Job ID = 6498769 SRX = SRX760383 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:00:25 prefetch.2.10.7: 1) Downloading 'SRR1653484'... 2020-06-26T00:00:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:23 prefetch.2.10.7: 1) 'SRR1653484' was downloaded successfully Read 19472584 spots for SRR1653484/SRR1653484.sra Written 19472584 spots for SRR1653484/SRR1653484.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: 00:10:00 19472584 reads; of these: 19472584 (100.00%) were unpaired; of these: 1940213 (9.96%) aligned 0 times 7691261 (39.50%) aligned exactly 1 time 9841110 (50.54%) aligned >1 times 90.04% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 8459587 / 17532371 = 0.4825 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 @ Fri, 26 Jun 2020 09:17:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.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 @ Fri, 26 Jun 2020 09:17:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:36: 1000000 INFO @ Fri, 26 Jun 2020 09:17:42: 2000000 INFO @ Fri, 26 Jun 2020 09:17:49: 3000000 INFO @ Fri, 26 Jun 2020 09:17:55: 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 @ Fri, 26 Jun 2020 09:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.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 @ Fri, 26 Jun 2020 09:18:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:02: 5000000 INFO @ Fri, 26 Jun 2020 09:18:07: 1000000 INFO @ Fri, 26 Jun 2020 09:18:09: 6000000 INFO @ Fri, 26 Jun 2020 09:18:13: 2000000 INFO @ Fri, 26 Jun 2020 09:18:16: 7000000 INFO @ Fri, 26 Jun 2020 09:18:20: 3000000 INFO @ Fri, 26 Jun 2020 09:18:23: 8000000 INFO @ Fri, 26 Jun 2020 09:18:27: 4000000 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 @ Fri, 26 Jun 2020 09:18:30: 9000000 INFO @ Fri, 26 Jun 2020 09:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.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 @ Fri, 26 Jun 2020 09:18:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:18:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:18:30: #1 total tags in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:18:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:18:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:18:30: #1 tags after filtering in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:18:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:18:30: #1 finished! INFO @ Fri, 26 Jun 2020 09:18:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:18:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:18:31: #2 number of paired peaks: 473 WARNING @ Fri, 26 Jun 2020 09:18:31: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Fri, 26 Jun 2020 09:18:31: start model_add_line... INFO @ Fri, 26 Jun 2020 09:18:31: start X-correlation... INFO @ Fri, 26 Jun 2020 09:18:31: end of X-cor INFO @ Fri, 26 Jun 2020 09:18:31: #2 finished! INFO @ Fri, 26 Jun 2020 09:18:31: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 09:18:31: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 26 Jun 2020 09:18:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05_model.r WARNING @ Fri, 26 Jun 2020 09:18:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:18:31: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 26 Jun 2020 09:18:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:18:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:18:34: 5000000 INFO @ Fri, 26 Jun 2020 09:18:37: 1000000 INFO @ Fri, 26 Jun 2020 09:18:40: 6000000 INFO @ Fri, 26 Jun 2020 09:18:43: 2000000 INFO @ Fri, 26 Jun 2020 09:18:47: 7000000 INFO @ Fri, 26 Jun 2020 09:18:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:18:50: 3000000 INFO @ Fri, 26 Jun 2020 09:18:54: 8000000 INFO @ Fri, 26 Jun 2020 09:18:56: 4000000 INFO @ Fri, 26 Jun 2020 09:18:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:18:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:18:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.05_summits.bed INFO @ Fri, 26 Jun 2020 09:18:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2010 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:19:01: 9000000 INFO @ Fri, 26 Jun 2020 09:19:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:19:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:19:02: #1 total tags in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:19:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:02: #1 tags after filtering in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:02: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:02: #2 number of paired peaks: 473 WARNING @ Fri, 26 Jun 2020 09:19:02: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Fri, 26 Jun 2020 09:19:02: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:02: 5000000 INFO @ Fri, 26 Jun 2020 09:19:02: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:02: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:02: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:02: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 09:19:02: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 26 Jun 2020 09:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10_model.r WARNING @ Fri, 26 Jun 2020 09:19:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:02: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 26 Jun 2020 09:19:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:08: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:19:14: 7000000 INFO @ Fri, 26 Jun 2020 09:19:20: 8000000 INFO @ Fri, 26 Jun 2020 09:19:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:19:26: 9000000 INFO @ Fri, 26 Jun 2020 09:19:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:19:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:19:27: #1 total tags in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:19:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:27: #1 tags after filtering in treatment: 9072784 INFO @ Fri, 26 Jun 2020 09:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:28: #2 number of paired peaks: 473 WARNING @ Fri, 26 Jun 2020 09:19:28: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Fri, 26 Jun 2020 09:19:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:28: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 09:19:28: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 26 Jun 2020 09:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20_model.r WARNING @ Fri, 26 Jun 2020 09:19:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:28: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 26 Jun 2020 09:19:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.10_summits.bed INFO @ Fri, 26 Jun 2020 09:19:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1562 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:19:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX760383/SRX760383.20_summits.bed INFO @ Fri, 26 Jun 2020 09:19:56: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1132 records, 4 fields): 3 millis CompletedMACS2peakCalling