Job ID = 6508893 SRX = SRX495288 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:07:00 prefetch.2.10.7: 1) Downloading 'SRR1198793'... 2020-06-26T15:07:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:09:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:09:44 prefetch.2.10.7: 1) 'SRR1198793' was downloaded successfully Read 25162813 spots for SRR1198793/SRR1198793.sra Written 25162813 spots for SRR1198793/SRR1198793.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: 00:07:45 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1448184 (5.76%) aligned 0 times 16797579 (66.76%) aligned exactly 1 time 6917050 (27.49%) aligned >1 times 94.24% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 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] 6319372 / 23714629 = 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 @ Sat, 27 Jun 2020 00:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.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 @ Sat, 27 Jun 2020 00:24:42: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:24:42: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:24:48: 1000000 INFO @ Sat, 27 Jun 2020 00:24:54: 2000000 INFO @ Sat, 27 Jun 2020 00:25:00: 3000000 INFO @ Sat, 27 Jun 2020 00:25:07: 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 @ Sat, 27 Jun 2020 00:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.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 @ Sat, 27 Jun 2020 00:25:12: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:12: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:13: 5000000 INFO @ Sat, 27 Jun 2020 00:25:19: 1000000 INFO @ Sat, 27 Jun 2020 00:25:20: 6000000 INFO @ Sat, 27 Jun 2020 00:25:25: 2000000 INFO @ Sat, 27 Jun 2020 00:25:26: 7000000 INFO @ Sat, 27 Jun 2020 00:25:31: 3000000 INFO @ Sat, 27 Jun 2020 00:25:32: 8000000 INFO @ Sat, 27 Jun 2020 00:25:37: 4000000 INFO @ Sat, 27 Jun 2020 00:25:39: 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 @ Sat, 27 Jun 2020 00:25:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.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 @ Sat, 27 Jun 2020 00:25:42: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:42: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:43: 5000000 INFO @ Sat, 27 Jun 2020 00:25:45: 10000000 INFO @ Sat, 27 Jun 2020 00:25:49: 1000000 INFO @ Sat, 27 Jun 2020 00:25:49: 6000000 INFO @ Sat, 27 Jun 2020 00:25:52: 11000000 INFO @ Sat, 27 Jun 2020 00:25:55: 2000000 INFO @ Sat, 27 Jun 2020 00:25:55: 7000000 INFO @ Sat, 27 Jun 2020 00:25:58: 12000000 INFO @ Sat, 27 Jun 2020 00:26:02: 8000000 INFO @ Sat, 27 Jun 2020 00:26:02: 3000000 INFO @ Sat, 27 Jun 2020 00:26:05: 13000000 INFO @ Sat, 27 Jun 2020 00:26:08: 9000000 INFO @ Sat, 27 Jun 2020 00:26:08: 4000000 INFO @ Sat, 27 Jun 2020 00:26:11: 14000000 INFO @ Sat, 27 Jun 2020 00:26:13: 10000000 INFO @ Sat, 27 Jun 2020 00:26:15: 5000000 INFO @ Sat, 27 Jun 2020 00:26:18: 15000000 INFO @ Sat, 27 Jun 2020 00:26:19: 11000000 INFO @ Sat, 27 Jun 2020 00:26:22: 6000000 INFO @ Sat, 27 Jun 2020 00:26:25: 16000000 INFO @ Sat, 27 Jun 2020 00:26:25: 12000000 INFO @ Sat, 27 Jun 2020 00:26:28: 7000000 INFO @ Sat, 27 Jun 2020 00:26:31: 13000000 INFO @ Sat, 27 Jun 2020 00:26:32: 17000000 INFO @ Sat, 27 Jun 2020 00:26:35: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:26:35: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:26:35: #1 total tags in treatment: 17395257 INFO @ Sat, 27 Jun 2020 00:26:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:35: 8000000 INFO @ Sat, 27 Jun 2020 00:26:35: #1 tags after filtering in treatment: 17395193 INFO @ Sat, 27 Jun 2020 00:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:35: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:35: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:36: #2 number of paired peaks: 246 WARNING @ Sat, 27 Jun 2020 00:26:36: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 27 Jun 2020 00:26:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:36: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:36: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:36: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:36: #2 predicted fragment length is 58 bps INFO @ Sat, 27 Jun 2020 00:26:36: #2 alternative fragment length(s) may be 2,36,40,58,199,226,338,538 bps INFO @ Sat, 27 Jun 2020 00:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05_model.r WARNING @ Sat, 27 Jun 2020 