Job ID = 6453836 SRX = SRX152091 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:41:32 prefetch.2.10.7: 1) Downloading 'SRR504947'... 2020-06-21T08:41:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:31 prefetch.2.10.7: 'SRR504947' is valid 2020-06-21T08:43:31 prefetch.2.10.7: 1) 'SRR504947' was downloaded successfully Read 13804609 spots for SRR504947/SRR504947.sra Written 13804609 spots for SRR504947/SRR504947.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: 00:03:14 13804609 reads; of these: 13804609 (100.00%) were unpaired; of these: 770661 (5.58%) aligned 0 times 11561357 (83.75%) aligned exactly 1 time 1472591 (10.67%) aligned >1 times 94.42% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 3948454 / 13033948 = 0.3029 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 17:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.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 17:51:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:18: 1000000 INFO @ Sun, 21 Jun 2020 17:51:24: 2000000 INFO @ Sun, 21 Jun 2020 17:51:31: 3000000 INFO @ Sun, 21 Jun 2020 17:51:38: 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 17:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.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 17:51:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:46: 5000000 INFO @ Sun, 21 Jun 2020 17:51:49: 1000000 INFO @ Sun, 21 Jun 2020 17:51:54: 6000000 INFO @ Sun, 21 Jun 2020 17:51:57: 2000000 INFO @ Sun, 21 Jun 2020 17:52:01: 7000000 INFO @ Sun, 21 Jun 2020 17:52:05: 3000000 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 17:52:10: 8000000 INFO @ Sun, 21 Jun 2020 17:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.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 17:52:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:12: 4000000 INFO @ Sun, 21 Jun 2020 17:52:18: 9000000 INFO @ Sun, 21 Jun 2020 17:52:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:18: #1 total tags in treatment: 9085494 INFO @ Sun, 21 Jun 2020 17:52:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:18: #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 17:52:19: #1 tags after filtering in treatment: 9085447 INFO @ Sun, 21 Jun 2020 17:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:19: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:19: 1000000 INFO @ Sun, 21 Jun 2020 17:52:19: #2 number of paired peaks: 2090 INFO @ Sun, 21 Jun 2020 17:52:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:20: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 17:52:20: #2 alternative fragment length(s) may be 4,33 bps INFO @ Sun, 21 Jun 2020 17:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:20: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:20: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Sun, 21 Jun 2020 17:52:20: #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 17:52:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:21: 5000000 INFO @ Sun, 21 Jun 2020 17:52:27: 2000000 INFO @ Sun, 21 Jun 2020 17:52:28: 6000000 INFO @ Sun, 21 Jun 2020 17:52:34: 3000000 INFO @ Sun, 21 Jun 2020 17:52:36: 7000000 INFO @ Sun, 21 Jun 2020 17:52:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:42: 4000000 INFO @ Sun, 21 Jun 2020 17:52:45: 8000000 INFO @ Sun, 21 Jun 2020 17:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:47: Done! pass1 - making usageList (79 chroms): 2 millis pass2 - checking and writing primary data (3108 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:50: 5000000 INFO @ Sun, 21 Jun 2020 17:52:53: 9000000 INFO @ Sun, 21 Jun 2020 17:52:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:54: #1 total tags in treatment: 9085494 INFO @ Sun, 21 Jun 2020 17:52:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:54: #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 17:52:54: #1 tags after filtering in treatment: 9085447 INFO @ Sun, 21 Jun 2020 17:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:55: #2 number of paired peaks: 2090 INFO @ Sun, 21 Jun 2020 17:52:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:55: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 17:52:55: #2 alternative fragment length(s) may be 4,33 bps INFO @ Sun, 21 Jun 2020 17:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10_model.r WARNING @ Sun, 21 Jun 2020 17:52:55: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:55: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Sun, 21 Jun 2020 17:52:55: #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 17:52:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:57: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:05: 7000000 INFO @ Sun, 21 Jun 2020 17:53:12: 8000000 INFO @ Sun, 21 Jun 2020 17:53:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:20: 9000000 INFO @ Sun, 21 Jun 2020 17:53:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:53:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:53:20: #1 total tags in treatment: 9085494 INFO @ Sun, 21 Jun 2020 17:53:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:20: #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 17:53:21: #1 tags after filtering in treatment: 9085447 INFO @ Sun, 21 Jun 2020 17:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:21: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:21: #2 number of paired peaks: 2090 INFO @ Sun, 21 Jun 2020 17:53:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:21: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 17:53:21: #2 alternative fragment length(s) may be 4,33 bps INFO @ Sun, 21 Jun 2020 17:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:21: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:21: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Sun, 21 Jun 2020 17:53:21: #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 17:53:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:23: Done! pass1 - making usageList (33 chroms): 3 millis pass2 - checking and writing primary data (589 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152091/SRX152091.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:49: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling