Job ID = 6453707 SRX = SRX1433353 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:54 prefetch.2.10.7: 1) Downloading 'SRR2919818'... 2020-06-21T08:34:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:39:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:39:42 prefetch.2.10.7: 1) 'SRR2919818' was downloaded successfully Read 23001437 spots for SRR2919818/SRR2919818.sra Written 23001437 spots for SRR2919818/SRR2919818.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: 00:06:11 23001437 reads; of these: 23001437 (100.00%) were unpaired; of these: 751074 (3.27%) aligned 0 times 17686520 (76.89%) aligned exactly 1 time 4563843 (19.84%) aligned >1 times 96.73% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 3935638 / 22250363 = 0.1769 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 17:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.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 17:52:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:07: 1000000 INFO @ Sun, 21 Jun 2020 17:52:14: 2000000 INFO @ Sun, 21 Jun 2020 17:52:20: 3000000 INFO @ Sun, 21 Jun 2020 17:52:26: 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 17:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.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 17:52:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:31: 5000000 INFO @ Sun, 21 Jun 2020 17:52:37: 6000000 INFO @ Sun, 21 Jun 2020 17:52:38: 1000000 INFO @ Sun, 21 Jun 2020 17:52:44: 7000000 INFO @ Sun, 21 Jun 2020 17:52:45: 2000000 INFO @ Sun, 21 Jun 2020 17:52:50: 8000000 INFO @ Sun, 21 Jun 2020 17:52:52: 3000000 INFO @ Sun, 21 Jun 2020 17:52:56: 9000000 INFO @ Sun, 21 Jun 2020 17:52:59: 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 17:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.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 17:53:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:03: 10000000 INFO @ Sun, 21 Jun 2020 17:53:06: 5000000 INFO @ Sun, 21 Jun 2020 17:53:08: 1000000 INFO @ Sun, 21 Jun 2020 17:53:09: 11000000 INFO @ Sun, 21 Jun 2020 17:53:13: 6000000 INFO @ Sun, 21 Jun 2020 17:53:14: 2000000 INFO @ Sun, 21 Jun 2020 17:53:15: 12000000 INFO @ Sun, 21 Jun 2020 17:53:20: 7000000 INFO @ Sun, 21 Jun 2020 17:53:20: 3000000 INFO @ Sun, 21 Jun 2020 17:53:21: 13000000 INFO @ Sun, 21 Jun 2020 17:53:27: 4000000 INFO @ Sun, 21 Jun 2020 17:53:27: 8000000 INFO @ Sun, 21 Jun 2020 17:53:28: 14000000 INFO @ Sun, 21 Jun 2020 17:53:33: 5000000 INFO @ Sun, 21 Jun 2020 17:53:34: 9000000 INFO @ Sun, 21 Jun 2020 17:53:34: 15000000 INFO @ Sun, 21 Jun 2020 17:53:39: 6000000 INFO @ Sun, 21 Jun 2020 17:53:41: 16000000 INFO @ Sun, 21 Jun 2020 17:53:41: 10000000 INFO @ Sun, 21 Jun 2020 17:53:46: 7000000 INFO @ Sun, 21 Jun 2020 17:53:47: 17000000 INFO @ Sun, 21 Jun 2020 17:53:48: 11000000 INFO @ Sun, 21 Jun 2020 17:53:52: 8000000 INFO @ Sun, 21 Jun 2020 17:53:53: 18000000 INFO @ Sun, 21 Jun 2020 17:53:55: 12000000 INFO @ Sun, 21 Jun 2020 17:53:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:53:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:53:55: #1 total tags in treatment: 18314725 INFO @ Sun, 21 Jun 2020 17:53:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:55: #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 17:53:56: #1 tags after filtering in treatment: 18314665 INFO @ Sun, 21 Jun 2020 17:53:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:57: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 17:53:57: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 17:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:57: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:53:57: #2 alternative fragment length(s) may be 3,63,75,584 bps INFO @ Sun, 21 Jun 2020 17:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05_model.r WARNING @ Sun, 21 Jun 2020 17:53:57: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:57: #2 You may need to consider one of the other alternative d(s): 3,63,75,584 WARNING @ Sun, 21 Jun 2020 17:53:57: #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 17:53:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:58: 9000000 INFO @ Sun, 21 Jun 2020 17:54:01: 13000000 INFO @ Sun, 21 Jun 2020 17:54:05: 10000000 INFO @ Sun, 21 Jun 2020 17:54:08: 14000000 INFO @ Sun, 21 Jun 2020 17:54:11: 11000000 INFO @ Sun, 21 Jun 2020 17:54:15: 15000000 INFO @ Sun, 21 Jun 2020 17:54:17: 12000000 INFO @ Sun, 21 Jun 2020 17:54:22: 16000000 INFO @ Sun, 21 Jun 2020 17:54:23: 13000000 INFO @ Sun, 21 Jun 2020 17:54:28: 17000000 INFO @ Sun, 21 Jun 2020 17:54:29: 14000000 INFO @ Sun, 21 Jun 2020 17:54:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:54:35: 15000000 INFO @ Sun, 21 Jun 2020 17:54:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:37: #1 total tags in treatment: 18314725 INFO @ Sun, 21 Jun 2020 17:54:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:37: #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 17:54:38: #1 tags after filtering in treatment: 18314665 INFO @ Sun, 21 Jun 2020 17:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:39: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 17:54:39: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 17:54:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:39: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:54:39: #2 alternative fragment length(s) may be 3,63,75,584 bps INFO @ Sun, 21 Jun 2020 17:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10_model.r WARNING @ Sun, 21 Jun 2020 17:54:39: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:54:39: #2 You may need to consider one of the other alternative d(s): 3,63,75,584 WARNING @ Sun, 21 Jun 2020 17:54:39: #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 17:54:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:41: 16000000 INFO @ Sun, 21 Jun 2020 17:54:47: 17000000 INFO @ Sun, 21 Jun 2020 17:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.05_summits.bed INFO @ Sun, 21 Jun 2020 17:54:50: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (1254 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:52: 18000000 INFO @ Sun, 21 Jun 2020 17:54:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:54: #1 total tags in treatment: 18314725 INFO @ Sun, 21 Jun 2020 17:54:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:54: #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 17:54:55: #1 tags after filtering in treatment: 18314665 INFO @ Sun, 21 Jun 2020 17:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:56: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 17:54:56: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 17:54:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:56: #2 predicted fragment length is 75 bps INFO @ Sun, 21 Jun 2020 17:54:56: #2 alternative fragment length(s) may be 3,63,75,584 bps INFO @ Sun, 21 Jun 2020 17:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20_model.r WARNING @ Sun, 21 Jun 2020 17:54:56: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:54:56: #2 You may need to consider one of the other alternative d(s): 3,63,75,584 WARNING @ Sun, 21 Jun 2020 17:54:56: #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 17:54:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.10_summits.bed INFO @ Sun, 21 Jun 2020 17:55:30: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:55:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433353/SRX1433353.20_summits.bed INFO @ Sun, 21 Jun 2020 17:55:48: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis CompletedMACS2peakCalling