Job ID = 5721151 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,619,066 reads read : 27,238,132 reads written : 27,238,132 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: 00:18:30 13619066 reads; of these: 13619066 (100.00%) were paired; of these: 3930930 (28.86%) aligned concordantly 0 times 7920969 (58.16%) aligned concordantly exactly 1 time 1767167 (12.98%) aligned concordantly >1 times ---- 3930930 pairs aligned concordantly 0 times; of these: 183908 (4.68%) aligned discordantly 1 time ---- 3747022 pairs aligned 0 times concordantly or discordantly; of these: 7494044 mates make up the pairs; of these: 7054349 (94.13%) aligned 0 times 229232 (3.06%) aligned exactly 1 time 210463 (2.81%) aligned >1 times 74.10% overall alignment rate Time searching: 00:18:30 Overall time: 00:18:30 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] 561116 / 9866133 = 0.0569 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 05:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.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 05:51:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:51:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:52:06: 1000000 INFO @ Thu, 16 Apr 2020 05:52:14: 2000000 INFO @ Thu, 16 Apr 2020 05:52:21: 3000000 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 05:52:28: 4000000 INFO @ Thu, 16 Apr 2020 05:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.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 05:52:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:52:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:52:36: 5000000 INFO @ Thu, 16 Apr 2020 05:52:36: 1000000 INFO @ Thu, 16 Apr 2020 05:52:44: 6000000 INFO @ Thu, 16 Apr 2020 05:52:44: 2000000 INFO @ Thu, 16 Apr 2020 05:52:51: 3000000 INFO @ Thu, 16 Apr 2020 05:52:52: 7000000 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 05:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.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 05:52:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:52:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:52:59: 4000000 INFO @ Thu, 16 Apr 2020 05:52:59: 8000000 INFO @ Thu, 16 Apr 2020 05:53:07: 5000000 INFO @ Thu, 16 Apr 2020 05:53:07: 1000000 INFO @ Thu, 16 Apr 2020 05:53:08: 9000000 INFO @ Thu, 16 Apr 2020 05:53:14: 6000000 INFO @ Thu, 16 Apr 2020 05:53:15: 2000000 INFO @ Thu, 16 Apr 2020 05:53:17: 10000000 INFO @ Thu, 16 Apr 2020 05:53:22: 7000000 INFO @ Thu, 16 Apr 2020 05:53:23: 3000000 INFO @ Thu, 16 Apr 2020 05:53:25: 11000000 INFO @ Thu, 16 Apr 2020 05:53:30: 8000000 INFO @ Thu, 16 Apr 2020 05:53:32: 4000000 INFO @ Thu, 16 Apr 2020 05:53:34: 12000000 INFO @ Thu, 16 Apr 2020 05:53:38: 9000000 INFO @ Thu, 16 Apr 2020 05:53:40: 5000000 INFO @ Thu, 16 Apr 2020 05:53:42: 13000000 INFO @ Thu, 16 Apr 2020 05:53:46: 10000000 INFO @ Thu, 16 Apr 2020 05:53:48: 6000000 INFO @ Thu, 16 Apr 2020 05:53:50: 14000000 INFO @ Thu, 16 Apr 2020 05:53:54: 11000000 INFO @ Thu, 16 Apr 2020 05:53:57: 7000000 INFO @ Thu, 16 Apr 2020 05:53:59: 15000000 INFO @ Thu, 16 Apr 2020 05:54:02: 12000000 INFO @ Thu, 16 Apr 2020 05:54:05: 8000000 INFO @ Thu, 16 Apr 2020 05:54:08: 16000000 INFO @ Thu, 16 Apr 2020 05:54:10: 13000000 INFO @ Thu, 16 Apr 2020 05:54:14: 9000000 INFO @ Thu, 16 Apr 2020 05:54:17: 17000000 INFO @ Thu, 16 Apr 2020 05:54:18: 14000000 INFO @ Thu, 16 Apr 2020 05:54:23: 10000000 INFO @ Thu, 16 Apr 2020 05:54:25: 18000000 INFO @ Thu, 16 Apr 2020 05:54:26: 15000000 INFO @ Thu, 16 Apr 2020 05:54:31: 11000000 INFO @ Thu, 16 Apr 2020 05:54:33: 19000000 INFO @ Thu, 16 Apr 2020 05:54:34: 16000000 INFO @ Thu, 16 Apr 2020 05:54:34: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:54:34: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:54:34: #1 total tags in treatment: 9133011 INFO @ Thu, 16 Apr 2020 05:54:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:54:34: #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 05:54:34: #1 tags after filtering in treatment: 7718916 INFO @ Thu, 16 Apr 2020 