Job ID = 5720548 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,123,727 reads read : 24,123,727 reads written : 24,123,727 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289697.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: 00:06:54 24123727 reads; of these: 24123727 (100.00%) were unpaired; of these: 1983796 (8.22%) aligned 0 times 17889047 (74.16%) aligned exactly 1 time 4250884 (17.62%) aligned >1 times 91.78% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 7460100 / 22139931 = 0.3370 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 00:43:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.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 00:43:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:18: 1000000 INFO @ Thu, 16 Apr 2020 00:43:24: 2000000 INFO @ Thu, 16 Apr 2020 00:43:31: 3000000 INFO @ Thu, 16 Apr 2020 00:43:38: 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 00:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.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 00:43:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:43:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:43:45: 5000000 INFO @ Thu, 16 Apr 2020 00:43:48: 1000000 INFO @ Thu, 16 Apr 2020 00:43:52: 6000000 INFO @ Thu, 16 Apr 2020 00:43:56: 2000000 INFO @ Thu, 16 Apr 2020 00:44:00: 7000000 INFO @ Thu, 16 Apr 2020 00:44:03: 3000000 INFO @ Thu, 16 Apr 2020 00:44:07: 8000000 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 00:44:10: 4000000 INFO @ Thu, 16 Apr 2020 00:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.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 00:44:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:15: 9000000 INFO @ Thu, 16 Apr 2020 00:44:18: 5000000 INFO @ Thu, 16 Apr 2020 00:44:18: 1000000 INFO @ Thu, 16 Apr 2020 00:44:22: 10000000 INFO @ Thu, 16 Apr 2020 00:44:26: 6000000 INFO @ Thu, 16 Apr 2020 00:44:26: 2000000 INFO @ Thu, 16 Apr 2020 00:44:30: 11000000 INFO @ Thu, 16 Apr 2020 00:44:34: 7000000 INFO @ Thu, 16 Apr 2020 00:44:34: 3000000 INFO @ Thu, 16 Apr 2020 00:44:38: 12000000 INFO @ Thu, 16 Apr 2020 00:44:41: 8000000 INFO @ Thu, 16 Apr 2020 00:44:41: 4000000 INFO @ Thu, 16 Apr 2020 00:44:45: 13000000 INFO @ Thu, 16 Apr 2020 00:44:49: 9000000 INFO @ Thu, 16 Apr 2020 00:44:49: 5000000 INFO @ Thu, 16 Apr 2020 00:44:53: 14000000 INFO @ Thu, 16 Apr 2020 00:44:57: 10000000 INFO @ Thu, 16 Apr 2020 00:44:57: 6000000 INFO @ Thu, 16 Apr 2020 00:44:58: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:44:58: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:44:58: #1 total tags in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:44:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:44:58: #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 00:44:58: #1 tags after filtering in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:44:58: #1 finished! INFO @ Thu, 16 Apr 2020 00:44:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:44:59: #2 number of paired peaks: 2631 INFO @ Thu, 16 Apr 2020 00:44:59: start model_add_line... INFO @ Thu, 16 Apr 2020 00:44:59: start X-correlation... INFO @ Thu, 16 Apr 2020 00:44:59: end of X-cor INFO @ Thu, 16 Apr 2020 00:44:59: #2 finished! INFO @ Thu, 16 Apr 2020 00:44:59: #2 predicted fragment length is 191 bps INFO @ Thu, 16 Apr 2020 00:44:59: #2 alternative fragment length(s) may be 4,191 bps INFO @ Thu, 16 Apr 2020 00:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05_model.r INFO @ Thu, 16 Apr 2020 00:44:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:04: 11000000 INFO @ Thu, 16 Apr 2020 00:45:05: 7000000 INFO @ Thu, 16 Apr 2020 00:45:12: 12000000 INFO @ Thu, 16 Apr 2020 00:45:13: 8000000 INFO @ Thu, 16 Apr 2020 00:45:20: 13000000 INFO @ Thu, 16 Apr 2020 00:45:20: 9000000 INFO @ Thu, 16 Apr 2020 00:45:27: 14000000 INFO @ Thu, 16 Apr 2020 00:45:28: 10000000 INFO @ Thu, 16 Apr 2020 00:45:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:45:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:45:32: #1 total tags in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:45:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:45:32: #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 00:45:32: #1 tags after filtering in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:45:32: #1 finished! INFO @ Thu, 16 Apr 2020 00:45:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:45:33: #2 number of paired peaks: 2631 INFO @ Thu, 16 Apr 2020 00:45:33: start model_add_line... INFO @ Thu, 16 Apr 2020 00:45:34: start X-correlation... INFO @ Thu, 16 Apr 2020 00:45:34: end of X-cor INFO @ Thu, 16 Apr 2020 00:45:34: #2 finished! INFO @ Thu, 16 Apr 2020 00:45:34: #2 predicted fragment length is 191 bps INFO @ Thu, 16 Apr 2020 00:45:34: #2 alternative fragment length(s) may be 4,191 bps INFO @ Thu, 16 Apr 2020 00:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10_model.r INFO @ Thu, 16 Apr 2020 00:45:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:45:36: 11000000 INFO @ Thu, 16 Apr 2020 00:45:44: 12000000 INFO @ Thu, 16 Apr 2020 00:45:51: 13000000 INFO @ Thu, 16 Apr 2020 00:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.05_summits.bed INFO @ Thu, 16 Apr 2020 00:45:52: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (16470 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:45:58: 14000000 INFO @ Thu, 16 Apr 2020 00:46:03: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:03: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:03: #1 total tags in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:46:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:03: #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 00:46:03: #1 tags after filtering in treatment: 14679831 INFO @ Thu, 16 Apr 2020 00:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:03: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:05: #2 number of paired peaks: 2631 INFO @ Thu, 16 Apr 2020 00:46:05: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:06: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:06: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:06: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:06: #2 predicted fragment length is 191 bps INFO @ Thu, 16 Apr 2020 00:46:06: #2 alternative fragment length(s) may be 4,191 bps INFO @ Thu, 16 Apr 2020 00:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20_model.r INFO @ Thu, 16 Apr 2020 00:46:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.10_summits.bed INFO @ Thu, 16 Apr 2020 00:46:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (11717 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:46:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592420/SRX2592420.20_summits.bed INFO @ Thu, 16 Apr 2020 00:47:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6007 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。