Job ID = 6498758 SRX = SRX750081 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:04:40 prefetch.2.10.7: 1) Downloading 'SRR1638774'... 2020-06-26T00:04:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:17:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:17:56 prefetch.2.10.7: 1) 'SRR1638774' was downloaded successfully Read 55955788 spots for SRR1638774/SRR1638774.sra Written 55955788 spots for SRR1638774/SRR1638774.sra 2020-06-26T00:22:11 prefetch.2.10.7: 1) Downloading 'SRR1638775'... 2020-06-26T00:22:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:33:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:33:43 prefetch.2.10.7: 1) 'SRR1638775' was downloaded successfully Read 55027158 spots for SRR1638775/SRR1638775.sra Written 55027158 spots for SRR1638775/SRR1638775.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: 01:19:39 110982946 reads; of these: 110982946 (100.00%) were unpaired; of these: 36282513 (32.69%) aligned 0 times 50359864 (45.38%) aligned exactly 1 time 24340569 (21.93%) aligned >1 times 67.31% overall alignment rate Time searching: 01:19:39 Overall time: 01:19:39 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 56 files... [bam_rmdupse_core] 70338918 / 74700433 = 0.9416 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 11:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.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 11:19:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:19:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:20:07: 1000000 INFO @ Fri, 26 Jun 2020 11:20:15: 2000000 INFO @ Fri, 26 Jun 2020 11:20:23: 3000000 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 11:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.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 11:20:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:20:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:20:30: 4000000 INFO @ Fri, 26 Jun 2020 11:20:33: #1 tag size is determined as 141 bps INFO @ Fri, 26 Jun 2020 11:20:33: #1 tag size = 141 INFO @ Fri, 26 Jun 2020 11:20:33: #1 total tags in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:20:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:20:33: #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 11:20:33: #1 tags after filtering in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:20:33: #1 finished! INFO @ Fri, 26 Jun 2020 11:20:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:20:34: #2 number of paired peaks: 7977 INFO @ Fri, 26 Jun 2020 11:20:34: start model_add_line... INFO @ Fri, 26 Jun 2020 11:20:34: start X-correlation... INFO @ Fri, 26 Jun 2020 11:20:34: end of X-cor INFO @ Fri, 26 Jun 2020 11:20:34: #2 finished! INFO @ Fri, 26 Jun 2020 11:20:34: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 11:20:34: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 11:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05_model.r WARNING @ Fri, 26 Jun 2020 11:20:34: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:20:34: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 11:20:34: #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 11:20:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:20:39: 1000000 INFO @ Fri, 26 Jun 2020 11:20:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:20:48: 2000000 INFO @ Fri, 26 Jun 2020 11:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05_peaks.xls INFO @ Fri, 26 Jun 2020 11:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:20:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.05_summits.bed INFO @ Fri, 26 Jun 2020 11:20:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10475 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:20:57: 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 @ Fri, 26 Jun 2020 11:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.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 11:20:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 11:20:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 11:21:06: 4000000 INFO @ Fri, 26 Jun 2020 11:21:08: 1000000 INFO @ Fri, 26 Jun 2020 11:21:10: #1 tag size is determined as 141 bps INFO @ Fri, 26 Jun 2020 11:21:10: #1 tag size = 141 INFO @ Fri, 26 Jun 2020 11:21:10: #1 total tags in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:21:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:21:10: #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 11:21:10: #1 tags after filtering in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:21:10: #1 finished! INFO @ Fri, 26 Jun 2020 11:21:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:21:11: #2 number of paired peaks: 7977 INFO @ Fri, 26 Jun 2020 11:21:11: start model_add_line... INFO @ Fri, 26 Jun 2020 11:21:11: start X-correlation... INFO @ Fri, 26 Jun 2020 11:21:11: end of X-cor INFO @ Fri, 26 Jun 2020 11:21:11: #2 finished! INFO @ Fri, 26 Jun 2020 11:21:11: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 11:21:11: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 11:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10_model.r WARNING @ Fri, 26 Jun 2020 11:21:11: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:21:11: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 11:21:11: #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 11:21:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:21:17: 2000000 INFO @ Fri, 26 Jun 2020 11:21:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 11:21:25: 3000000 INFO @ Fri, 26 Jun 2020 11:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10_peaks.xls INFO @ Fri, 26 Jun 2020 11:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.10_summits.bed INFO @ Fri, 26 Jun 2020 11:21:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7101 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:21:33: 4000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 11:21:36: #1 tag size is determined as 141 bps INFO @ Fri, 26 Jun 2020 11:21:36: #1 tag size = 141 INFO @ Fri, 26 Jun 2020 11:21:36: #1 total tags in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:21:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:21:36: #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 11:21:36: #1 tags after filtering in treatment: 4361515 INFO @ Fri, 26 Jun 2020 11:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:21:36: #1 finished! INFO @ Fri, 26 Jun 2020 11:21:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:21:36: #2 number of paired peaks: 7977 INFO @ Fri, 26 Jun 2020 11:21:36: start model_add_line... INFO @ Fri, 26 Jun 2020 11:21:36: start X-correlation... INFO @ Fri, 26 Jun 2020 11:21:36: end of X-cor INFO @ Fri, 26 Jun 2020 11:21:36: #2 finished! INFO @ Fri, 26 Jun 2020 11:21:36: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 11:21:36: #2 alternative fragment length(s) may be 133 bps INFO @ Fri, 26 Jun 2020 11:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20_model.r WARNING @ Fri, 26 Jun 2020 11:21:36: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:21:36: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Fri, 26 Jun 2020 11:21:36: #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 11:21:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:21:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20_peaks.xls INFO @ Fri, 26 Jun 2020 11:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750081/SRX750081.20_summits.bed INFO @ Fri, 26 Jun 2020 11:21:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4579 records, 4 fields): 6 millis CompletedMACS2peakCalling