Job ID = 6454667 SRX = SRX2458928 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:29 prefetch.2.10.7: 1) Downloading 'SRR5140277'... 2020-06-21T09:27:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:31:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:31:34 prefetch.2.10.7: 1) 'SRR5140277' was downloaded successfully Read 19642448 spots for SRR5140277/SRR5140277.sra Written 19642448 spots for SRR5140277/SRR5140277.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: 00:05:28 19642448 reads; of these: 19642448 (100.00%) were unpaired; of these: 1476771 (7.52%) aligned 0 times 12431764 (63.29%) aligned exactly 1 time 5733913 (29.19%) aligned >1 times 92.48% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3519989 / 18165677 = 0.1938 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 18:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.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 18:42:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:42: 1000000 INFO @ Sun, 21 Jun 2020 18:42:47: 2000000 INFO @ Sun, 21 Jun 2020 18:42:53: 3000000 INFO @ Sun, 21 Jun 2020 18:42:59: 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 18:43:04: 5000000 INFO @ Sun, 21 Jun 2020 18:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.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 18:43:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:11: 6000000 INFO @ Sun, 21 Jun 2020 18:43:12: 1000000 INFO @ Sun, 21 Jun 2020 18:43:17: 7000000 INFO @ Sun, 21 Jun 2020 18:43:19: 2000000 INFO @ Sun, 21 Jun 2020 18:43:23: 8000000 INFO @ Sun, 21 Jun 2020 18:43:25: 3000000 INFO @ Sun, 21 Jun 2020 18:43:29: 9000000 INFO @ Sun, 21 Jun 2020 18:43:31: 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 @ Sun, 21 Jun 2020 18:43:36: 10000000 INFO @ Sun, 21 Jun 2020 18:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.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 18:43:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:38: 5000000 INFO @ Sun, 21 Jun 2020 18:43:42: 11000000 INFO @ Sun, 21 Jun 2020 18:43:43: 1000000 INFO @ Sun, 21 Jun 2020 18:43:44: 6000000 INFO @ Sun, 21 Jun 2020 18:43:49: 12000000 INFO @ Sun, 21 Jun 2020 18:43:49: 2000000 INFO @ Sun, 21 Jun 2020 18:43:51: 7000000 INFO @ Sun, 21 Jun 2020 18:43:56: 13000000 INFO @ Sun, 21 Jun 2020 18:43:56: 3000000 INFO @ Sun, 21 Jun 2020 18:43:57: 8000000 INFO @ Sun, 21 Jun 2020 18:44:02: 14000000 INFO @ Sun, 21 Jun 2020 18:44:02: 4000000 INFO @ Sun, 21 Jun 2020 18:44:04: 9000000 INFO @ Sun, 21 Jun 2020 18:44:07: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:44:07: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:44:07: #1 total tags in treatment: 14645688 INFO @ Sun, 21 Jun 2020 18:44:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:07: #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 18:44:07: #1 tags after filtering in treatment: 14645613 INFO @ Sun, 21 Jun 2020 18:44:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:08: #2 number of paired peaks: 2031 INFO @ Sun, 21 Jun 2020 18:44:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:08: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:44:08: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 18:44:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05_model.r WARNING @ Sun, 21 Jun 2020 18:44:08: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:08: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 18:44:08: #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 18:44:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:09: 5000000 INFO @ Sun, 21 Jun 2020 18:44:10: 10000000 INFO @ Sun, 21 Jun 2020 18:44:15: 6000000 INFO @ Sun, 21 Jun 2020 18:44:17: 11000000 INFO @ Sun, 21 Jun 2020 18:44:22: 7000000 INFO @ Sun, 21 Jun 2020 18:44:23: 12000000 INFO @ Sun, 21 Jun 2020 18:44:28: 8000000 INFO @ Sun, 21 Jun 2020 18:44:30: 13000000 INFO @ Sun, 21 Jun 2020 18:44:34: 9000000 INFO @ Sun, 21 Jun 2020 18:44:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:36: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:41: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:44:41: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:44:41: #1 total tags in treatment: 14645688 INFO @ Sun, 21 Jun 2020 18:44:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:41: #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 18:44:41: 10000000 INFO @ Sun, 21 Jun 2020 18:44:41: #1 tags after filtering in treatment: 14645613 INFO @ Sun, 21 Jun 2020 18:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:42: #2 number of paired peaks: 2031 INFO @ Sun, 21 Jun 2020 18:44:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:43: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:44:43: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 18:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10_model.r WARNING @ Sun, 21 Jun 2020 18:44:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:43: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 18:44:43: #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 18:44:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:47: 11000000 INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:50: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:53: 12000000 INFO @ Sun, 21 Jun 2020 18:44:59: 13000000 INFO @ Sun, 21 Jun 2020 18:45:04: 14000000 INFO @ Sun, 21 Jun 2020 18:45:08: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:45:08: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:45:08: #1 total tags in treatment: 14645688 INFO @ Sun, 21 Jun 2020 18:45:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:08: #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 18:45:09: #1 tags after filtering in treatment: 14645613 INFO @ Sun, 21 Jun 2020 18:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:10: #2 number of paired peaks: 2031 INFO @ Sun, 21 Jun 2020 18:45:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:10: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:45:10: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 18:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20_model.r WARNING @ Sun, 21 Jun 2020 18:45:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:10: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 18:45:10: #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 18:45:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.10_summits.bed INFO @ Sun, 21 Jun 2020 18:45:24: Done! pass1 - making usageList (535 chroms): 1 millis pass2 - checking and writing primary data (2211 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458928/SRX2458928.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:53: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (1573 records, 4 fields): 14 millis CompletedMACS2peakCalling