Job ID = 6457999 SRX = SRX4933902 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:01:32 prefetch.2.10.7: 1) Downloading 'SRR8107293'... 2020-06-21T12:01:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:06:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:06:31 prefetch.2.10.7: 1) 'SRR8107293' was downloaded successfully Read 28078010 spots for SRR8107293/SRR8107293.sra Written 28078010 spots for SRR8107293/SRR8107293.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:12 28078010 reads; of these: 28078010 (100.00%) were unpaired; of these: 871876 (3.11%) aligned 0 times 19464741 (69.32%) aligned exactly 1 time 7741393 (27.57%) aligned >1 times 96.89% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 4810266 / 27206134 = 0.1768 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 21:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.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 21:23:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:21: 1000000 INFO @ Sun, 21 Jun 2020 21:23:27: 2000000 INFO @ Sun, 21 Jun 2020 21:23:32: 3000000 INFO @ Sun, 21 Jun 2020 21:23:38: 4000000 INFO @ Sun, 21 Jun 2020 21:23:43: 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 @ Sun, 21 Jun 2020 21:23:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.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 21:23:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:23:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:23:50: 6000000 INFO @ Sun, 21 Jun 2020 21:23:53: 1000000 INFO @ Sun, 21 Jun 2020 21:23:56: 7000000 INFO @ Sun, 21 Jun 2020 21:24:00: 2000000 INFO @ Sun, 21 Jun 2020 21:24:03: 8000000 INFO @ Sun, 21 Jun 2020 21:24:07: 3000000 INFO @ Sun, 21 Jun 2020 21:24:10: 9000000 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 21:24:14: 4000000 INFO @ Sun, 21 Jun 2020 21:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.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 21:24:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:16: 10000000 INFO @ Sun, 21 Jun 2020 21:24:22: 5000000 INFO @ Sun, 21 Jun 2020 21:24:22: 1000000 INFO @ Sun, 21 Jun 2020 21:24:23: 11000000 INFO @ Sun, 21 Jun 2020 21:24:29: 6000000 INFO @ Sun, 21 Jun 2020 21:24:29: 2000000 INFO @ Sun, 21 Jun 2020 21:24:30: 12000000 INFO @ Sun, 21 Jun 2020 21:24:36: 7000000 INFO @ Sun, 21 Jun 2020 21:24:36: 3000000 INFO @ Sun, 21 Jun 2020 21:24:37: 13000000 INFO @ Sun, 21 Jun 2020 21:24:43: 4000000 INFO @ Sun, 21 Jun 2020 21:24:43: 8000000 INFO @ Sun, 21 Jun 2020 21:24:44: 14000000 INFO @ Sun, 21 Jun 2020 21:24:50: 5000000 INFO @ Sun, 21 Jun 2020 21:24:50: 9000000 INFO @ Sun, 21 Jun 2020 21:24:51: 15000000 INFO @ Sun, 21 Jun 2020 21:24:57: 6000000 INFO @ Sun, 21 Jun 2020 21:24:58: 10000000 INFO @ Sun, 21 Jun 2020 21:24:58: 16000000 INFO @ Sun, 21 Jun 2020 21:25:03: 7000000 INFO @ Sun, 21 Jun 2020 21:25:04: 17000000 INFO @ Sun, 21 Jun 2020 21:25:05: 11000000 INFO @ Sun, 21 Jun 2020 21:25:10: 8000000 INFO @ Sun, 21 Jun 2020 21:25:11: 18000000 INFO @ Sun, 21 Jun 2020 21:25:12: 12000000 INFO @ Sun, 21 Jun 2020 21:25:17: 9000000 INFO @ Sun, 21 Jun 2020 21:25:18: 19000000 INFO @ Sun, 21 Jun 2020 21:25:19: 13000000 INFO @ Sun, 21 Jun 2020 21:25:24: 10000000 INFO @ Sun, 21 Jun 2020 21:25:25: 20000000 INFO @ Sun, 21 Jun 2020 21:25:26: 14000000 INFO @ Sun, 21 Jun 2020 21:25:30: 11000000 INFO @ Sun, 21 Jun 2020 21:25:32: 21000000 INFO @ Sun, 21 Jun 2020 21:25:33: 15000000 INFO @ Sun, 21 Jun 2020 21:25:37: 12000000 INFO @ Sun, 21 Jun 2020 21:25:39: 22000000 INFO @ Sun, 21 Jun 2020 21:25:40: 16000000 INFO @ Sun, 21 Jun 2020 21:25:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:25:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:25:42: #1 total tags in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:25:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:42: #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 21:25:42: #1 tags after filtering in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:44: #2 number of paired peaks: 368 WARNING @ Sun, 21 Jun 2020 21:25:44: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sun, 21 Jun 2020 21:25:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:44: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 