Job ID = 6498433 SRX = SRX495290 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:58:31 prefetch.2.10.7: 1) Downloading 'SRR1198795'... 2020-06-25T23:58:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:30 prefetch.2.10.7: 1) 'SRR1198795' was downloaded successfully Read 35725350 spots for SRR1198795/SRR1198795.sra Written 35725350 spots for SRR1198795/SRR1198795.sra 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: 00:18:00 35725350 reads; of these: 35725350 (100.00%) were unpaired; of these: 2291724 (6.41%) aligned 0 times 13704296 (38.36%) aligned exactly 1 time 19729330 (55.23%) aligned >1 times 93.59% overall alignment rate Time searching: 00:18:00 Overall time: 00:18:00 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 16 files... [bam_rmdupse_core] 17517755 / 33433626 = 0.5240 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 @ Fri, 26 Jun 2020 09:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.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 @ Fri, 26 Jun 2020 09:29:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:29:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:29:11: 1000000 INFO @ Fri, 26 Jun 2020 09:29:16: 2000000 INFO @ Fri, 26 Jun 2020 09:29:22: 3000000 INFO @ Fri, 26 Jun 2020 09:29:28: 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 @ Fri, 26 Jun 2020 09:29:34: 5000000 INFO @ Fri, 26 Jun 2020 09:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.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 @ Fri, 26 Jun 2020 09:29:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:29:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:29:40: 6000000 INFO @ Fri, 26 Jun 2020 09:29:41: 1000000 INFO @ Fri, 26 Jun 2020 09:29:46: 7000000 INFO @ Fri, 26 Jun 2020 09:29:47: 2000000 INFO @ Fri, 26 Jun 2020 09:29:52: 8000000 INFO @ Fri, 26 Jun 2020 09:29:53: 3000000 INFO @ Fri, 26 Jun 2020 09:29:58: 9000000 INFO @ Fri, 26 Jun 2020 09:30:00: 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 @ Fri, 26 Jun 2020 09:30:04: 10000000 INFO @ Fri, 26 Jun 2020 09:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.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 @ Fri, 26 Jun 2020 09:30:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:30:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:30:06: 5000000 INFO @ Fri, 26 Jun 2020 09:30:11: 11000000 INFO @ Fri, 26 Jun 2020 09:30:11: 1000000 INFO @ Fri, 26 Jun 2020 09:30:12: 6000000 INFO @ Fri, 26 Jun 2020 09:30:17: 12000000 INFO @ Fri, 26 Jun 2020 09:30:18: 2000000 INFO @ Fri, 26 Jun 2020 09:30:19: 7000000 INFO @ Fri, 26 Jun 2020 09:30:24: 13000000 INFO @ Fri, 26 Jun 2020 09:30:24: 3000000 INFO @ Fri, 26 Jun 2020 09:30:25: 8000000 INFO @ Fri, 26 Jun 2020 09:30:30: 4000000 INFO @ Fri, 26 Jun 2020 09:30:30: 14000000 INFO @ Fri, 26 Jun 2020 09:30:32: 9000000 INFO @ Fri, 26 Jun 2020 09:30:36: 5000000 INFO @ Fri, 26 Jun 2020 09:30:37: 15000000 INFO @ Fri, 26 Jun 2020 09:30:38: 10000000 INFO @ Fri, 26 Jun 2020 09:30:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:30:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:30:43: #1 total tags in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:30:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:30:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:30:43: 6000000 INFO @ Fri, 26 Jun 2020 09:30:43: #1 tags after filtering in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:30:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:30:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:44: #2 number of paired peaks: 1831 INFO @ Fri, 26 Jun 2020 09:30:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:44: 11000000 INFO @ Fri, 26 Jun 2020 09:30:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:44: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:30:44: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 09:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05_model.r WARNING @ Fri, 26 Jun 2020 09:30:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:30:44: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 09:30:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:30:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:30:49: 7000000 INFO @ Fri, 26 Jun 2020 09:30:51: 12000000 INFO @ Fri, 26 Jun 2020 09:30:55: 8000000 INFO @ Fri, 26 Jun 2020 09:30:57: 13000000 INFO @ Fri, 26 Jun 2020 09:31:01: 9000000 INFO @ Fri, 26 Jun 2020 09:31:03: 14000000 INFO @ Fri, 26 Jun 2020 09:31:08: 10000000 INFO @ Fri, 26 Jun 2020 09:31:10: 15000000 INFO @ Fri, 26 Jun 2020 09:31:14: 11000000 INFO @ Fri, 26 Jun 2020 09:31:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:31:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:31:15: #1 total tags in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:31:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:31:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:31:16: #1 tags after filtering in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:31:16: #1 finished! INFO @ Fri, 26 Jun 2020 09:31:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:31:17: #2 number of paired peaks: 1831 INFO @ Fri, 26 Jun 2020 09:31:17: start model_add_line... INFO @ Fri, 26 Jun 2020 09:31:17: start X-correlation... INFO @ Fri, 26 Jun 2020 09:31:17: end of X-cor INFO @ Fri, 26 Jun 2020 09:31:17: #2 finished! INFO @ Fri, 26 Jun 2020 09:31:17: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:31:17: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 09:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10_model.r WARNING @ Fri, 26 Jun 2020 09:31:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:31:17: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 09:31:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:31:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:31:20: 12000000 INFO @ Fri, 26 Jun 2020 09:31:26: 13000000 INFO @ Fri, 26 Jun 2020 09:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.05_summits.bed INFO @ Fri, 26 Jun 2020 09:31:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:31:32: 14000000 INFO @ Fri, 26 Jun 2020 09:31:38: 15000000 INFO @ Fri, 26 Jun 2020 09:31:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:31:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:31:43: #1 total tags in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:31:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:31:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:31:44: #1 tags after filtering in treatment: 15915871 INFO @ Fri, 26 Jun 2020 09:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:31:44: #1 finished! INFO @ Fri, 26 Jun 2020 09:31:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:31:45: #2 number of paired peaks: 1831 INFO @ Fri, 26 Jun 2020 09:31:45: start model_add_line... INFO @ Fri, 26 Jun 2020 09:31:45: start X-correlation... INFO @ Fri, 26 Jun 2020 09:31:45: end of X-cor INFO @ Fri, 26 Jun 2020 09:31:45: #2 finished! INFO @ Fri, 26 Jun 2020 09:31:45: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:31:45: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 09:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20_model.r WARNING @ Fri, 26 Jun 2020 09:31:45: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:31:45: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 09:31:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:31:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:31:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.10_summits.bed INFO @ Fri, 26 Jun 2020 09:32:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:32:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495290/SRX495290.20_summits.bed INFO @ Fri, 26 Jun 2020 09:32:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling