Job ID = 6527820 SRX = SRX287757 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:06:20 prefetch.2.10.7: 1) Downloading 'SRR869946'... 2020-06-29T14:06:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:10:21 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:10:21 prefetch.2.10.7: 1) 'SRR869946' was downloaded successfully Read 22133183 spots for SRR869946/SRR869946.sra Written 22133183 spots for SRR869946/SRR869946.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: 00:08:21 22133183 reads; of these: 22133183 (100.00%) were unpaired; of these: 1088503 (4.92%) aligned 0 times 13883107 (62.73%) aligned exactly 1 time 7161573 (32.36%) aligned >1 times 95.08% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 3985032 / 21044680 = 0.1894 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 @ Mon, 29 Jun 2020 23:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.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 @ Mon, 29 Jun 2020 23:30:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:30:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:30:19: 1000000 INFO @ Mon, 29 Jun 2020 23:30:24: 2000000 INFO @ Mon, 29 Jun 2020 23:30:29: 3000000 INFO @ Mon, 29 Jun 2020 23:30:35: 4000000 INFO @ Mon, 29 Jun 2020 23:30:40: 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 @ Mon, 29 Jun 2020 23:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.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 @ Mon, 29 Jun 2020 23:30:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:30:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:30:45: 6000000 INFO @ Mon, 29 Jun 2020 23:30:49: 1000000 INFO @ Mon, 29 Jun 2020 23:30:51: 7000000 INFO @ Mon, 29 Jun 2020 23:30:55: 2000000 INFO @ Mon, 29 Jun 2020 23:30:56: 8000000 INFO @ Mon, 29 Jun 2020 23:31:00: 3000000 INFO @ Mon, 29 Jun 2020 23:31:02: 9000000 INFO @ Mon, 29 Jun 2020 23:31:06: 4000000 INFO @ Mon, 29 Jun 2020 23:31:07: 10000000 INFO @ Mon, 29 Jun 2020 23:31:12: 5000000 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 @ Mon, 29 Jun 2020 23:31:13: 11000000 INFO @ Mon, 29 Jun 2020 23:31:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.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 @ Mon, 29 Jun 2020 23:31:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:31:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:17: 6000000 INFO @ Mon, 29 Jun 2020 23:31:19: 12000000 INFO @ Mon, 29 Jun 2020 23:31:19: 1000000 INFO @ Mon, 29 Jun 2020 23:31:23: 7000000 INFO @ Mon, 29 Jun 2020 23:31:24: 13000000 INFO @ Mon, 29 Jun 2020 23:31:25: 2000000 INFO @ Mon, 29 Jun 2020 23:31:28: 8000000 INFO @ Mon, 29 Jun 2020 23:31:30: 14000000 INFO @ Mon, 29 Jun 2020 23:31:31: 3000000 INFO @ Mon, 29 Jun 2020 23:31:34: 9000000 INFO @ Mon, 29 Jun 2020 23:31:36: 15000000 INFO @ Mon, 29 Jun 2020 23:31:37: 4000000 INFO @ Mon, 29 Jun 2020 23:31:40: 10000000 INFO @ Mon, 29 Jun 2020 23:31:42: 16000000 INFO @ Mon, 29 Jun 2020 23:31:42: 5000000 INFO @ Mon, 29 Jun 2020 23:31:45: 11000000 INFO @ Mon, 29 Jun 2020 23:31:47: 17000000 INFO @ Mon, 29 Jun 2020 23:31:48: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:31:48: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:31:48: #1 total tags in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:31:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:31:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:31:48: #1 tags after filtering in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:31:48: #1 finished! INFO @ Mon, 29 Jun 2020 23:31:48: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:31:48: 6000000 INFO @ Mon, 29 Jun 2020 23:31:49: #2 number of paired peaks: 238 WARNING @ Mon, 29 Jun 2020 23:31:49: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 29 Jun 2020 23:31:49: start model_add_line... INFO @ Mon, 29 Jun 2020 23:31:49: start X-correlation... INFO @ Mon, 29 Jun 2020 23:31:49: end of X-cor INFO @ Mon, 29 Jun 2020 23:31:49: #2 finished! INFO @ Mon, 29 Jun 2020 23:31:49: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:31:49: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05_model.r WARNING @ Mon, 29 Jun 2020 23:31:49: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:31:49: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:31:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:31:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:31:51: 12000000 INFO @ Mon, 29 Jun 2020 23:31:54: 7000000 INFO @ Mon, 29 Jun 2020 23:31:56: 13000000 INFO @ Mon, 29 Jun 2020 23:31:59: 8000000 INFO @ Mon, 29 Jun 2020 23:32:02: 14000000 INFO @ Mon, 29 Jun 2020 23:32:05: 9000000 INFO @ Mon, 29 Jun 2020 23:32:07: 15000000 INFO @ Mon, 29 Jun 2020 23:32:11: 10000000 INFO @ Mon, 29 Jun 2020 23:32:13: 16000000 INFO @ Mon, 29 Jun 2020 23:32:16: 11000000 INFO @ Mon, 29 Jun 2020 23:32:19: 17000000 INFO @ Mon, 29 Jun 2020 23:32:19: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:32:19: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:32:19: #1 total tags in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:32:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:32:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:32:19: #1 tags after filtering in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:32:19: #1 finished! INFO @ Mon, 29 Jun 2020 23:32:19: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:32:21: #2 number of paired peaks: 238 WARNING @ Mon, 29 Jun 2020 23:32:21: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 29 Jun 2020 23:32:21: start model_add_line... INFO @ Mon, 29 Jun 2020 23:32:21: start X-correlation... INFO @ Mon, 29 Jun 2020 23:32:21: end of X-cor INFO @ Mon, 29 Jun 2020 23:32:21: #2 finished! INFO @ Mon, 29 Jun 2020 23:32:21: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:32:21: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10_model.r WARNING @ Mon, 29 Jun 2020 23:32:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:32:21: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:32:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:32:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:32:22: 12000000 INFO @ Mon, 29 Jun 2020 23:32:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:32:27: 13000000 INFO @ Mon, 29 Jun 2020 23:32:32: 14000000 INFO @ Mon, 29 Jun 2020 23:32:38: 15000000 INFO @ Mon, 29 Jun 2020 23:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.05_summits.bed INFO @ Mon, 29 Jun 2020 23:32:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2226 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:32:43: 16000000 INFO @ Mon, 29 Jun 2020 23:32:49: 17000000 INFO @ Mon, 29 Jun 2020 23:32:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:32:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:32:49: #1 total tags in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:32:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:32:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:32:49: #1 tags after filtering in treatment: 17059648 INFO @ Mon, 29 Jun 2020 23:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:32:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:32:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:32:50: #2 number of paired peaks: 238 WARNING @ Mon, 29 Jun 2020 23:32:50: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 29 Jun 2020 23:32:50: start model_add_line... INFO @ Mon, 29 Jun 2020 23:32:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:32:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:32:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:32:50: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:32:50: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20_model.r WARNING @ Mon, 29 Jun 2020 23:32:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:32:50: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:32:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:32:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:32:54: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.10_summits.bed INFO @ Mon, 29 Jun 2020 23:33:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1867 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:33:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:33:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:33:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:33:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287757/SRX287757.20_summits.bed INFO @ Mon, 29 Jun 2020 23:33:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1433 records, 4 fields): 3 millis CompletedMACS2peakCalling