Job ID = 6454412 SRX = SRX2055944 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:04:19 prefetch.2.10.7: 1) Downloading 'SRR4069176'... 2020-06-21T09:04:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:44 prefetch.2.10.7: 'SRR4069176' is valid 2020-06-21T09:06:44 prefetch.2.10.7: 1) 'SRR4069176' was downloaded successfully Read 21130231 spots for SRR4069176/SRR4069176.sra Written 21130231 spots for SRR4069176/SRR4069176.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: 00:08:04 21130231 reads; of these: 21130231 (100.00%) were unpaired; of these: 761006 (3.60%) aligned 0 times 9544177 (45.17%) aligned exactly 1 time 10825048 (51.23%) aligned >1 times 96.40% overall alignment rate Time searching: 00:08:04 Overall time: 00:08:04 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] 4981684 / 20369225 = 0.2446 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 18:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.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 18:19:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:44: 1000000 INFO @ Sun, 21 Jun 2020 18:19:49: 2000000 INFO @ Sun, 21 Jun 2020 18:19:55: 3000000 INFO @ Sun, 21 Jun 2020 18:20:00: 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 18:20:06: 5000000 INFO @ Sun, 21 Jun 2020 18:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.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 18:20:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:13: 6000000 INFO @ Sun, 21 Jun 2020 18:20:15: 1000000 INFO @ Sun, 21 Jun 2020 18:20:19: 7000000 INFO @ Sun, 21 Jun 2020 18:20:21: 2000000 INFO @ Sun, 21 Jun 2020 18:20:26: 8000000 INFO @ Sun, 21 Jun 2020 18:20:28: 3000000 INFO @ Sun, 21 Jun 2020 18:20:33: 9000000 INFO @ Sun, 21 Jun 2020 18:20:35: 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 18:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.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 18:20:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:20:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:40: 10000000 INFO @ Sun, 21 Jun 2020 18:20:41: 5000000 INFO @ Sun, 21 Jun 2020 18:20:45: 1000000 INFO @ Sun, 21 Jun 2020 18:20:46: 11000000 INFO @ Sun, 21 Jun 2020 18:20:48: 6000000 INFO @ Sun, 21 Jun 2020 18:20:51: 2000000 INFO @ Sun, 21 Jun 2020 18:20:53: 12000000 INFO @ Sun, 21 Jun 2020 18:20:55: 7000000 INFO @ Sun, 21 Jun 2020 18:20:58: 3000000 INFO @ Sun, 21 Jun 2020 18:21:00: 13000000 INFO @ Sun, 21 Jun 2020 18:21:02: 8000000 INFO @ Sun, 21 Jun 2020 18:21:05: 4000000 INFO @ Sun, 21 Jun 2020 18:21:07: 14000000 INFO @ Sun, 21 Jun 2020 18:21:08: 9000000 INFO @ Sun, 21 Jun 2020 18:21:12: 5000000 INFO @ Sun, 21 Jun 2020 18:21:14: 15000000 INFO @ Sun, 21 Jun 2020 18:21:15: 10000000 INFO @ Sun, 21 Jun 2020 18:21:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:17: #1 total tags in treatment: 15387541 INFO @ Sun, 21 Jun 2020 18:21:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:17: #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 18:21:17: #1 tags after filtering in treatment: 15387492 INFO @ Sun, 21 Jun 2020 18:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:18: 6000000 INFO @ Sun, 21 Jun 2020 18:21:18: #2 number of paired peaks: 2385 INFO @ Sun, 21 Jun 2020 18:21:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:18: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:21:18: #2 alternative fragment length(s) may be 2,41,583,588 bps INFO @ Sun, 21 Jun 2020 18:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05_model.r WARNING @ Sun, 21 Jun 2020 18:21:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:18: #2 You may need to consider one of the other alternative d(s): 2,41,583,588 WARNING @ Sun, 21 Jun 2020 18:21:18: #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 18:21:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:21: 11000000 INFO @ Sun, 21 Jun 2020 18:21:24: 7000000 INFO @ Sun, 21 Jun 2020 18:21:27: 12000000 INFO @ Sun, 21 Jun 2020 18:21:30: 8000000 INFO @ Sun, 21 Jun 2020 18:21:34: 13000000 INFO @ Sun, 21 Jun 2020 18:21:36: 9000000 INFO @ Sun, 21 Jun 2020 18:21:40: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:42: 10000000 INFO @ Sun, 21 Jun 2020 18:21:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:46: 15000000 INFO @ Sun, 21 Jun 2020 18:21:48: 11000000 INFO @ Sun, 21 Jun 2020 18:21:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:48: #1 total tags in treatment: 15387541 INFO @ Sun, 21 Jun 2020 18:21:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:48: #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 18:21:49: #1 tags after filtering in treatment: 15387492 INFO @ Sun, 21 Jun 2020 18:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:50: #2 number of paired peaks: 2385 INFO @ Sun, 21 Jun 2020 18:21:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:50: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:21:50: #2 alternative fragment length(s) may be 2,41,583,588 bps INFO @ Sun, 21 Jun 2020 18:21:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10_model.r WARNING @ Sun, 21 Jun 2020 18:21:50: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:50: #2 You may need to consider one of the other alternative d(s): 2,41,583,588 WARNING @ Sun, 21 Jun 2020 18:21:50: #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 18:21:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:54: 12000000 INFO @ Sun, 21 Jun 2020 18:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.05_summits.bed INFO @ Sun, 21 Jun 2020 18:22:00: Done! INFO @ Sun, 21 Jun 2020 18:22:00: 13000000 pass1 - making usageList (848 chroms): 2 millis pass2 - checking and writing primary data (4041 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:05: 14000000 INFO @ Sun, 21 Jun 2020 18:22:11: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:22:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:22:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:22:13: #1 total tags in treatment: 15387541 INFO @ Sun, 21 Jun 2020 18:22:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:13: #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 18:22:14: #1 tags after filtering in treatment: 15387492 INFO @ Sun, 21 Jun 2020 18:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:15: #2 number of paired peaks: 2385 INFO @ Sun, 21 Jun 2020 18:22:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:15: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:22:15: #2 alternative fragment length(s) may be 2,41,583,588 bps INFO @ Sun, 21 Jun 2020 18:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20_model.r WARNING @ Sun, 21 Jun 2020 18:22:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:22:15: #2 You may need to consider one of the other alternative d(s): 2,41,583,588 WARNING @ Sun, 21 Jun 2020 18:22:15: #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 18:22:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.10_summits.bed INFO @ Sun, 21 Jun 2020 18:22:33: Done! pass1 - making usageList (708 chroms): 2 millis pass2 - checking and writing primary data (2838 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055944/SRX2055944.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:57: Done! pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (1793 records, 4 fields): 15 millis CompletedMACS2peakCalling