05:54:34: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:54:34: #1 finished! INFO @ Thu, 16 Apr 2020 05:54:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:54:35: #2 number of paired peaks: 4962 INFO @ Thu, 16 Apr 2020 05:54:35: start model_add_line... INFO @ Thu, 16 Apr 2020 05:54:35: start X-correlation... INFO @ Thu, 16 Apr 2020 05:54:35: end of X-cor INFO @ Thu, 16 Apr 2020 05:54:35: #2 finished! INFO @ Thu, 16 Apr 2020 05:54:35: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:54:35: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05_model.r INFO @ Thu, 16 Apr 2020 05:54:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:54:39: 12000000 INFO @ Thu, 16 Apr 2020 05:54:41: 17000000 INFO @ Thu, 16 Apr 2020 05:54:47: 13000000 INFO @ Thu, 16 Apr 2020 05:54:49: 18000000 INFO @ Thu, 16 Apr 2020 05:54:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:54:55: 14000000 INFO @ Thu, 16 Apr 2020 05:54:56: 19000000 INFO @ Thu, 16 Apr 2020 05:54:57: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:54:57: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:54:57: #1 total tags in treatment: 9133011 INFO @ Thu, 16 Apr 2020 05:54:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:54:57: #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 05:54:57: #1 tags after filtering in treatment: 7718916 INFO @ Thu, 16 Apr 2020 05:54:57: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:54:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:54:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:54:58: #2 number of paired peaks: 4962 INFO @ Thu, 16 Apr 2020 05:54:58: start model_add_line... INFO @ Thu, 16 Apr 2020 05:54:58: start X-correlation... INFO @ Thu, 16 Apr 2020 05:54:58: end of X-cor INFO @ Thu, 16 Apr 2020 05:54:58: #2 finished! INFO @ Thu, 16 Apr 2020 05:54:58: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:54:58: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10_model.r INFO @ Thu, 16 Apr 2020 05:54:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:55:03: 15000000 INFO @ Thu, 16 Apr 2020 05:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.05_summits.bed INFO @ Thu, 16 Apr 2020 05:55:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8789 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:55:10: 16000000 INFO @ Thu, 16 Apr 2020 05:55:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:55:18: 17000000 INFO @ Thu, 16 Apr 2020 05:55:25: 18000000 INFO @ Thu, 16 Apr 2020 05:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.10_summits.bed INFO @ Thu, 16 Apr 2020 05:55:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6952 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:55:32: 19000000 INFO @ Thu, 16 Apr 2020 05:55:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:55:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:55:33: #1 total tags in treatment: 9133011 INFO @ Thu, 16 Apr 2020 05:55:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:55:33: #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 05:55:33: #1 tags after filtering in treatment: 7718916 INFO @ Thu, 16 Apr 2020 05:55:33: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:55:33: #1 finished! INFO @ Thu, 16 Apr 2020 05:55:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:55:34: #2 number of paired peaks: 4962 INFO @ Thu, 16 Apr 2020 05:55:34: start model_add_line... INFO @ Thu, 16 Apr 2020 05:55:34: start X-correlation... INFO @ Thu, 16 Apr 2020 05:55:34: end of X-cor INFO @ Thu, 16 Apr 2020 05:55:34: #2 finished! INFO @ Thu, 16 Apr 2020 05:55:34: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:55:34: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20_model.r INFO @ Thu, 16 Apr 2020 05:55:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:55:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:55:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708289/SRX6708289.20_summits.bed INFO @ Thu, 16 Apr 2020 05:56:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5265 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。