Job ID = 5721104 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,500,612 reads read : 21,001,224 reads written : 21,001,224 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:15 10500612 reads; of these: 10500612 (100.00%) were paired; of these: 1081429 (10.30%) aligned concordantly 0 times 6813735 (64.89%) aligned concordantly exactly 1 time 2605448 (24.81%) aligned concordantly >1 times ---- 1081429 pairs aligned concordantly 0 times; of these: 342143 (31.64%) aligned discordantly 1 time ---- 739286 pairs aligned 0 times concordantly or discordantly; of these: 1478572 mates make up the pairs; of these: 799404 (54.07%) aligned 0 times 358313 (24.23%) aligned exactly 1 time 320855 (21.70%) aligned >1 times 96.19% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 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] 786410 / 9715489 = 0.0809 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.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 @ Thu, 16 Apr 2020 05:11:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:11:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:11:24: 1000000 INFO @ Thu, 16 Apr 2020 05:11:29: 2000000 INFO @ Thu, 16 Apr 2020 05:11:34: 3000000 INFO @ Thu, 16 Apr 2020 05:11:39: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:11:45: 5000000 INFO @ Thu, 16 Apr 2020 05:11:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.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 @ Thu, 16 Apr 2020 05:11:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:11:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:11:50: 6000000 INFO @ Thu, 16 Apr 2020 05:11:54: 1000000 INFO @ Thu, 16 Apr 2020 05:11:56: 7000000 INFO @ Thu, 16 Apr 2020 05:12:01: 2000000 INFO @ Thu, 16 Apr 2020 05:12:02: 8000000 INFO @ Thu, 16 Apr 2020 05:12:08: 9000000 INFO @ Thu, 16 Apr 2020 05:12:08: 3000000 INFO @ Thu, 16 Apr 2020 05:12:13: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 05:12:14: 4000000 INFO @ Thu, 16 Apr 2020 05:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.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 @ Thu, 16 Apr 2020 05:12:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:12:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:12:19: 11000000 INFO @ Thu, 16 Apr 2020 05:12:21: 5000000 INFO @ Thu, 16 Apr 2020 05:12:24: 1000000 INFO @ Thu, 16 Apr 2020 05:12:25: 12000000 INFO @ Thu, 16 Apr 2020 05:12:28: 6000000 INFO @ Thu, 16 Apr 2020 05:12:30: 2000000 INFO @ Thu, 16 Apr 2020 05:12:31: 13000000 INFO @ Thu, 16 Apr 2020 05:12:35: 7000000 INFO @ Thu, 16 Apr 2020 05:12:36: 3000000 INFO @ Thu, 16 Apr 2020 05:12:37: 14000000 INFO @ Thu, 16 Apr 2020 05:12:42: 4000000 INFO @ Thu, 16 Apr 2020 05:12:42: 8000000 INFO @ Thu, 16 Apr 2020 05:12:43: 15000000 INFO @ Thu, 16 Apr 2020 05:12:47: 5000000 INFO @ Thu, 16 Apr 2020 05:12:48: 16000000 INFO @ Thu, 16 Apr 2020 05:12:49: 9000000 INFO @ Thu, 16 Apr 2020 05:12:53: 6000000 INFO @ Thu, 16 Apr 2020 05:12:54: 17000000 INFO @ Thu, 16 Apr 2020 05:12:56: 10000000 INFO @ Thu, 16 Apr 2020 05:12:59: 7000000 INFO @ Thu, 16 Apr 2020 05:13:00: 18000000 INFO @ Thu, 16 Apr 2020 05:13:03: 11000000 INFO @ Thu, 16 Apr 2020 05:13:04: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:13:04: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:13:04: #1 total tags in treatment: 8648041 INFO @ Thu, 16 Apr 2020 05:13:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:13:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:13:04: #1 tags after filtering in treatment: 8122490 INFO @ Thu, 16 Apr 2020 05:13:04: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:13:04: #1 finished! INFO @ Thu, 16 Apr 2020 05:13:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:13:05: #2 number of paired peaks: 1004 INFO @ Thu, 16 Apr 2020 05:13:05: start model_add_line... INFO @ Thu, 16 Apr 2020 05:13:05: start X-correlation... INFO @ Thu, 16 Apr 2020 05:13:05: end of X-cor INFO @ Thu, 16 Apr 2020 05:13:05: #2 finished! INFO @ Thu, 16 Apr 2020 05:13:05: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:13:05: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05_model.r INFO @ Thu, 16 Apr 2020 05:13:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:13:05: 8000000 INFO @ Thu, 16 Apr 2020 05:13:10: 12000000 INFO @ Thu, 16 Apr 2020 05:13:11: 9000000 INFO @ Thu, 16 Apr 2020 05:13:17: 10000000 INFO @ Thu, 16 Apr 2020 05:13:17: 13000000 INFO @ Thu, 16 Apr 2020 05:13:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:13:23: 11000000 INFO @ Thu, 16 Apr 2020 05:13:24: 14000000 INFO @ Thu, 16 Apr 2020 05:13:28: 12000000 INFO @ Thu, 16 Apr 2020 05:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.05_summits.bed INFO @ Thu, 16 Apr 2020 05:13:31: Done! INFO @ Thu, 16 Apr 2020 05:13:31: 15000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1771 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:13:34: 13000000 INFO @ Thu, 16 Apr 2020 05:13:38: 16000000 INFO @ Thu, 16 Apr 2020 05:13:40: 14000000 INFO @ Thu, 16 Apr 2020 05:13:45: 17000000 INFO @ Thu, 16 Apr 2020 05:13:46: 15000000 INFO @ Thu, 16 Apr 2020 05:13:52: 18000000 INFO @ Thu, 16 Apr 2020 05:13:52: 16000000 INFO @ Thu, 16 Apr 2020 05:13:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:13:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:13:56: #1 total tags in treatment: 8648041 INFO @ Thu, 16 Apr 2020 05:13:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:13:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:13:56: #1 tags after filtering in treatment: 8122490 INFO @ Thu, 16 Apr 2020 05:13:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:13:56: #1 finished! INFO @ Thu, 16 Apr 2020 05:13:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:13:57: #2 number of paired peaks: 1004 INFO @ Thu, 16 Apr 2020 05:13:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:13:57: start X-correlation... INFO @ Thu, 16 Apr 2020 05:13:57: end of X-cor INFO @ Thu, 16 Apr 2020 05:13:57: #2 finished! INFO @ Thu, 16 Apr 2020 05:13:57: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:13:57: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10_model.r INFO @ Thu, 16 Apr 2020 05:13:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:13:58: 17000000 INFO @ Thu, 16 Apr 2020 05:14:03: 18000000 INFO @ Thu, 16 Apr 2020 05:14:07: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:14:07: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:14:07: #1 total tags in treatment: 8648041 INFO @ Thu, 16 Apr 2020 05:14:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:14:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:14:07: #1 tags after filtering in treatment: 8122490 INFO @ Thu, 16 Apr 2020 05:14:07: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:14:07: #1 finished! INFO @ Thu, 16 Apr 2020 05:14:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:14:08: #2 number of paired peaks: 1004 INFO @ Thu, 16 Apr 2020 05:14:08: start model_add_line... INFO @ Thu, 16 Apr 2020 05:14:08: start X-correlation... INFO @ Thu, 16 Apr 2020 05:14:08: end of X-cor INFO @ Thu, 16 Apr 2020 05:14:08: #2 finished! INFO @ Thu, 16 Apr 2020 05:14:08: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 05:14:08: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 05:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20_model.r INFO @ Thu, 16 Apr 2020 05:14:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:14:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.10_summits.bed INFO @ Thu, 16 Apr 2020 05:14:23: Done! INFO @ Thu, 16 Apr 2020 05:14:25: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1091 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708248/SRX6708248.20_summits.bed INFO @ Thu, 16 Apr 2020 05:14:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。