Job ID = 6453682 SRX = SRX1361351 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:39 prefetch.2.10.7: 1) Downloading 'SRR2749789'... 2020-06-21T08:34:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:44:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:44:18 prefetch.2.10.7: 1) 'SRR2749789' was downloaded successfully Read 49142444 spots for SRR2749789/SRR2749789.sra Written 49142444 spots for SRR2749789/SRR2749789.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: 00:18:26 49142444 reads; of these: 49142444 (100.00%) were unpaired; of these: 3550819 (7.23%) aligned 0 times 22475932 (45.74%) aligned exactly 1 time 23115693 (47.04%) aligned >1 times 92.77% overall alignment rate Time searching: 00:18:26 Overall time: 00:18:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 18575891 / 45591625 = 0.4074 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 @ Sun, 21 Jun 2020 18:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.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 @ Sun, 21 Jun 2020 18:16:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:54: 1000000 INFO @ Sun, 21 Jun 2020 18:17:01: 2000000 INFO @ Sun, 21 Jun 2020 18:17:08: 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 @ Sun, 21 Jun 2020 18:17:15: 4000000 INFO @ Sun, 21 Jun 2020 18:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.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 @ Sun, 21 Jun 2020 18:17:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:23: 5000000 INFO @ Sun, 21 Jun 2020 18:17:24: 1000000 INFO @ Sun, 21 Jun 2020 18:17:31: 6000000 INFO @ Sun, 21 Jun 2020 18:17:31: 2000000 INFO @ Sun, 21 Jun 2020 18:17:39: 7000000 INFO @ Sun, 21 Jun 2020 18:17:39: 3000000 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 @ Sun, 21 Jun 2020 18:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.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 @ Sun, 21 Jun 2020 18:17:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:46: 4000000 INFO @ Sun, 21 Jun 2020 18:17:47: 8000000 INFO @ Sun, 21 Jun 2020 18:17:54: 5000000 INFO @ Sun, 21 Jun 2020 18:17:54: 1000000 INFO @ Sun, 21 Jun 2020 18:17:55: 9000000 INFO @ Sun, 21 Jun 2020 18:18:01: 6000000 INFO @ Sun, 21 Jun 2020 18:18:02: 2000000 INFO @ Sun, 21 Jun 2020 18:18:03: 10000000 INFO @ Sun, 21 Jun 2020 18:18:09: 7000000 INFO @ Sun, 21 Jun 2020 18:18:09: 3000000 INFO @ Sun, 21 Jun 2020 18:18:10: 11000000 INFO @ Sun, 21 Jun 2020 18:18:16: 8000000 INFO @ Sun, 21 Jun 2020 18:18:17: 4000000 INFO @ Sun, 21 Jun 2020 18:18:18: 12000000 INFO @ Sun, 21 Jun 2020 18:18:24: 9000000 INFO @ Sun, 21 Jun 2020 18:18:25: 5000000 INFO @ Sun, 21 Jun 2020 18:18:26: 13000000 INFO @ Sun, 21 Jun 2020 18:18:31: 10000000 INFO @ Sun, 21 Jun 2020 18:18:32: 6000000 INFO @ Sun, 21 Jun 2020 18:18:34: 14000000 INFO @ Sun, 21 Jun 2020 18:18:39: 11000000 INFO @ Sun, 21 Jun 2020 18:18:40: 7000000 INFO @ Sun, 21 Jun 2020 18:18:41: 15000000 INFO @ Sun, 21 Jun 2020 18:18:47: 12000000 INFO @ Sun, 21 Jun 2020 18:18:48: 8000000 INFO @ Sun, 21 Jun 2020 18:18:49: 16000000 INFO @ Sun, 21 Jun 2020 18:18:54: 13000000 INFO @ Sun, 21 Jun 2020 18:18:55: 9000000 INFO @ Sun, 21 Jun 2020 18:18:57: 17000000 INFO @ Sun, 21 Jun 2020 18:19:02: 14000000 INFO @ Sun, 21 Jun 2020 18:19:03: 10000000 INFO @ Sun, 21 Jun 2020 18:19:04: 18000000 INFO @ Sun, 21 Jun 2020 18:19:10: 15000000 INFO @ Sun, 21 Jun 2020 18:19:11: 11000000 INFO @ Sun, 21 Jun 2020 18:19:12: 19000000 INFO @ Sun, 21 Jun 2020 18:19:17: 16000000 INFO @ Sun, 21 Jun 2020 18:19:18: 12000000 INFO @ Sun, 21 Jun 2020 18:19:20: 20000000 INFO @ Sun, 21 Jun 2020 18:19:24: 17000000 INFO @ Sun, 21 Jun 2020 18:19:26: 13000000 INFO @ Sun, 21 Jun 2020 18:19:28: 21000000 INFO @ Sun, 21 Jun 2020 18:19:32: 18000000 INFO @ Sun, 21 Jun 2020 18:19:33: 14000000 INFO @ Sun, 21 Jun 2020 18:19:36: 22000000 INFO @ Sun, 21 Jun 2020 18:19:40: 19000000 INFO @ Sun, 21 Jun 2020 18:19:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:44: 23000000 INFO @ Sun, 21 Jun 2020 18:19:47: 20000000 INFO @ Sun, 21 Jun 2020 18:19:48: 16000000 INFO @ Sun, 21 Jun 2020 18:19:52: 24000000 INFO @ Sun, 21 Jun 2020 18:19:55: 21000000 INFO @ Sun, 21 Jun 2020 18:19:56: 17000000 INFO @ Sun, 21 Jun 2020 18:20:00: 25000000 INFO @ Sun, 21 Jun 2020 18:20:03: 22000000 INFO @ Sun, 21 Jun 2020 18:20:03: 18000000 INFO @ Sun, 21 Jun 2020 18:20:07: 26000000 INFO @ Sun, 21 Jun 2020 18:20:10: 23000000 INFO @ Sun, 21 Jun 2020 18:20:11: 19000000 INFO @ Sun, 21 Jun 2020 18:20:16: 27000000 INFO @ Sun, 21 Jun 2020 18:20:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:16: #1 total tags in treatment: 27015734 INFO @ Sun, 21 Jun 2020 18:20:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:20:17: #1 tags after filtering in treatment: 27015706 INFO @ Sun, 21 Jun 2020 18:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:18: 24000000 INFO @ Sun, 21 Jun 2020 18:20:19: #2 number of paired peaks: 2117 INFO @ Sun, 21 Jun 2020 18:20:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:19: 20000000 INFO @ Sun, 21 Jun 2020 18:20:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:19: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:20:19: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:19: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:20:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:20:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:25: 25000000 INFO @ Sun, 21 Jun 2020 18:20:26: 21000000 INFO @ Sun, 21 Jun 2020 18:20:32: 26000000 INFO @ Sun, 21 Jun 2020 18:20:33: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:20:39: 27000000 INFO @ Sun, 21 Jun 2020 18:20:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:39: #1 total tags in treatment: 27015734 INFO @ Sun, 21 Jun 2020 18:20:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:20:40: #1 tags after filtering in treatment: 27015706 INFO @ Sun, 21 Jun 2020 18:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:40: 23000000 INFO @ Sun, 21 Jun 2020 18:20:42: #2 number of paired peaks: 2117 INFO @ Sun, 21 Jun 2020 18:20:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:42: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:20:42: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:42: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:20:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:20:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:47: 24000000 INFO @ Sun, 21 Jun 2020 18:20:53: 25000000 INFO @ Sun, 21 Jun 2020 18:20:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:59: 26000000 INFO @ Sun, 21 Jun 2020 18:21:05: 27000000 INFO @ Sun, 21 Jun 2020 18:21:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:06: #1 total tags in treatment: 27015734 INFO @ Sun, 21 Jun 2020 18:21:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:21:07: #1 tags after filtering in treatment: 27015706 INFO @ Sun, 21 Jun 2020 18:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:08: #2 number of paired peaks: 2117 INFO @ Sun, 21 Jun 2020 18:21:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:09: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:21:09: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:09: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:21:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:21:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361351/SRX1361351.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling