Job ID = 6458235 SRX = SRX495788 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:24:20 prefetch.2.10.7: 1) Downloading 'SRR1199486'... 2020-06-21T12:24:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:28:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:28:01 prefetch.2.10.7: 1) 'SRR1199486' was downloaded successfully Read 25162813 spots for SRR1199486/SRR1199486.sra Written 25162813 spots for SRR1199486/SRR1199486.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: 00:07:36 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1448098 (5.75%) aligned 0 times 16797680 (66.76%) aligned exactly 1 time 6917035 (27.49%) aligned >1 times 94.25% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 6320706 / 23714715 = 0.2665 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 21:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.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 21:42:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:53: 1000000 INFO @ Sun, 21 Jun 2020 21:42:59: 2000000 INFO @ Sun, 21 Jun 2020 21:43:04: 3000000 INFO @ Sun, 21 Jun 2020 21:43:10: 4000000 INFO @ Sun, 21 Jun 2020 21:43:15: 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 21:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.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 21:43:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:20: 6000000 INFO @ Sun, 21 Jun 2020 21:43:23: 1000000 INFO @ Sun, 21 Jun 2020 21:43:26: 7000000 INFO @ Sun, 21 Jun 2020 21:43:29: 2000000 INFO @ Sun, 21 Jun 2020 21:43:31: 8000000 INFO @ Sun, 21 Jun 2020 21:43:34: 3000000 INFO @ Sun, 21 Jun 2020 21:43:37: 9000000 INFO @ Sun, 21 Jun 2020 21:43:40: 4000000 INFO @ Sun, 21 Jun 2020 21:43:42: 10000000 INFO @ Sun, 21 Jun 2020 21:43:45: 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 @ Sun, 21 Jun 2020 21:43:47: 11000000 INFO @ Sun, 21 Jun 2020 21:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.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 21:43:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:50: 6000000 INFO @ Sun, 21 Jun 2020 21:43:53: 12000000 INFO @ Sun, 21 Jun 2020 21:43:54: 1000000 INFO @ Sun, 21 Jun 2020 21:43:56: 7000000 INFO @ Sun, 21 Jun 2020 21:43:58: 13000000 INFO @ Sun, 21 Jun 2020 21:43:59: 2000000 INFO @ Sun, 21 Jun 2020 21:44:01: 8000000 INFO @ Sun, 21 Jun 2020 21:44:03: 14000000 INFO @ Sun, 21 Jun 2020 21:44:04: 3000000 INFO @ Sun, 21 Jun 2020 21:44:07: 9000000 INFO @ Sun, 21 Jun 2020 21:44:09: 15000000 INFO @ Sun, 21 Jun 2020 21:44:10: 4000000 INFO @ Sun, 21 Jun 2020 21:44:12: 10000000 INFO @ Sun, 21 Jun 2020 21:44:14: 16000000 INFO @ Sun, 21 Jun 2020 21:44:15: 5000000 INFO @ Sun, 21 Jun 2020 21:44:17: 11000000 INFO @ Sun, 21 Jun 2020 21:44:20: 17000000 INFO @ Sun, 21 Jun 2020 21:44:20: 6000000 INFO @ Sun, 21 Jun 2020 21:44:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:22: #1 total tags in treatment: 17394009 INFO @ Sun, 21 Jun 2020 21:44:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:22: #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 21:44:23: #1 tags after filtering in treatment: 17393919 INFO @ Sun, 21 Jun 2020 21:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:23: 12000000 INFO @ Sun, 21 Jun 2020 21:44:24: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:44:24: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:44:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:24: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:44:24: #2 alternative fragment length(s) may be 2,11,50,471 bps INFO @ Sun, 21 Jun 2020 21:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05_model.r WARNING @ Sun, 21 Jun 2020 21:44:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:24: #2 You may need to consider one of the other alternative d(s): 2,11,50,471 WARNING @ Sun, 21 Jun 2020 21:44:24: #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 21:44:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:26: 7000000 INFO @ Sun, 21 Jun 2020 21:44:28: 13000000 INFO @ Sun, 21 Jun 2020 21:44:31: 8000000 INFO @ Sun, 21 Jun 2020 21:44:33: 14000000 INFO @ Sun, 21 Jun 2020 21:44:36: 9000000 INFO @ Sun, 21 Jun 2020 21:44:39: 15000000 INFO @ Sun, 21 Jun 2020 21:44:42: 10000000 INFO @ Sun, 21 Jun 2020 21:44:44: 16000000 INFO @ Sun, 21 Jun 2020 21:44:47: 11000000 INFO @ Sun, 21 Jun 2020 21:44:50: 17000000 INFO @ Sun, 21 Jun 2020 21:44:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:52: #1 total tags in treatment: 17394009 INFO @ Sun, 21 Jun 2020 21:44:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:52: #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 21:44:52: 12000000 INFO @ Sun, 21 Jun 2020 21:44:53: #1 tags after filtering in treatment: 17393919 INFO @ Sun, 21 Jun 2020 21:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:54: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:44:54: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:44:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:54: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:44:54: #2 alternative fragment length(s) may be 2,11,50,471 bps INFO @ Sun, 21 Jun 2020 21:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10_model.r WARNING @ Sun, 21 Jun 2020 21:44:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:54: #2 You may need to consider one of the other alternative d(s): 2,11,50,471 WARNING @ Sun, 21 Jun 2020 21:44:54: #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 21:44:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:57: 13000000 INFO @ Sun, 21 Jun 2020 21:45:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:02: 14000000 INFO @ Sun, 21 Jun 2020 21:45:08: 15000000 INFO @ Sun, 21 Jun 2020 21:45:13: 16000000 INFO @ Sun, 21 Jun 2020 21:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.05_summits.bed INFO @ Sun, 21 Jun 2020 21:45:17: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1689 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:45:18: 17000000 INFO @ Sun, 21 Jun 2020 21:45:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:20: #1 total tags in treatment: 17394009 INFO @ Sun, 21 Jun 2020 21:45:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:20: #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 21:45:21: #1 tags after filtering in treatment: 17393919 INFO @ Sun, 21 Jun 2020 21:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:45:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:45:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:45:22: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:45:22: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:45:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:45:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:45:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:45:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:45:22: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 21:45:22: #2 alternative fragment length(s) may be 2,11,50,471 bps INFO @ Sun, 21 Jun 2020 21:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20_model.r WARNING @ Sun, 21 Jun 2020 21:45:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:45:22: #2 You may need to consider one of the other alternative d(s): 2,11,50,471 WARNING @ Sun, 21 Jun 2020 21:45:22: #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 21:45:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:45:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:45:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.10_summits.bed INFO @ Sun, 21 Jun 2020 21:45:44: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:45:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495788/SRX495788.20_summits.bed INFO @ Sun, 21 Jun 2020 21:46:09: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 5 millis CompletedMACS2peakCalling