Job ID = 5720547 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,670,138 reads read : 25,670,138 reads written : 25,670,138 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289696.sra.cache’: 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: 00:07:56 25670138 reads; of these: 25670138 (100.00%) were unpaired; of these: 2017859 (7.86%) aligned 0 times 19138704 (74.56%) aligned exactly 1 time 4513575 (17.58%) aligned >1 times 92.14% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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_rmdupse_core] 6407425 / 23652279 = 0.2709 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 00:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.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 00:44:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:48: 1000000 INFO @ Thu, 16 Apr 2020 00:44:54: 2000000 INFO @ Thu, 16 Apr 2020 00:45:00: 3000000 INFO @ Thu, 16 Apr 2020 00:45:06: 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 00:45:12: 5000000 INFO @ Thu, 16 Apr 2020 00:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.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 00:45:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:18: 6000000 INFO @ Thu, 16 Apr 2020 00:45:19: 1000000 INFO @ Thu, 16 Apr 2020 00:45:24: 7000000 INFO @ Thu, 16 Apr 2020 00:45:25: 2000000 INFO @ Thu, 16 Apr 2020 00:45:30: 8000000 INFO @ Thu, 16 Apr 2020 00:45:31: 3000000 INFO @ Thu, 16 Apr 2020 00:45:36: 9000000 INFO @ Thu, 16 Apr 2020 00:45:36: 4000000 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 00:45:42: 10000000 INFO @ Thu, 16 Apr 2020 00:45:42: 5000000 INFO @ Thu, 16 Apr 2020 00:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.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 00:45:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:47: 11000000 INFO @ Thu, 16 Apr 2020 00:45:48: 6000000 INFO @ Thu, 16 Apr 2020 00:45:49: 1000000 INFO @ Thu, 16 Apr 2020 00:45:53: 12000000 INFO @ Thu, 16 Apr 2020 00:45:54: 7000000 INFO @ Thu, 16 Apr 2020 00:45:55: 2000000 INFO @ Thu, 16 Apr 2020 00:45:59: 13000000 INFO @ Thu, 16 Apr 2020 00:46:00: 8000000 INFO @ Thu, 16 Apr 2020 00:46:01: 3000000 INFO @ Thu, 16 Apr 2020 00:46:05: 14000000 INFO @ Thu, 16 Apr 2020 00:46:06: 9000000 INFO @ Thu, 16 Apr 2020 00:46:08: 4000000 INFO @ Thu, 16 Apr 2020 00:46:11: 15000000 INFO @ Thu, 16 Apr 2020 00:46:11: 10000000 INFO @ Thu, 16 Apr 2020 00:46:14: 5000000 INFO @ Thu, 16 Apr 2020 00:46:17: 16000000 INFO @ Thu, 16 Apr 2020 00:46:17: 11000000 INFO @ Thu, 16 Apr 2020 00:46:20: 6000000 INFO @ Thu, 16 Apr 2020 00:46:23: 17000000 INFO @ Thu, 16 Apr 2020 00:46:23: 12000000 INFO @ Thu, 16 Apr 2020 00:46:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:24: #1 total tags in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:46:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:24: #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 00:46:25: #1 tags after filtering in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:25: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:26: 7000000 INFO @ Thu, 16 Apr 2020 00:46:26: #2 number of paired peaks: 2664 INFO @ Thu, 16 Apr 2020 00:46:26: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:26: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:26: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:26: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:26: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:46:26: #2 alternative fragment length(s) may be 4,189 bps INFO @ Thu, 16 Apr 2020 00:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05_model.r INFO @ Thu, 16 Apr 2020 00:46:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:28: 13000000 INFO @ Thu, 16 Apr 2020 00:46:32: 8000000 INFO @ Thu, 16 Apr 2020 00:46:34: 14000000 INFO @ Thu, 16 Apr 2020 00:46:38: 9000000 INFO @ Thu, 16 Apr 2020 00:46:40: 15000000 INFO @ Thu, 16 Apr 2020 00:46:44: 10000000 INFO @ Thu, 16 Apr 2020 00:46:46: 16000000 INFO @ Thu, 16 Apr 2020 00:46:49: 11000000 INFO @ Thu, 16 Apr 2020 00:46:51: 17000000 INFO @ Thu, 16 Apr 2020 00:46:53: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:53: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:53: #1 total tags in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:46:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:53: #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 00:46:53: #1 tags after filtering in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:55: #2 number of paired peaks: 2664 INFO @ Thu, 16 Apr 2020 00:46:55: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:55: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:55: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:55: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:55: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:46:55: #2 alternative fragment length(s) may be 4,189 bps INFO @ Thu, 16 Apr 2020 00:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10_model.r INFO @ Thu, 16 Apr 2020 00:46:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:55: 12000000 INFO @ Thu, 16 Apr 2020 00:47:01: 13000000 INFO @ Thu, 16 Apr 2020 00:47:06: 14000000 INFO @ Thu, 16 Apr 2020 00:47:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:12: 15000000 INFO @ Thu, 16 Apr 2020 00:47:17: 16000000 INFO @ Thu, 16 Apr 2020 00:47:23: 17000000 INFO @ Thu, 16 Apr 2020 00:47:25: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:47:25: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:47:25: #1 total tags in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:47:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:25: #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 00:47:25: #1 tags after filtering in treatment: 17244854 INFO @ Thu, 16 Apr 2020 00:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:25: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:27: #2 number of paired peaks: 2664 INFO @ Thu, 16 Apr 2020 00:47:27: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:27: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:27: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:27: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:27: #2 predicted fragment length is 189 bps INFO @ Thu, 16 Apr 2020 00:47:27: #2 alternative fragment length(s) may be 4,189 bps INFO @ Thu, 16 Apr 2020 00:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20_model.r INFO @ Thu, 16 Apr 2020 00:47:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.05_summits.bed INFO @ Thu, 16 Apr 2020 00:47:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14367 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:47:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.10_summits.bed INFO @ Thu, 16 Apr 2020 00:48:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10059 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:48:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592419/SRX2592419.20_summits.bed INFO @ Thu, 16 Apr 2020 00:48:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5051 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。