Job ID = 6527681 SRX = SRX2055953 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:46:14 prefetch.2.10.7: 1) Downloading 'SRR4069185'... 2020-06-29T14:46:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:48:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:48:11 prefetch.2.10.7: 1) 'SRR4069185' was downloaded successfully Read 27968435 spots for SRR4069185/SRR4069185.sra Written 27968435 spots for SRR4069185/SRR4069185.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: 00:14:10 27968435 reads; of these: 27968435 (100.00%) were unpaired; of these: 867528 (3.10%) aligned 0 times 13389765 (47.87%) aligned exactly 1 time 13711142 (49.02%) aligned >1 times 96.90% overall alignment rate Time searching: 00:14:10 Overall time: 00:14:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4263780 / 27100907 = 0.1573 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 @ Tue, 30 Jun 2020 00:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.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 @ Tue, 30 Jun 2020 00:18:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:18:18: 1000000 INFO @ Tue, 30 Jun 2020 00:18:23: 2000000 INFO @ Tue, 30 Jun 2020 00:18:28: 3000000 INFO @ Tue, 30 Jun 2020 00:18:34: 4000000 INFO @ Tue, 30 Jun 2020 00:18:40: 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 @ Tue, 30 Jun 2020 00:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.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 @ Tue, 30 Jun 2020 00:18:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:18:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:18:46: 6000000 INFO @ Tue, 30 Jun 2020 00:18:49: 1000000 INFO @ Tue, 30 Jun 2020 00:18:52: 7000000 INFO @ Tue, 30 Jun 2020 00:18:56: 2000000 INFO @ Tue, 30 Jun 2020 00:18:59: 8000000 INFO @ Tue, 30 Jun 2020 00:19:02: 3000000 INFO @ Tue, 30 Jun 2020 00:19:05: 9000000 INFO @ Tue, 30 Jun 2020 00:19:09: 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 @ Tue, 30 Jun 2020 00:19:11: 10000000 INFO @ Tue, 30 Jun 2020 00:19:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.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 @ Tue, 30 Jun 2020 00:19:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:19:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:19:16: 5000000 INFO @ Tue, 30 Jun 2020 00:19:18: 11000000 INFO @ Tue, 30 Jun 2020 00:19:19: 1000000 INFO @ Tue, 30 Jun 2020 00:19:22: 6000000 INFO @ Tue, 30 Jun 2020 00:19:24: 12000000 INFO @ Tue, 30 Jun 2020 00:19:25: 2000000 INFO @ Tue, 30 Jun 2020 00:19:29: 7000000 INFO @ Tue, 30 Jun 2020 00:19:31: 3000000 INFO @ Tue, 30 Jun 2020 00:19:31: 13000000 INFO @ Tue, 30 Jun 2020 00:19:36: 8000000 INFO @ Tue, 30 Jun 2020 00:19:37: 4000000 INFO @ Tue, 30 Jun 2020 00:19:38: 14000000 INFO @ Tue, 30 Jun 2020 00:19:43: 5000000 INFO @ Tue, 30 Jun 2020 00:19:44: 9000000 INFO @ Tue, 30 Jun 2020 00:19:44: 15000000 INFO @ Tue, 30 Jun 2020 00:19:49: 6000000 INFO @ Tue, 30 Jun 2020 00:19:51: 10000000 INFO @ Tue, 30 Jun 2020 00:19:51: 16000000 INFO @ Tue, 30 Jun 2020 00:19:55: 7000000 INFO @ Tue, 30 Jun 2020 00:19:57: 17000000 INFO @ Tue, 30 Jun 2020 00:19:58: 11000000 INFO @ Tue, 30 Jun 2020 00:20:01: 8000000 INFO @ Tue, 30 Jun 2020 00:20:04: 18000000 INFO @ Tue, 30 Jun 2020 00:20:05: 12000000 INFO @ Tue, 30 Jun 2020 00:20:07: 9000000 INFO @ Tue, 30 Jun 2020 00:20:11: 19000000 INFO @ Tue, 30 Jun 2020 00:20:11: 13000000 INFO @ Tue, 30 Jun 2020 00:20:13: 10000000 INFO @ Tue, 30 Jun 2020 00:20:17: 20000000 INFO @ Tue, 30 Jun 2020 00:20:18: 14000000 INFO @ Tue, 30 Jun 2020 00:20:19: 11000000 INFO @ Tue, 30 Jun 2020 00:20:24: 21000000 INFO @ Tue, 30 Jun 2020 00:20:25: 15000000 INFO @ Tue, 30 Jun 2020 00:20:25: 12000000 INFO @ Tue, 30 Jun 2020 00:20:30: 22000000 INFO @ Tue, 30 Jun 2020 00:20:31: 13000000 INFO @ Tue, 30 Jun 2020 00:20:31: 16000000 INFO @ Tue, 30 Jun 2020 00:20:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:20:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:20:35: #1 total tags in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:20:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:20:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:20:36: #1 tags after filtering in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:20:36: #1 finished! INFO @ Tue, 30 Jun 2020 00:20:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:20:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:20:36: 14000000 INFO @ Tue, 30 Jun 2020 00:20:37: #2 number of paired peaks: 503 WARNING @ Tue, 30 Jun 2020 00:20:37: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Tue, 30 Jun 2020 00:20:37: start model_add_line... INFO @ Tue, 30 Jun 2020 00:20:37: 17000000 INFO @ Tue, 30 Jun 2020 00:20:38: start X-correlation... INFO @ Tue, 30 Jun 2020 00:20:38: end of X-cor INFO @ Tue, 30 Jun 2020 00:20:38: #2 finished! INFO @ Tue, 30 