21:25:44: #2 alternative fragment length(s) may be 2,40,580 bps INFO @ Sun, 21 Jun 2020 21:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05_model.r WARNING @ Sun, 21 Jun 2020 21:25:44: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:44: #2 You may need to consider one of the other alternative d(s): 2,40,580 WARNING @ Sun, 21 Jun 2020 21:25:44: #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 21:25:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:44: 13000000 INFO @ Sun, 21 Jun 2020 21:25:48: 17000000 INFO @ Sun, 21 Jun 2020 21:25:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:25:55: 18000000 INFO @ Sun, 21 Jun 2020 21:25:58: 15000000 INFO @ Sun, 21 Jun 2020 21:26:02: 19000000 INFO @ Sun, 21 Jun 2020 21:26:05: 16000000 INFO @ Sun, 21 Jun 2020 21:26:10: 20000000 INFO @ Sun, 21 Jun 2020 21:26:11: 17000000 INFO @ Sun, 21 Jun 2020 21:26:17: 21000000 INFO @ Sun, 21 Jun 2020 21:26:18: 18000000 INFO @ Sun, 21 Jun 2020 21:26:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:24: 22000000 INFO @ Sun, 21 Jun 2020 21:26:25: 19000000 INFO @ Sun, 21 Jun 2020 21:26:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:26:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:26:27: #1 total tags in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:26:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:27: #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 21:26:27: #1 tags after filtering in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:29: #2 number of paired peaks: 368 WARNING @ Sun, 21 Jun 2020 21:26:29: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sun, 21 Jun 2020 21:26:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:29: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 21:26:29: #2 alternative fragment length(s) may be 2,40,580 bps INFO @ Sun, 21 Jun 2020 21:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10_model.r WARNING @ Sun, 21 Jun 2020 21:26:29: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:29: #2 You may need to consider one of the other alternative d(s): 2,40,580 WARNING @ Sun, 21 Jun 2020 21:26:29: #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 21:26:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:32: 20000000 INFO @ Sun, 21 Jun 2020 21:26:38: 21000000 INFO @ Sun, 21 Jun 2020 21:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.05_summits.bed INFO @ Sun, 21 Jun 2020 21:26:41: Done! pass1 - making usageList (695 chroms): 2 millis pass2 - checking and writing primary data (2887 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:26:44: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:26:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:26:47: #1 total tags in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:47: #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 21:26:47: #1 tags after filtering in treatment: 22395868 INFO @ Sun, 21 Jun 2020 21:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:49: #2 number of paired peaks: 368 WARNING @ Sun, 21 Jun 2020 21:26:49: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sun, 21 Jun 2020 21:26:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:49: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 21:26:49: #2 alternative fragment length(s) may be 2,40,580 bps INFO @ Sun, 21 Jun 2020 21:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20_model.r WARNING @ Sun, 21 Jun 2020 21:26:49: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:49: #2 You may need to consider one of the other alternative d(s): 2,40,580 WARNING @ Sun, 21 Jun 2020 21:26:49: #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 21:26:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.10_summits.bed INFO @ Sun, 21 Jun 2020 21:27:26: Done! pass1 - making usageList (588 chroms): 2 millis pass2 - checking and writing primary data (2181 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:27:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933902/SRX4933902.20_summits.bed INFO @ Sun, 21 Jun 2020 21:27:46: Done! pass1 - making usageList (383 chroms): 1 millis pass2 - checking and writing primary data (1021 records, 4 fields): 12 millis CompletedMACS2peakCalling