Job ID = 16438673 SRX = SRX14748152 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6554761 spots for SRR18645011/SRR18645011.sra Written 6554761 spots for SRR18645011/SRR18645011.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438962 ("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: 00:11:43 6554761 reads; of these: 6554761 (100.00%) were paired; of these: 698339 (10.65%) aligned concordantly 0 times 4313502 (65.81%) aligned concordantly exactly 1 time 1542920 (23.54%) aligned concordantly >1 times ---- 698339 pairs aligned concordantly 0 times; of these: 16545 (2.37%) aligned discordantly 1 time ---- 681794 pairs aligned 0 times concordantly or discordantly; of these: 1363588 mates make up the pairs; of these: 1053776 (77.28%) aligned 0 times 190657 (13.98%) aligned exactly 1 time 119155 (8.74%) aligned >1 times 91.96% overall alignment rate Time searching: 00:11:43 Overall time: 00:11:43 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 8 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] 189681 / 5868077 = 0.0323 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.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 @ Tue, 02 Aug 2022 14:18:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:36: 1000000 INFO @ Tue, 02 Aug 2022 14:18:41: 2000000 INFO @ Tue, 02 Aug 2022 14:18:47: 3000000 INFO @ Tue, 02 Aug 2022 14:18:52: 4000000 INFO @ Tue, 02 Aug 2022 14:18:57: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.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 @ Tue, 02 Aug 2022 14:19:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:03: 6000000 INFO @ Tue, 02 Aug 2022 14:19:06: 1000000 INFO @ Tue, 02 Aug 2022 14:19:08: 7000000 INFO @ Tue, 02 Aug 2022 14:19:13: 2000000 INFO @ Tue, 02 Aug 2022 14:19:14: 8000000 INFO @ Tue, 02 Aug 2022 14:19:19: 3000000 INFO @ Tue, 02 Aug 2022 14:19:20: 9000000 INFO @ Tue, 02 Aug 2022 14:19:25: 4000000 INFO @ Tue, 02 Aug 2022 14:19:26: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.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 @ Tue, 02 Aug 2022 14:19:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:31: 11000000 INFO @ Tue, 02 Aug 2022 14:19:32: 5000000 INFO @ Tue, 02 Aug 2022 14:19:35: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:19:35: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:19:35: #1 total tags in treatment: 5667123 INFO @ Tue, 02 Aug 2022 14:19:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:19:35: #1 tags after filtering in treatment: 5367315 INFO @ Tue, 02 Aug 2022 14:19:35: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 14:19:35: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:36: 1000000 INFO @ Tue, 02 Aug 2022 14:19:36: #2 number of paired peaks: 2092 INFO @ Tue, 02 Aug 2022 14:19:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:36: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:19:36: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05_model.r INFO @ Tue, 02 Aug 2022 14:19:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:38: 6000000 INFO @ Tue, 02 Aug 2022 14:19:41: 2000000 INFO @ Tue, 02 Aug 2022 14:19:44: 7000000 INFO @ Tue, 02 Aug 2022 14:19:47: 3000000 INFO @ Tue, 02 Aug 2022 14:19:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:50: 8000000 INFO @ Tue, 02 Aug 2022 14:19:52: 4000000 INFO @ Tue, 02 Aug 2022 14:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.05_summits.bed INFO @ Tue, 02 Aug 2022 14:19:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4261 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:19:56: 9000000 INFO @ Tue, 02 Aug 2022 14:19:58: 5000000 INFO @ Tue, 02 Aug 2022 14:20:03: 10000000 INFO @ Tue, 02 Aug 2022 14:20:03: 6000000 INFO @ Tue, 02 Aug 2022 14:20:09: 7000000 INFO @ Tue, 02 Aug 2022 14:20:09: 11000000 INFO @ Tue, 02 Aug 2022 14:20:13: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:20:13: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:20:13: #1 total tags in treatment: 5667123 INFO @ Tue, 02 Aug 2022 14:20:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:20:13: #1 tags after filtering in treatment: 5367315 INFO @ Tue, 02 Aug 2022 14:20:13: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 14:20:13: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:14: #2 number of paired peaks: 2092 INFO @ Tue, 02 Aug 2022 14:20:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:14: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:20:14: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10_model.r INFO @ Tue, 02 Aug 2022 14:20:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:14: 8000000 INFO @ Tue, 02 Aug 2022 14:20:19: 9000000 INFO @ Tue, 02 Aug 2022 14:20:24: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:20:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:29: 11000000 INFO @ Tue, 02 Aug 2022 14:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.10_summits.bed INFO @ Tue, 02 Aug 2022 14:20:33: #1 tag size is determined as 65 bps INFO @ Tue, 02 Aug 2022 14:20:33: #1 tag size = 65 INFO @ Tue, 02 Aug 2022 14:20:33: #1 total tags in treatment: 5667123 INFO @ Tue, 02 Aug 2022 14:20:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:20:33: Done! INFO @ Tue, 02 Aug 2022 14:20:33: #1 tags after filtering in treatment: 5367315 INFO @ Tue, 02 Aug 2022 14:20:33: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 14:20:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:33: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2680 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:20:33: #2 number of paired peaks: 2092 INFO @ Tue, 02 Aug 2022 14:20:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:34: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 14:20:34: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 14:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20_model.r INFO @ Tue, 02 Aug 2022 14:20:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:20:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748152/SRX14748152.20_summits.bed INFO @ Tue, 02 Aug 2022 14:20:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1401 records, 4 fields): 34 millis CompletedMACS2peakCalling