Jun 2020 00:20:38: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 00:20:38: #2 alternative fragment length(s) may be 4,39,515 bps INFO @ Tue, 30 Jun 2020 00:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05_model.r WARNING @ Tue, 30 Jun 2020 00:20:38: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:20:38: #2 You may need to consider one of the other alternative d(s): 4,39,515 WARNING @ Tue, 30 Jun 2020 00:20:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:20:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:20:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:20:42: 15000000 INFO @ Tue, 30 Jun 2020 00:20:43: 18000000 INFO @ Tue, 30 Jun 2020 00:20:47: 16000000 INFO @ Tue, 30 Jun 2020 00:20:49: 19000000 INFO @ Tue, 30 Jun 2020 00:20:52: 17000000 INFO @ Tue, 30 Jun 2020 00:20:55: 20000000 INFO @ Tue, 30 Jun 2020 00:20:57: 18000000 INFO @ Tue, 30 Jun 2020 00:21:01: 21000000 INFO @ Tue, 30 Jun 2020 00:21:03: 19000000 INFO @ Tue, 30 Jun 2020 00:21:07: 22000000 INFO @ Tue, 30 Jun 2020 00:21:08: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:21:13: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:21:13: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:21:13: #1 total tags in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:21:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:21:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:21:13: 21000000 INFO @ Tue, 30 Jun 2020 00:21:13: #1 tags after filtering in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:21:13: #1 finished! INFO @ Tue, 30 Jun 2020 00:21:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:21:15: #2 number of paired peaks: 503 WARNING @ Tue, 30 Jun 2020 00:21:15: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Tue, 30 Jun 2020 00:21:15: start model_add_line... INFO @ Tue, 30 Jun 2020 00:21:15: start X-correlation... INFO @ Tue, 30 Jun 2020 00:21:15: end of X-cor INFO @ Tue, 30 Jun 2020 00:21:15: #2 finished! INFO @ Tue, 30 Jun 2020 00:21:15: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 00:21:15: #2 alternative fragment length(s) may be 4,39,515 bps INFO @ Tue, 30 Jun 2020 00:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10_model.r WARNING @ Tue, 30 Jun 2020 00:21:15: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:21:15: #2 You may need to consider one of the other alternative d(s): 4,39,515 WARNING @ Tue, 30 Jun 2020 00:21:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:21:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:21:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:21:18: 22000000 INFO @ Tue, 30 Jun 2020 00:21:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:21:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:21:23: #1 total tags in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:21:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:21:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:21:23: #1 tags after filtering in treatment: 22837127 INFO @ Tue, 30 Jun 2020 00:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:21:23: #1 finished! INFO @ Tue, 30 Jun 2020 00:21:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:21:25: #2 number of paired peaks: 503 WARNING @ Tue, 30 Jun 2020 00:21:25: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Tue, 30 Jun 2020 00:21:25: start model_add_line... INFO @ Tue, 30 Jun 2020 00:21:25: start X-correlation... INFO @ Tue, 30 Jun 2020 00:21:25: end of X-cor INFO @ Tue, 30 Jun 2020 00:21:25: #2 finished! INFO @ Tue, 30 Jun 2020 00:21:25: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 00:21:25: #2 alternative fragment length(s) may be 4,39,515 bps INFO @ Tue, 30 Jun 2020 00:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20_model.r WARNING @ Tue, 30 Jun 2020 00:21:25: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:21:25: #2 You may need to consider one of the other alternative d(s): 4,39,515 WARNING @ Tue, 30 Jun 2020 00:21:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:21:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.05_summits.bed INFO @ Tue, 30 Jun 2020 00:21:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5813 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:21:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:22:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:22:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:22:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:22:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.10_summits.bed INFO @ Tue, 30 Jun 2020 00:22:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2913 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2055953/SRX2055953.20_summits.bed INFO @ Tue, 30 Jun 2020 00:22:22: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1402 records, 4 fields): 4 millis CompletedMACS2peakCalling