Job ID = 6456121 SRX = SRX318794 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:14 prefetch.2.10.7: 1) Downloading 'SRR927110'... 2020-06-21T10:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:00 prefetch.2.10.7: 1) 'SRR927110' was downloaded successfully Read 21575683 spots for SRR927110/SRR927110.sra Written 21575683 spots for SRR927110/SRR927110.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: 00:06:00 21575683 reads; of these: 21575683 (100.00%) were unpaired; of these: 3111440 (14.42%) aligned 0 times 12219124 (56.63%) aligned exactly 1 time 6245119 (28.95%) aligned >1 times 85.58% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3001014 / 18464243 = 0.1625 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 19:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.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 19:52:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:50: 1000000 INFO @ Sun, 21 Jun 2020 19:52:56: 2000000 INFO @ Sun, 21 Jun 2020 19:53:02: 3000000 INFO @ Sun, 21 Jun 2020 19:53:08: 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 @ Sun, 21 Jun 2020 19:53:13: 5000000 INFO @ Sun, 21 Jun 2020 19:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.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 19:53:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:19: 6000000 INFO @ Sun, 21 Jun 2020 19:53:20: 1000000 INFO @ Sun, 21 Jun 2020 19:53:25: 7000000 INFO @ Sun, 21 Jun 2020 19:53:26: 2000000 INFO @ Sun, 21 Jun 2020 19:53:30: 8000000 INFO @ Sun, 21 Jun 2020 19:53:32: 3000000 INFO @ Sun, 21 Jun 2020 19:53:36: 9000000 INFO @ Sun, 21 Jun 2020 19:53:38: 4000000 INFO @ Sun, 21 Jun 2020 19:53:42: 10000000 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 19:53:43: 5000000 INFO @ Sun, 21 Jun 2020 19:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.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 19:53:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:47: 11000000 INFO @ Sun, 21 Jun 2020 19:53:49: 6000000 INFO @ Sun, 21 Jun 2020 19:53:50: 1000000 INFO @ Sun, 21 Jun 2020 19:53:54: 12000000 INFO @ Sun, 21 Jun 2020 19:53:55: 7000000 INFO @ Sun, 21 Jun 2020 19:53:55: 2000000 INFO @ Sun, 21 Jun 2020 19:54:00: 13000000 INFO @ Sun, 21 Jun 2020 19:54:01: 8000000 INFO @ Sun, 21 Jun 2020 19:54:01: 3000000 INFO @ Sun, 21 Jun 2020 19:54:06: 14000000 INFO @ Sun, 21 Jun 2020 19:54:06: 4000000 INFO @ Sun, 21 Jun 2020 19:54:07: 9000000 INFO @ Sun, 21 Jun 2020 19:54:11: 15000000 INFO @ Sun, 21 Jun 2020 19:54:12: 5000000 INFO @ Sun, 21 Jun 2020 19:54:12: 10000000 INFO @ Sun, 21 Jun 2020 19:54:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:14: #1 total tags in treatment: 15463229 INFO @ Sun, 21 Jun 2020 19:54:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:14: #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 19:54:15: #1 tags after filtering in treatment: 15463157 INFO @ Sun, 21 Jun 2020 19:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:16: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 19:54:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:16: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:54:16: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 21 Jun 2020 19:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05_model.r WARNING @ Sun, 21 Jun 2020 19:54:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:16: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 21 Jun 2020 19:54:16: #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 19:54:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:17: 6000000 INFO @ Sun, 21 Jun 2020 19:54:18: 11000000 INFO @ Sun, 21 Jun 2020 19:54:22: 7000000 INFO @ Sun, 21 Jun 2020 19:54:24: 12000000 INFO @ Sun, 21 Jun 2020 19:54:27: 8000000 INFO @ Sun, 21 Jun 2020 19:54:30: 13000000 INFO @ Sun, 21 Jun 2020 19:54:33: 9000000 INFO @ Sun, 21 Jun 2020 19:54:36: 14000000 INFO @ Sun, 21 Jun 2020 19:54:38: 10000000 INFO @ Sun, 21 Jun 2020 19:54:42: 15000000 INFO @ Sun, 21 Jun 2020 19:54:43: 11000000 INFO @ Sun, 21 Jun 2020 19:54:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:45: #1 total tags in treatment: 15463229 INFO @ Sun, 21 Jun 2020 19:54:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:45: #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 19:54:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:45: #1 tags after filtering in treatment: 15463157 INFO @ Sun, 21 Jun 2020 19:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:46: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 19:54:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:47: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:54:47: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 21 Jun 2020 19:54:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10_model.r WARNING @ Sun, 21 Jun 2020 19:54:47: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:47: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 21 Jun 2020 19:54:47: #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 19:54:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:49: 12000000 INFO @ Sun, 21 Jun 2020 19:54:54: 13000000 INFO @ Sun, 21 Jun 2020 19:54:59: 14000000 INFO @ Sun, 21 Jun 2020 19:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:00: Done! pass1 - making usageList (617 chroms): 1 millis pass2 - checking and writing primary data (2469 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:04: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:55:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:07: #1 total tags in treatment: 15463229 INFO @ Sun, 21 Jun 2020 19:55:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:07: #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 19:55:07: #1 tags after filtering in treatment: 15463157 INFO @ Sun, 21 Jun 2020 19:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:08: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 19:55:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:08: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:55:08: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 21 Jun 2020 19:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20_model.r WARNING @ Sun, 21 Jun 2020 19:55:08: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:08: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 21 Jun 2020 19:55:08: #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 19:55:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.10_summits.bed INFO @ Sun, 21 Jun 2020 19:55:28: Done! pass1 - making usageList (539 chroms): 1 millis pass2 - checking and writing primary data (2118 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318794/SRX318794.20_summits.bed INFO @ Sun, 21 Jun 2020 19:55:51: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (1486 records, 4 fields): 13 millis CompletedMACS2peakCalling