00:26:36: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:26:36: #2 You may need to consider one of the other alternative d(s): 2,36,40,58,199,226,338,538 WARNING @ Sat, 27 Jun 2020 00:26:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:26:36: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:26:37: 14000000 INFO @ Sat, 27 Jun 2020 00:26:41: 9000000 INFO @ Sat, 27 Jun 2020 00:26:44: 15000000 INFO @ Sat, 27 Jun 2020 00:26:47: 10000000 INFO @ Sat, 27 Jun 2020 00:26:50: 16000000 INFO @ Sat, 27 Jun 2020 00:26:54: 11000000 INFO @ Sat, 27 Jun 2020 00:26:55: 17000000 INFO @ Sat, 27 Jun 2020 00:26:58: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:26:58: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:26:58: #1 total tags in treatment: 17395257 INFO @ Sat, 27 Jun 2020 00:26:58: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:59: #1 tags after filtering in treatment: 17395193 INFO @ Sat, 27 Jun 2020 00:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:59: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:59: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:27:00: #2 number of paired peaks: 246 WARNING @ Sat, 27 Jun 2020 00:27:00: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 27 Jun 2020 00:27:00: start model_add_line... INFO @ Sat, 27 Jun 2020 00:27:00: start X-correlation... INFO @ Sat, 27 Jun 2020 00:27:00: end of X-cor INFO @ Sat, 27 Jun 2020 00:27:00: #2 finished! INFO @ Sat, 27 Jun 2020 00:27:00: #2 predicted fragment length is 58 bps INFO @ Sat, 27 Jun 2020 00:27:00: #2 alternative fragment length(s) may be 2,36,40,58,199,226,338,538 bps INFO @ Sat, 27 Jun 2020 00:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10_model.r WARNING @ Sat, 27 Jun 2020 00:27:00: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:27:00: #2 You may need to consider one of the other alternative d(s): 2,36,40,58,199,226,338,538 WARNING @ Sat, 27 Jun 2020 00:27:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:27:00: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:00: 12000000 INFO @ Sat, 27 Jun 2020 00:27:06: 13000000 INFO @ Sat, 27 Jun 2020 00:27:12: 14000000 INFO @ Sat, 27 Jun 2020 00:27:13: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:27:19: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:27:26: 16000000 INFO @ Sat, 27 Jun 2020 00:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.05_summits.bed INFO @ Sat, 27 Jun 2020 00:27:32: Done! INFO @ Sat, 27 Jun 2020 00:27:32: 17000000 pass1 - making usageList (465 chroms): 2 millis pass2 - checking and writing primary data (1726 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:27:35: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:27:35: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:27:35: #1 total tags in treatment: 17395257 INFO @ Sat, 27 Jun 2020 00:27:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:27:35: #1 tags after filtering in treatment: 17395193 INFO @ Sat, 27 Jun 2020 00:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:27:35: #1 finished! INFO @ Sat, 27 Jun 2020 00:27:35: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:27:36: #2 number of paired peaks: 246 WARNING @ Sat, 27 Jun 2020 00:27:36: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 27 Jun 2020 00:27:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:27:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:27:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:27:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:27:37: #2 predicted fragment length is 58 bps INFO @ Sat, 27 Jun 2020 00:27:37: #2 alternative fragment length(s) may be 2,36,40,58,199,226,338,538 bps INFO @ Sat, 27 Jun 2020 00:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20_model.r WARNING @ Sat, 27 Jun 2020 00:27:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:27:37: #2 You may need to consider one of the other alternative d(s): 2,36,40,58,199,226,338,538 WARNING @ Sat, 27 Jun 2020 00:27:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:27:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:37: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.10_summits.bed INFO @ Sat, 27 Jun 2020 00:27:55: Done! pass1 - making usageList (213 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:28:14: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495288/SRX495288.20_summits.bed INFO @ Sat, 27 Jun 2020 00:28:33: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (205 records, 4 fields): 5 millis CompletedMACS2peakCalling