Job ID = 6457968 SRX = SRX4933876 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:19:04 prefetch.2.10.7: 1) Downloading 'SRR8107266'... 2020-06-21T12:19:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:26:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:26:19 prefetch.2.10.7: 1) 'SRR8107266' was downloaded successfully Read 51562425 spots for SRR8107266/SRR8107266.sra Written 51562425 spots for SRR8107266/SRR8107266.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: 00:14:42 51562425 reads; of these: 51562425 (100.00%) were unpaired; of these: 1486303 (2.88%) aligned 0 times 35990038 (69.80%) aligned exactly 1 time 14086084 (27.32%) aligned >1 times 97.12% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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 24 files... [bam_rmdupse_core] 34983980 / 50076122 = 0.6986 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 21:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.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 21:53:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:25: 1000000 INFO @ Sun, 21 Jun 2020 21:53:31: 2000000 INFO @ Sun, 21 Jun 2020 21:53:38: 3000000 INFO @ Sun, 21 Jun 2020 21:53:44: 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 21:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.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 21:53:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:51: 5000000 INFO @ Sun, 21 Jun 2020 21:53:56: 1000000 INFO @ Sun, 21 Jun 2020 21:53:58: 6000000 INFO @ Sun, 21 Jun 2020 21:54:03: 2000000 INFO @ Sun, 21 Jun 2020 21:54:05: 7000000 INFO @ Sun, 21 Jun 2020 21:54:10: 3000000 INFO @ Sun, 21 Jun 2020 21:54:12: 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 @ Sun, 21 Jun 2020 21:54:17: 4000000 INFO @ Sun, 21 Jun 2020 21:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.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 21:54:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:20: 9000000 INFO @ Sun, 21 Jun 2020 21:54:25: 5000000 INFO @ Sun, 21 Jun 2020 21:54:28: 1000000 INFO @ Sun, 21 Jun 2020 21:54:28: 10000000 INFO @ Sun, 21 Jun 2020 21:54:34: 6000000 INFO @ Sun, 21 Jun 2020 21:54:36: 2000000 INFO @ Sun, 21 Jun 2020 21:54:37: 11000000 INFO @ Sun, 21 Jun 2020 21:54:42: 7000000 INFO @ Sun, 21 Jun 2020 21:54:45: 3000000 INFO @ Sun, 21 Jun 2020 21:54:45: 12000000 INFO @ Sun, 21 Jun 2020 21:54:50: 8000000 INFO @ Sun, 21 Jun 2020 21:54:54: 13000000 INFO @ Sun, 21 Jun 2020 21:54:54: 4000000 INFO @ Sun, 21 Jun 2020 21:54:58: 9000000 INFO @ Sun, 21 Jun 2020 21:55:02: 14000000 INFO @ Sun, 21 Jun 2020 21:55:03: 5000000 INFO @ Sun, 21 Jun 2020 21:55:07: 10000000 INFO @ Sun, 21 Jun 2020 21:55:11: 15000000 INFO @ Sun, 21 Jun 2020 21:55:11: 6000000 INFO @ Sun, 21 Jun 2020 21:55:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:55:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:55:12: #1 total tags in treatment: 15092142 INFO @ Sun, 21 Jun 2020 21:55:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:12: #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 21:55:12: #1 tags after filtering in treatment: 15092140 INFO @ Sun, 21 Jun 2020 21:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:13: #2 number of paired peaks: 2003 INFO @ Sun, 21 Jun 2020 21:55:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:14: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:14: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:14: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:14: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:55:14: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 21:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:14: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:14: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 21:55:14: #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 21:55:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:15: 11000000 INFO @ Sun, 21 Jun 2020 21:55:20: 7000000 INFO @ Sun, 21 Jun 2020 21:55:24: 12000000 INFO @ Sun, 21 Jun 2020 21:55:28: 8000000 INFO @ Sun, 21 Jun 2020 21:55:32: 13000000 INFO @ Sun, 21 Jun 2020 21:55:37: 9000000 INFO @ Sun, 21 Jun 2020 21:55:40: 14000000 INFO @ Sun, 21 Jun 2020 21:55:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:45: 10000000 INFO @ Sun, 21 Jun 2020 21:55:48: 15000000 INFO @ Sun, 21 Jun 2020 21:55:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:55:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:55:49: #1 total tags in treatment: 15092142 INFO @ Sun, 21 Jun 2020 21:55:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:49: #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 21:55:49: #1 tags after filtering in treatment: 15092140 INFO @ Sun, 21 Jun 2020 21:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:50: #2 number of paired peaks: 2003 INFO @ Sun, 21 Jun 2020 21:55:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:50: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:55:50: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 21:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:50: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 21:55:50: #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 21:55:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:53: 11000000 INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:00: Done! pass1 - making usageList (1149 chroms): 2 millis pass2 - checking and writing primary data (6545 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:01: 12000000 INFO @ Sun, 21 Jun 2020 21:56:09: 13000000 INFO @ Sun, 21 Jun 2020 21:56:16: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:24: 15000000 INFO @ Sun, 21 Jun 2020 21:56:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:56:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:56:25: #1 total tags in treatment: 15092142 INFO @ Sun, 21 Jun 2020 21:56:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:25: #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 21:56:25: #1 tags after filtering in treatment: 15092140 INFO @ Sun, 21 Jun 2020 21:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:26: #2 number of paired peaks: 2003 INFO @ Sun, 21 Jun 2020 21:56:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:26: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 21:56:26: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 21:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:26: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:26: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 21:56:26: #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 21:56:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:36: Done! pass1 - making usageList (851 chroms): 2 millis pass2 - checking and writing primary data (3708 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:56:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933876/SRX4933876.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:10: Done! pass1 - making usageList (594 chroms): 2 millis pass2 - checking and writing primary data (2120 records, 4 fields): 19 millis CompletedMACS2peakCalling