Job ID = 16439468 SRX = SRX9518324 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8405270 spots for SRR13070807/SRR13070807.sra Written 8405270 spots for SRR13070807/SRR13070807.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439642 ("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: 00:26:01 8405270 reads; of these: 8405270 (100.00%) were paired; of these: 725828 (8.64%) aligned concordantly 0 times 6282175 (74.74%) aligned concordantly exactly 1 time 1397267 (16.62%) aligned concordantly >1 times ---- 725828 pairs aligned concordantly 0 times; of these: 293389 (40.42%) aligned discordantly 1 time ---- 432439 pairs aligned 0 times concordantly or discordantly; of these: 864878 mates make up the pairs; of these: 572912 (66.24%) aligned 0 times 134563 (15.56%) aligned exactly 1 time 157403 (18.20%) aligned >1 times 96.59% overall alignment rate Time searching: 00:26:01 Overall time: 00:26:01 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] 342856 / 7960113 = 0.0431 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 15:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.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 15:49:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:49:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:49:58: 1000000 INFO @ Tue, 02 Aug 2022 15:50:05: 2000000 INFO @ Tue, 02 Aug 2022 15:50:12: 3000000 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 15:50:19: 4000000 INFO @ Tue, 02 Aug 2022 15:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.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 15:50:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:50:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:50:27: 5000000 INFO @ Tue, 02 Aug 2022 15:50:29: 1000000 INFO @ Tue, 02 Aug 2022 15:50:35: 6000000 INFO @ Tue, 02 Aug 2022 15:50:38: 2000000 INFO @ Tue, 02 Aug 2022 15:50:42: 7000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 15:50:47: 3000000 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 15:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.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 15:50:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:50:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:50:50: 8000000 INFO @ Tue, 02 Aug 2022 15:50:57: 4000000 INFO @ Tue, 02 Aug 2022 15:50:58: 9000000 INFO @ Tue, 02 Aug 2022 15:50:59: 1000000 INFO @ Tue, 02 Aug 2022 15:51:06: 10000000 INFO @ Tue, 02 Aug 2022 15:51:07: 5000000 INFO @ Tue, 02 Aug 2022 15:51:10: 2000000 INFO @ Tue, 02 Aug 2022 15:51:14: 11000000 INFO @ Tue, 02 Aug 2022 15:51:16: 6000000 INFO @ Tue, 02 Aug 2022 15:51:19: 3000000 INFO @ Tue, 02 Aug 2022 15:51:22: 12000000 INFO @ Tue, 02 Aug 2022 15:51:26: 7000000 INFO @ Tue, 02 Aug 2022 15:51:30: 4000000 INFO @ Tue, 02 Aug 2022 15:51:30: 13000000 INFO @ Tue, 02 Aug 2022 15:51:36: 8000000 INFO @ Tue, 02 Aug 2022 15:51:38: 14000000 INFO @ Tue, 02 Aug 2022 15:51:41: 5000000 INFO @ Tue, 02 Aug 2022 15:51:45: 9000000 INFO @ Tue, 02 Aug 2022 15:51:46: 15000000 INFO @ Tue, 02 Aug 2022 15:51:50: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:51:50: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:51:50: #1 total tags in treatment: 7347018 INFO @ Tue, 02 Aug 2022 15:51:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:51:50: #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 15:51:50: #1 tags after filtering in treatment: 6706172 INFO @ Tue, 02 Aug 2022 15:51:50: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:51:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:51:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:51:50: 6000000 INFO @ Tue, 02 Aug 2022 15:51:51: #2 number of paired peaks: 3864 INFO @ Tue, 02 Aug 2022 15:51:51: start model_add_line... INFO @ Tue, 02 Aug 2022 15:51:51: start X-correlation... INFO @ Tue, 02 Aug 2022 15:51:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:51:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:51:51: #2 predicted fragment length is 211 bps INFO @ Tue, 02 Aug 2022 15:51:51: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 02 Aug 2022 15:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05_model.r INFO @ Tue, 02 Aug 2022 15:51:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:51:55: 10000000 INFO @ Tue, 02 Aug 2022 15:51:59: 7000000 INFO @ Tue, 02 Aug 2022 15:52:04: 11000000 INFO @ Tue, 02 Aug 2022 15:52:08: 8000000 INFO @ Tue, 02 Aug 2022 15:52:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:52:14: 12000000 INFO @ Tue, 02 Aug 2022 15:52:16: 9000000 INFO @ Tue, 02 Aug 2022 15:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.05_summits.bed INFO @ Tue, 02 Aug 2022 15:52:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4017 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:52:23: 13000000 INFO @ Tue, 02 Aug 2022 15:52:24: 10000000 INFO @ Tue, 02 Aug 2022 15:52:33: 14000000 INFO @ Tue, 02 Aug 2022 15:52:33: 11000000 INFO @ Tue, 02 Aug 2022 15:52:42: 12000000 INFO @ Tue, 02 Aug 2022 15:52:42: 15000000 INFO @ Tue, 02 Aug 2022 15:52:47: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:52:47: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:52:47: #1 total tags in treatment: 7347018 INFO @ Tue, 02 Aug 2022 15:52:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:52:47: #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 15:52:47: #1 tags after filtering in treatment: 6706172 INFO @ Tue, 02 Aug 2022 15:52:47: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:52:47: #1 finished! INFO @ Tue, 02 Aug 2022 15:52:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:52:48: #2 number of paired peaks: 3864 INFO @ Tue, 02 Aug 2022 15:52:48: start model_add_line... INFO @ Tue, 02 Aug 2022 15:52:48: start X-correlation... INFO @ Tue, 02 Aug 2022 15:52:48: end of X-cor INFO @ Tue, 02 Aug 2022 15:52:48: #2 finished! INFO @ Tue, 02 Aug 2022 15:52:48: #2 predicted fragment length is 211 bps INFO @ Tue, 02 Aug 2022 15:52:48: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 02 Aug 2022 15:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10_model.r INFO @ Tue, 02 Aug 2022 15:52:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:52:50: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:52:58: 14000000 INFO @ Tue, 02 Aug 2022 15:53:06: 15000000 INFO @ Tue, 02 Aug 2022 15:53:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:53:10: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:53:10: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:53:10: #1 total tags in treatment: 7347018 INFO @ Tue, 02 Aug 2022 15:53:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:10: #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 15:53:10: #1 tags after filtering in treatment: 6706172 INFO @ Tue, 02 Aug 2022 15:53:10: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 15:53:10: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:11: #2 number of paired peaks: 3864 INFO @ Tue, 02 Aug 2022 15:53:11: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:11: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:11: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:11: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:11: #2 predicted fragment length is 211 bps INFO @ Tue, 02 Aug 2022 15:53:11: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 02 Aug 2022 15:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20_model.r INFO @ Tue, 02 Aug 2022 15:53:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.10_summits.bed INFO @ Tue, 02 Aug 2022 15:53:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2588 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:53:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518324/SRX9518324.20_summits.bed INFO @ Tue, 02 Aug 2022 15:53:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1591 records, 4 fields): 16 millis CompletedMACS2peakCalling