Job ID = 6458202 SRX = SRX495311 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:15:34 prefetch.2.10.7: 1) Downloading 'SRR1198816'... 2020-06-21T12:15:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:50 prefetch.2.10.7: 1) 'SRR1198816' was downloaded successfully Read 37981047 spots for SRR1198816/SRR1198816.sra Written 37981047 spots for SRR1198816/SRR1198816.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: 00:22:52 37981047 reads; of these: 37981047 (100.00%) were unpaired; of these: 2314650 (6.09%) aligned 0 times 16142163 (42.50%) aligned exactly 1 time 19524234 (51.41%) aligned >1 times 93.91% overall alignment rate Time searching: 00:22:52 Overall time: 00:22:52 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 16 files... [bam_rmdupse_core] 25075950 / 35666397 = 0.7031 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 21:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.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 21:52:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:13: 1000000 INFO @ Sun, 21 Jun 2020 21:52:19: 2000000 INFO @ Sun, 21 Jun 2020 21:52:24: 3000000 INFO @ Sun, 21 Jun 2020 21:52:30: 4000000 INFO @ Sun, 21 Jun 2020 21:52:35: 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 21:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.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 21:52:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:41: 6000000 INFO @ Sun, 21 Jun 2020 21:52:43: 1000000 INFO @ Sun, 21 Jun 2020 21:52:46: 7000000 INFO @ Sun, 21 Jun 2020 21:52:49: 2000000 INFO @ Sun, 21 Jun 2020 21:52:52: 8000000 INFO @ Sun, 21 Jun 2020 21:52:54: 3000000 INFO @ Sun, 21 Jun 2020 21:52:58: 9000000 INFO @ Sun, 21 Jun 2020 21:53:00: 4000000 INFO @ Sun, 21 Jun 2020 21:53:03: 10000000 INFO @ Sun, 21 Jun 2020 21:53:05: 5000000 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 21:53:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:07: #1 total tags in treatment: 10590447 INFO @ Sun, 21 Jun 2020 21:53:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:07: #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 21:53:07: #1 tags after filtering in treatment: 10590444 INFO @ Sun, 21 Jun 2020 21:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.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 21:53:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:08: #2 number of paired peaks: 2859 INFO @ Sun, 21 Jun 2020 21:53:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:08: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:53:08: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 21:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05_model.r WARNING @ Sun, 21 Jun 2020 21:53:08: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:53:08: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 21:53:08: #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 21:53:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:11: 6000000 INFO @ Sun, 21 Jun 2020 21:53:13: 1000000 INFO @ Sun, 21 Jun 2020 21:53:16: 7000000 INFO @ Sun, 21 Jun 2020 21:53:19: 2000000 INFO @ Sun, 21 Jun 2020 21:53:22: 8000000 INFO @ Sun, 21 Jun 2020 21:53:24: 3000000 INFO @ Sun, 21 Jun 2020 21:53:28: 9000000 INFO @ Sun, 21 Jun 2020 21:53:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:29: 4000000 INFO @ Sun, 21 Jun 2020 21:53:33: 10000000 INFO @ Sun, 21 Jun 2020 21:53:35: 5000000 INFO @ Sun, 21 Jun 2020 21:53:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:37: #1 total tags in treatment: 10590447 INFO @ Sun, 21 Jun 2020 21:53:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:37: #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 21:53:37: #1 tags after filtering in treatment: 10590444 INFO @ Sun, 21 Jun 2020 21:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:38: #2 number of paired peaks: 2859 INFO @ Sun, 21 Jun 2020 21:53:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:39: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:53:39: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 21:53:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10_model.r WARNING @ Sun, 21 Jun 2020 21:53:39: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:53:39: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 21:53:39: #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 21:53:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.05_summits.bed INFO @ Sun, 21 Jun 2020 21:53:39: Done! INFO @ Sun, 21 Jun 2020 21:53:40: 6000000 pass1 - making usageList (839 chroms): 2 millis pass2 - checking and writing primary data (9222 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:53:46: 7000000 INFO @ Sun, 21 Jun 2020 21:53:51: 8000000 INFO @ Sun, 21 Jun 2020 21:53:57: 9000000 INFO @ Sun, 21 Jun 2020 21:54:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:03: 10000000 INFO @ Sun, 21 Jun 2020 21:54:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:54:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:54:06: #1 total tags in treatment: 10590447 INFO @ Sun, 21 Jun 2020 21:54:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:06: #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 21:54:07: #1 tags after filtering in treatment: 10590444 INFO @ Sun, 21 Jun 2020 21:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:08: #2 number of paired peaks: 2859 INFO @ Sun, 21 Jun 2020 21:54:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:08: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 21:54:08: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 21:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20_model.r WARNING @ Sun, 21 Jun 2020 21:54:08: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:08: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 21:54:08: #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 21:54:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:11: Done! pass1 - making usageList (652 chroms): 2 millis pass2 - checking and writing primary data (6079 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:54:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495311/SRX495311.20_summits.bed INFO @ Sun, 21 Jun 2020 21:54:39: Done! pass1 - making usageList (202 chroms): 1 millis pass2 - checking and writing primary data (2699 records, 4 fields): 9 millis CompletedMACS2peakCalling