Job ID = 6455409 SRX = SRX287764 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:08:21 prefetch.2.10.7: 1) Downloading 'SRR869953'... 2020-06-21T10:08:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:12 prefetch.2.10.7: 1) 'SRR869953' was downloaded successfully Read 17131262 spots for SRR869953/SRR869953.sra Written 17131262 spots for SRR869953/SRR869953.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: 00:04:55 17131262 reads; of these: 17131262 (100.00%) were unpaired; of these: 1024781 (5.98%) aligned 0 times 10827847 (63.21%) aligned exactly 1 time 5278634 (30.81%) aligned >1 times 94.02% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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 8 files... [bam_rmdupse_core] 2679675 / 16106481 = 0.1664 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 19:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.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 19:21:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:11: 1000000 INFO @ Sun, 21 Jun 2020 19:21:16: 2000000 INFO @ Sun, 21 Jun 2020 19:21:21: 3000000 INFO @ Sun, 21 Jun 2020 19:21:26: 4000000 INFO @ Sun, 21 Jun 2020 19:21:31: 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 19:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.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 19:21:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:36: 6000000 INFO @ Sun, 21 Jun 2020 19:21:41: 1000000 INFO @ Sun, 21 Jun 2020 19:21:41: 7000000 INFO @ Sun, 21 Jun 2020 19:21:46: 2000000 INFO @ Sun, 21 Jun 2020 19:21:47: 8000000 INFO @ Sun, 21 Jun 2020 19:21:51: 3000000 INFO @ Sun, 21 Jun 2020 19:21:52: 9000000 INFO @ Sun, 21 Jun 2020 19:21:57: 4000000 INFO @ Sun, 21 Jun 2020 19:21:58: 10000000 INFO @ Sun, 21 Jun 2020 19:22:02: 5000000 INFO @ Sun, 21 Jun 2020 19:22:03: 11000000 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 19:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.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 19:22:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:08: 6000000 INFO @ Sun, 21 Jun 2020 19:22:09: 12000000 INFO @ Sun, 21 Jun 2020 19:22:11: 1000000 INFO @ Sun, 21 Jun 2020 19:22:13: 7000000 INFO @ Sun, 21 Jun 2020 19:22:14: 13000000 INFO @ Sun, 21 Jun 2020 19:22:16: 2000000 INFO @ Sun, 21 Jun 2020 19:22:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:17: #1 total tags in treatment: 13426806 INFO @ Sun, 21 Jun 2020 19:22:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:17: #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 19:22:17: #1 tags after filtering in treatment: 13426805 INFO @ Sun, 21 Jun 2020 19:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:18: #2 number of paired peaks: 801 WARNING @ Sun, 21 Jun 2020 19:22:18: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:18: 8000000 INFO @ Sun, 21 Jun 2020 19:22:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:18: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:22:18: #2 alternative fragment length(s) may be 3,39,545 bps INFO @ Sun, 21 Jun 2020 19:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05_model.r WARNING @ Sun, 21 Jun 2020 19:22:18: #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 19:22:18: #2 You may need to consider one of the other alternative d(s): 3,39,545 WARNING @ Sun, 21 Jun 2020 19:22:18: #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 19:22:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:22: 3000000 INFO @ Sun, 21 Jun 2020 19:22:24: 9000000 INFO @ Sun, 21 Jun 2020 19:22:27: 4000000 INFO @ Sun, 21 Jun 2020 19:22:29: 10000000 INFO @ Sun, 21 Jun 2020 19:22:33: 5000000 INFO @ Sun, 21 Jun 2020 19:22:35: 11000000 INFO @ Sun, 21 Jun 2020 19:22:38: 6000000 INFO @ Sun, 21 Jun 2020 19:22:41: 12000000 INFO @ Sun, 21 Jun 2020 19:22:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:44: 7000000 INFO @ Sun, 21 Jun 2020 19:22:47: 13000000 INFO @ Sun, 21 Jun 2020 19:22:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:49: #1 total tags in treatment: 13426806 INFO @ Sun, 21 Jun 2020 19:22:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:49: #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 19:22:49: 8000000 INFO @ Sun, 21 Jun 2020 19:22:50: #1 tags after filtering in treatment: 13426805 INFO @ Sun, 21 Jun 2020 19:22:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:51: #2 number of paired peaks: 801 WARNING @ Sun, 21 Jun 2020 19:22:51: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:51: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:22:51: #2 alternative fragment length(s) may be 3,39,545 bps INFO @ Sun, 21 Jun 2020 19:22:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10_model.r WARNING @ Sun, 21 Jun 2020 19:22:51: #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 19:22:51: #2 You may need to consider one of the other alternative d(s): 3,39,545 WARNING @ Sun, 21 Jun 2020 19:22:51: #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 19:22:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:55: 9000000 INFO @ Sun, 21 Jun 2020 19:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.05_summits.bed INFO @ Sun, 21 Jun 2020 19:22:56: Done! pass1 - making usageList (639 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:00: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:06: 11000000 INFO @ Sun, 21 Jun 2020 19:23:11: 12000000 INFO @ Sun, 21 Jun 2020 19:23:16: 13000000 INFO @ Sun, 21 Jun 2020 19:23:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:18: #1 total tags in treatment: 13426806 INFO @ Sun, 21 Jun 2020 19:23:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:18: #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 19:23:19: #1 tags after filtering in treatment: 13426805 INFO @ Sun, 21 Jun 2020 19:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:20: #2 number of paired peaks: 801 WARNING @ Sun, 21 Jun 2020 19:23:20: Fewer paired peaks (801) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 801 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:20: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:23:20: #2 alternative fragment length(s) may be 3,39,545 bps INFO @ Sun, 21 Jun 2020 19:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20_model.r WARNING @ Sun, 21 Jun 2020 19:23:20: #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 19:23:20: #2 You may need to consider one of the other alternative d(s): 3,39,545 WARNING @ Sun, 21 Jun 2020 19:23:20: #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 19:23:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:29: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (2012 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287764/SRX287764.20_summits.bed INFO @ Sun, 21 Jun 2020 19:23:57: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (1104 records, 4 fields): 12 millis CompletedMACS2peakCalling