Job ID = 6457676 SRX = SRX467099 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:53:03 prefetch.2.10.7: 1) Downloading 'SRR1164523'... 2020-06-21T11:53:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:57:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:57:23 prefetch.2.10.7: 1) 'SRR1164523' was downloaded successfully Read 24101770 spots for SRR1164523/SRR1164523.sra Written 24101770 spots for SRR1164523/SRR1164523.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: 00:06:32 24101770 reads; of these: 24101770 (100.00%) were unpaired; of these: 1663068 (6.90%) aligned 0 times 17059064 (70.78%) aligned exactly 1 time 5379638 (22.32%) aligned >1 times 93.10% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 3878848 / 22438702 = 0.1729 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 21:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.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 21:10:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:42: 1000000 INFO @ Sun, 21 Jun 2020 21:10:47: 2000000 INFO @ Sun, 21 Jun 2020 21:10:53: 3000000 INFO @ Sun, 21 Jun 2020 21:10:58: 4000000 INFO @ Sun, 21 Jun 2020 21:11:03: 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 21:11:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.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 21:11:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:09: 6000000 INFO @ Sun, 21 Jun 2020 21:11:12: 1000000 INFO @ Sun, 21 Jun 2020 21:11:14: 7000000 INFO @ Sun, 21 Jun 2020 21:11:18: 2000000 INFO @ Sun, 21 Jun 2020 21:11:20: 8000000 INFO @ Sun, 21 Jun 2020 21:11:24: 3000000 INFO @ Sun, 21 Jun 2020 21:11:26: 9000000 INFO @ Sun, 21 Jun 2020 21:11:30: 4000000 INFO @ Sun, 21 Jun 2020 21:11:32: 10000000 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 21:11:36: 5000000 INFO @ Sun, 21 Jun 2020 21:11:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.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 21:11:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:38: 11000000 INFO @ Sun, 21 Jun 2020 21:11:42: 6000000 INFO @ Sun, 21 Jun 2020 21:11:42: 1000000 INFO @ Sun, 21 Jun 2020 21:11:44: 12000000 INFO @ Sun, 21 Jun 2020 21:11:48: 7000000 INFO @ Sun, 21 Jun 2020 21:11:48: 2000000 INFO @ Sun, 21 Jun 2020 21:11:50: 13000000 INFO @ Sun, 21 Jun 2020 21:11:54: 8000000 INFO @ Sun, 21 Jun 2020 21:11:54: 3000000 INFO @ Sun, 21 Jun 2020 21:11:56: 14000000 INFO @ Sun, 21 Jun 2020 21:12:00: 9000000 INFO @ Sun, 21 Jun 2020 21:12:00: 4000000 INFO @ Sun, 21 Jun 2020 21:12:02: 15000000 INFO @ Sun, 21 Jun 2020 21:12:06: 10000000 INFO @ Sun, 21 Jun 2020 21:12:06: 5000000 INFO @ Sun, 21 Jun 2020 21:12:08: 16000000 INFO @ Sun, 21 Jun 2020 21:12:12: 11000000 INFO @ Sun, 21 Jun 2020 21:12:12: 6000000 INFO @ Sun, 21 Jun 2020 21:12:14: 17000000 INFO @ Sun, 21 Jun 2020 21:12:18: 7000000 INFO @ Sun, 21 Jun 2020 21:12:18: 12000000 INFO @ Sun, 21 Jun 2020 21:12:20: 18000000 INFO @ Sun, 21 Jun 2020 21:12:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:12:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:12:23: #1 total tags in treatment: 18559854 INFO @ Sun, 21 Jun 2020 21:12:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:23: #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 21:12:23: 8000000 INFO @ Sun, 21 Jun 2020 21:12:24: 13000000 INFO @ Sun, 21 Jun 2020 21:12:24: #1 tags after filtering in treatment: 18559844 INFO @ Sun, 21 Jun 2020 21:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:25: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 21:12:25: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 21:12:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:25: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 21:12:25: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 21:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05_model.r WARNING @ Sun, 21 Jun 2020 21:12:25: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:12:25: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 21:12:25: #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 21:12:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:29: 9000000 INFO @ Sun, 21 Jun 2020 21:12:29: 14000000 INFO @ Sun, 21 Jun 2020 21:12:35: 10000000 INFO @ Sun, 21 Jun 2020 21:12:36: 15000000 INFO @ Sun, 21 Jun 2020 21:12:41: 11000000 INFO @ Sun, 21 Jun 2020 21:12:42: 16000000 INFO @ Sun, 21 Jun 2020 21:12:47: 12000000 INFO @ Sun, 21 Jun 2020 21:12:48: 17000000 INFO @ Sun, 21 Jun 2020 21:12:53: 13000000 INFO @ Sun, 21 Jun 2020 21:12:54: 18000000 INFO @ Sun, 21 Jun 2020 21:12:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:12:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:12:57: #1 total tags in treatment: 18559854 INFO @ Sun, 21 Jun 2020 21:12:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:12:58: #1 tags after filtering in treatment: 18559844 INFO @ Sun, 21 Jun 2020 21:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:12:59: 14000000 INFO @ Sun, 21 Jun 2020 21:12:59: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 21:12:59: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 21:12:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:59: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 21:12:59: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 21:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10_model.r WARNING @ Sun, 21 Jun 2020 21:12:59: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:12:59: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 21:12:59: #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 21:12:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:04: 15000000 INFO @ Sun, 21 Jun 2020 21:13:10: 16000000 INFO @ Sun, 21 Jun 2020 21:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.05_summits.bed INFO @ Sun, 21 Jun 2020 21:13:14: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (2665 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:16: 17000000 INFO @ Sun, 21 Jun 2020 21:13:21: 18000000 INFO @ Sun, 21 Jun 2020 21:13:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:24: #1 total tags in treatment: 18559854 INFO @ Sun, 21 Jun 2020 21:13:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:24: #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 21:13:25: #1 tags after filtering in treatment: 18559844 INFO @ Sun, 21 Jun 2020 21:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:26: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 21:13:26: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 21:13:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:26: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 21:13:26: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 21:13:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20_model.r WARNING @ Sun, 21 Jun 2020 21:13:26: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:26: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 21:13:26: #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 21:13:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.10_summits.bed INFO @ Sun, 21 Jun 2020 21:13:48: Done! pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (2033 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467099/SRX467099.20_summits.bed INFO @ Sun, 21 Jun 2020 21:14:16: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 33 millis CompletedMACS2peakCalling