Job ID = 14168261 SRX = ERX3978840 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13392756 spots for ERR3975909/ERR3975909.sra Written 13392756 spots for ERR3975909/ERR3975909.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169300 ("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: 00:34:03 13392756 reads; of these: 13392756 (100.00%) were paired; of these: 1779625 (13.29%) aligned concordantly 0 times 8511496 (63.55%) aligned concordantly exactly 1 time 3101635 (23.16%) aligned concordantly >1 times ---- 1779625 pairs aligned concordantly 0 times; of these: 192213 (10.80%) aligned discordantly 1 time ---- 1587412 pairs aligned 0 times concordantly or discordantly; of these: 3174824 mates make up the pairs; of these: 1972874 (62.14%) aligned 0 times 539337 (16.99%) aligned exactly 1 time 662613 (20.87%) aligned >1 times 92.63% overall alignment rate Time searching: 00:34:03 Overall time: 00:34:03 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 12 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] 7669411 / 11760126 = 0.6522 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 17:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.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 17:23:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:23:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:23:29: 1000000 INFO @ Fri, 10 Dec 2021 17:23:36: 2000000 INFO @ Fri, 10 Dec 2021 17:23:42: 3000000 INFO @ Fri, 10 Dec 2021 17:23:49: 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 17:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.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 17:23:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:23:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:23:55: 5000000 INFO @ Fri, 10 Dec 2021 17:23:58: 1000000 INFO @ Fri, 10 Dec 2021 17:24:01: 6000000 INFO @ Fri, 10 Dec 2021 17:24:04: 2000000 INFO @ Fri, 10 Dec 2021 17:24:07: 7000000 INFO @ Fri, 10 Dec 2021 17:24:10: 3000000 INFO @ Fri, 10 Dec 2021 17:24:14: 8000000 INFO @ Fri, 10 Dec 2021 17:24:16: 4000000 INFO @ Fri, 10 Dec 2021 17:24:20: 9000000 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 17:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.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 17:24:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:24:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:24:23: 5000000 INFO @ Fri, 10 Dec 2021 17:24:23: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:24:23: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:24:23: #1 total tags in treatment: 4064187 INFO @ Fri, 10 Dec 2021 17:24:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:24:23: #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 17:24:23: #1 tags after filtering in treatment: 3770010 INFO @ Fri, 10 Dec 2021 17:24:23: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:24:23: #1 finished! INFO @ Fri, 10 Dec 2021 17:24:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:24:23: #2 number of paired peaks: 1658 INFO @ Fri, 10 Dec 2021 17:24:23: start model_add_line... INFO @ Fri, 10 Dec 2021 17:24:23: start X-correlation... INFO @ Fri, 10 Dec 2021 17:24:23: end of X-cor INFO @ Fri, 10 Dec 2021 17:24:23: #2 finished! INFO @ Fri, 10 Dec 2021 17:24:23: #2 predicted fragment length is 173 bps INFO @ Fri, 10 Dec 2021 17:24:23: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 10 Dec 2021 17:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05_model.r INFO @ Fri, 10 Dec 2021 17:24:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:24:30: 1000000 INFO @ Fri, 10 Dec 2021 17:24:30: 6000000 INFO @ Fri, 10 Dec 2021 17:24:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.05_summits.bed INFO @ Fri, 10 Dec 2021 17:24:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4505 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:24:37: 2000000 INFO @ Fri, 10 Dec 2021 17:24:38: 7000000 INFO @ Fri, 10 Dec 2021 17:24:45: 8000000 INFO @ Fri, 10 Dec 2021 17:24:45: 3000000 INFO @ Fri, 10 Dec 2021 17:24:53: 9000000 INFO @ Fri, 10 Dec 2021 17:24:53: 4000000 INFO @ Fri, 10 Dec 2021 17:24:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:24:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:24:56: #1 total tags in treatment: 4064187 INFO @ Fri, 10 Dec 2021 17:24:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:24:56: #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 17:24:56: #1 tags after filtering in treatment: 3770010 INFO @ Fri, 10 Dec 2021 17:24:56: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:24:56: #1 finished! INFO @ Fri, 10 Dec 2021 17:24:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:24:56: #2 number of paired peaks: 1658 INFO @ Fri, 10 Dec 2021 17:24:56: start model_add_line... INFO @ Fri, 10 Dec 2021 17:24:56: start X-correlation... INFO @ Fri, 10 Dec 2021 17:24:56: end of X-cor INFO @ Fri, 10 Dec 2021 17:24:56: #2 finished! INFO @ Fri, 10 Dec 2021 17:24:56: #2 predicted fragment length is 173 bps INFO @ Fri, 10 Dec 2021 17:24:56: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 10 Dec 2021 17:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10_model.r INFO @ Fri, 10 Dec 2021 17:24:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:25:01: 5000000 INFO @ Fri, 10 Dec 2021 17:25:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:25:08: 6000000 INFO @ Fri, 10 Dec 2021 17:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.10_summits.bed INFO @ Fri, 10 Dec 2021 17:25:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1979 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:25:15: 7000000 INFO @ Fri, 10 Dec 2021 17:25:23: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:25:30: 9000000 INFO @ Fri, 10 Dec 2021 17:25:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:25:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:25:33: #1 total tags in treatment: 4064187 INFO @ Fri, 10 Dec 2021 17:25:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:25:33: #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 17:25:34: #1 tags after filtering in treatment: 3770010 INFO @ Fri, 10 Dec 2021 17:25:34: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 17:25:34: #1 finished! INFO @ Fri, 10 Dec 2021 17:25:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:25:34: #2 number of paired peaks: 1658 INFO @ Fri, 10 Dec 2021 17:25:34: start model_add_line... INFO @ Fri, 10 Dec 2021 17:25:34: start X-correlation... INFO @ Fri, 10 Dec 2021 17:25:34: end of X-cor INFO @ Fri, 10 Dec 2021 17:25:34: #2 finished! INFO @ Fri, 10 Dec 2021 17:25:34: #2 predicted fragment length is 173 bps INFO @ Fri, 10 Dec 2021 17:25:34: #2 alternative fragment length(s) may be 173 bps INFO @ Fri, 10 Dec 2021 17:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20_model.r INFO @ Fri, 10 Dec 2021 17:25:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:25:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978840/ERX3978840.20_summits.bed INFO @ Fri, 10 Dec 2021 17:25:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 3 millis CompletedMACS2peakCalling