:14: 6000000 INFO @ Fri, 10 Dec 2021 13:52:18: 2000000 INFO @ Fri, 10 Dec 2021 13:52:22: 12000000 INFO @ Fri, 10 Dec 2021 13:52:22: 7000000 INFO @ Fri, 10 Dec 2021 13:52:26: 3000000 INFO @ Fri, 10 Dec 2021 13:52:30: 8000000 INFO @ Fri, 10 Dec 2021 13:52:30: 13000000 INFO @ Fri, 10 Dec 2021 13:52:35: 4000000 INFO @ Fri, 10 Dec 2021 13:52:38: 9000000 INFO @ Fri, 10 Dec 2021 13:52:38: 14000000 INFO @ Fri, 10 Dec 2021 13:52:44: 5000000 INFO @ Fri, 10 Dec 2021 13:52:46: 10000000 INFO @ Fri, 10 Dec 2021 13:52:46: 15000000 INFO @ Fri, 10 Dec 2021 13:52:52: 6000000 INFO @ Fri, 10 Dec 2021 13:52:54: 11000000 INFO @ Fri, 10 Dec 2021 13:52:54: 16000000 INFO @ Fri, 10 Dec 2021 13:53:01: 7000000 INFO @ Fri, 10 Dec 2021 13:53:02: 17000000 INFO @ Fri, 10 Dec 2021 13:53:02: 12000000 INFO @ Fri, 10 Dec 2021 13:53:05: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:53:05: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:53:05: #1 total tags in treatment: 7214289 INFO @ Fri, 10 Dec 2021 13:53:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:53:05: #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 13:53:06: #1 tags after filtering in treatment: 6612851 INFO @ Fri, 10 Dec 2021 13:53:06: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 13:53:06: #1 finished! INFO @ Fri, 10 Dec 2021 13:53:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:53:06: #2 number of paired peaks: 2083 INFO @ Fri, 10 Dec 2021 13:53:06: start model_add_line... INFO @ Fri, 10 Dec 2021 13:53:06: start X-correlation... INFO @ Fri, 10 Dec 2021 13:53:06: end of X-cor INFO @ Fri, 10 Dec 2021 13:53:06: #2 finished! INFO @ Fri, 10 Dec 2021 13:53:06: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 13:53:06: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 13:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05_model.r INFO @ Fri, 10 Dec 2021 13:53:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:53:09: 8000000 INFO @ Fri, 10 Dec 2021 13:53:10: 13000000 INFO @ Fri, 10 Dec 2021 13:53:18: 14000000 INFO @ Fri, 10 Dec 2021 13:53:18: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:53:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:53:26: 15000000 INFO @ Fri, 10 Dec 2021 13:53:27: 10000000 INFO @ Fri, 10 Dec 2021 13:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.05_summits.bed INFO @ Fri, 10 Dec 2021 13:53:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9984 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:53:34: 16000000 INFO @ Fri, 10 Dec 2021 13:53:36: 11000000 INFO @ Fri, 10 Dec 2021 13:53:42: 17000000 INFO @ Fri, 10 Dec 2021 13:53:44: 12000000 INFO @ Fri, 10 Dec 2021 13:53:45: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:53:45: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:53:45: #1 total tags in treatment: 7214289 INFO @ Fri, 10 Dec 2021 13:53:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:53:45: #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 13:53:45: #1 tags after filtering in treatment: 6612851 INFO @ Fri, 10 Dec 2021 13:53:45: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 13:53:45: #1 finished! INFO @ Fri, 10 Dec 2021 13:53:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:53:46: #2 number of paired peaks: 2083 INFO @ Fri, 10 Dec 2021 13:53:46: start model_add_line... INFO @ Fri, 10 Dec 2021 13:53:46: start X-correlation... INFO @ Fri, 10 Dec 2021 13:53:46: end of X-cor INFO @ Fri, 10 Dec 2021 13:53:46: #2 finished! INFO @ Fri, 10 Dec 2021 13:53:46: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 13:53:46: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 13:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10_model.r INFO @ Fri, 10 Dec 2021 13:53:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:53:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:53:52: 13000000 INFO @ Fri, 10 Dec 2021 13:54:00: 14000000 INFO @ Fri, 10 Dec 2021 13:54:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:54:08: 15000000 INFO @ Fri, 10 Dec 2021 13:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.10_summits.bed INFO @ Fri, 10 Dec 2021 13:54:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6050 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:54:16: 16000000 INFO @ Fri, 10 Dec 2021 13:54:24: 17000000 INFO @ Fri, 10 Dec 2021 13:54:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 13:54:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 13:54:27: #1 total tags in treatment: 7214289 INFO @ Fri, 10 Dec 2021 13:54:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:54:27: #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 13:54:27: #1 tags after filtering in treatment: 6612851 INFO @ Fri, 10 Dec 2021 13:54:27: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 13:54:27: #1 finished! INFO @ Fri, 10 Dec 2021 13:54:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:54:28: #2 number of paired peaks: 2083 INFO @ Fri, 10 Dec 2021 13:54:28: start model_add_line... INFO @ Fri, 10 Dec 2021 13:54:28: start X-correlation... INFO @ Fri, 10 Dec 2021 13:54:28: end of X-cor INFO @ Fri, 10 Dec 2021 13:54:28: #2 finished! INFO @ Fri, 10 Dec 2021 13:54:28: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 13:54:28: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 13:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20_model.r INFO @ Fri, 10 Dec 2021 13:54:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:54:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978912/ERX3978912.20_summits.bed INFO @ Fri, 10 Dec 2021 13:54:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3111 records, 4 fields): 5 millis CompletedMACS2peakCalling