Job ID = 6455362 SRX = SRX287727 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:10 prefetch.2.10.7: 1) Downloading 'SRR869916'... 2020-06-21T09:53:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:57:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:57:43 prefetch.2.10.7: 1) 'SRR869916' was downloaded successfully Read 21366297 spots for SRR869916/SRR869916.sra Written 21366297 spots for SRR869916/SRR869916.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: 00:06:59 21366297 reads; of these: 21366297 (100.00%) were unpaired; of these: 1510248 (7.07%) aligned 0 times 9113777 (42.65%) aligned exactly 1 time 10742272 (50.28%) aligned >1 times 92.93% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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 12 files... [bam_rmdupse_core] 4149838 / 19856049 = 0.2090 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 19:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.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 19:10:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:44: 1000000 INFO @ Sun, 21 Jun 2020 19:10:49: 2000000 INFO @ Sun, 21 Jun 2020 19:10:54: 3000000 INFO @ Sun, 21 Jun 2020 19:10:59: 4000000 INFO @ Sun, 21 Jun 2020 19:11:04: 5000000 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 19:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.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 19:11:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:09: 6000000 INFO @ Sun, 21 Jun 2020 19:11:14: 1000000 INFO @ Sun, 21 Jun 2020 19:11:14: 7000000 INFO @ Sun, 21 Jun 2020 19:11:19: 2000000 INFO @ Sun, 21 Jun 2020 19:11:20: 8000000 INFO @ Sun, 21 Jun 2020 19:11:25: 3000000 INFO @ Sun, 21 Jun 2020 19:11:25: 9000000 INFO @ Sun, 21 Jun 2020 19:11:30: 4000000 INFO @ Sun, 21 Jun 2020 19:11:31: 10000000 INFO @ Sun, 21 Jun 2020 19:11:36: 5000000 INFO @ Sun, 21 Jun 2020 19:11:36: 11000000 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 19:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.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 19:11:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:41: 6000000 INFO @ Sun, 21 Jun 2020 19:11:42: 12000000 INFO @ Sun, 21 Jun 2020 19:11:44: 1000000 INFO @ Sun, 21 Jun 2020 19:11:47: 7000000 INFO @ Sun, 21 Jun 2020 19:11:47: 13000000 INFO @ Sun, 21 Jun 2020 19:11:49: 2000000 INFO @ Sun, 21 Jun 2020 19:11:52: 8000000 INFO @ Sun, 21 Jun 2020 19:11:53: 14000000 INFO @ Sun, 21 Jun 2020 19:11:55: 3000000 INFO @ Sun, 21 Jun 2020 19:11:58: 9000000 INFO @ Sun, 21 Jun 2020 19:11:58: 15000000 INFO @ Sun, 21 Jun 2020 19:12:00: 4000000 INFO @ Sun, 21 Jun 2020 19:12:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:02: #1 total tags in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:12:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:02: #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 19:12:03: #1 tags after filtering in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:03: 10000000 INFO @ Sun, 21 Jun 2020 19:12:04: #2 number of paired peaks: 1752 INFO @ Sun, 21 Jun 2020 19:12:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:04: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:12:04: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 19:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:04: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:04: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 19:12:04: #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 19:12:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:05: 5000000 INFO @ Sun, 21 Jun 2020 19:12:09: 11000000 INFO @ Sun, 21 Jun 2020 19:12:11: 6000000 INFO @ Sun, 21 Jun 2020 19:12:15: 12000000 INFO @ Sun, 21 Jun 2020 19:12:16: 7000000 INFO @ Sun, 21 Jun 2020 19:12:20: 13000000 INFO @ Sun, 21 Jun 2020 19:12:21: 8000000 INFO @ Sun, 21 Jun 2020 19:12:26: 14000000 INFO @ Sun, 21 Jun 2020 19:12:27: 9000000 INFO @ Sun, 21 Jun 2020 19:12:31: 15000000 INFO @ Sun, 21 Jun 2020 19:12:32: 10000000 INFO @ Sun, 21 Jun 2020 19:12:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:12:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:12:35: #1 total tags in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:12:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:35: #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 19:12:35: #1 tags after filtering in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:37: #2 number of paired peaks: 1752 INFO @ Sun, 21 Jun 2020 19:12:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:37: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:12:37: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 19:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:37: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:37: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 19:12:37: #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 19:12:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:37: 11000000 INFO @ Sun, 21 Jun 2020 19:12:43: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.05_summits.bed INFO @ Sun, 21 Jun 2020 19:12:47: Done! pass1 - making usageList (1099 chroms): 1 millis pass2 - checking and writing primary data (4527 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:12:48: 13000000 INFO @ Sun, 21 Jun 2020 19:12:53: 14000000 INFO @ Sun, 21 Jun 2020 19:12:59: 15000000 INFO @ Sun, 21 Jun 2020 19:13:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:03: #1 total tags in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:13:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:03: #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 19:13:03: #1 tags after filtering in treatment: 15706211 INFO @ Sun, 21 Jun 2020 19:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:04: #2 number of paired peaks: 1752 INFO @ Sun, 21 Jun 2020 19:13:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:04: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:13:04: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 19:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20_model.r WARNING @ Sun, 21 Jun 2020 19:13:04: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:04: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 19:13:04: #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 19:13:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:18: Done! pass1 - making usageList (836 chroms): 1 millis pass2 - checking and writing primary data (2960 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287727/SRX287727.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:47: Done! pass1 - making usageList (615 chroms): 1 millis pass2 - checking and writing primary data (1991 records, 4 fields): 17 millis CompletedMACS2peakCalling