Job ID = 6455001 SRX = SRX2618547 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:10 prefetch.2.10.7: 1) Downloading 'SRR5319101'... 2020-06-21T09:35:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:54 prefetch.2.10.7: 'SRR5319101' is valid 2020-06-21T09:37:54 prefetch.2.10.7: 1) 'SRR5319101' was downloaded successfully 2020-06-21T09:37:54 prefetch.2.10.7: 'SRR5319101' has 0 unresolved dependencies Read 21505423 spots for SRR5319101/SRR5319101.sra Written 21505423 spots for SRR5319101/SRR5319101.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: 00:06:14 21505423 reads; of these: 21505423 (100.00%) were unpaired; of these: 960347 (4.47%) aligned 0 times 13413146 (62.37%) aligned exactly 1 time 7131930 (33.16%) aligned >1 times 95.53% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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 12 files... [bam_rmdupse_core] 3795238 / 20545076 = 0.1847 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 18:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.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 18:49:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:00: 1000000 INFO @ Sun, 21 Jun 2020 18:50:05: 2000000 INFO @ Sun, 21 Jun 2020 18:50:10: 3000000 INFO @ Sun, 21 Jun 2020 18:50:16: 4000000 INFO @ Sun, 21 Jun 2020 18:50:21: 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 18:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.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 18:50:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:27: 6000000 INFO @ Sun, 21 Jun 2020 18:50:31: 1000000 INFO @ Sun, 21 Jun 2020 18:50:33: 7000000 INFO @ Sun, 21 Jun 2020 18:50:38: 2000000 INFO @ Sun, 21 Jun 2020 18:50:40: 8000000 INFO @ Sun, 21 Jun 2020 18:50:44: 3000000 INFO @ Sun, 21 Jun 2020 18:50:46: 9000000 INFO @ Sun, 21 Jun 2020 18:50:51: 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 @ Sun, 21 Jun 2020 18:50:53: 10000000 INFO @ Sun, 21 Jun 2020 18:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.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 18:50:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:58: 5000000 INFO @ Sun, 21 Jun 2020 18:50:59: 11000000 INFO @ Sun, 21 Jun 2020 18:51:01: 1000000 INFO @ Sun, 21 Jun 2020 18:51:05: 6000000 INFO @ Sun, 21 Jun 2020 18:51:05: 12000000 INFO @ Sun, 21 Jun 2020 18:51:08: 2000000 INFO @ Sun, 21 Jun 2020 18:51:12: 7000000 INFO @ Sun, 21 Jun 2020 18:51:12: 13000000 INFO @ Sun, 21 Jun 2020 18:51:15: 3000000 INFO @ Sun, 21 Jun 2020 18:51:19: 14000000 INFO @ Sun, 21 Jun 2020 18:51:19: 8000000 INFO @ Sun, 21 Jun 2020 18:51:22: 4000000 INFO @ Sun, 21 Jun 2020 18:51:25: 15000000 INFO @ Sun, 21 Jun 2020 18:51:26: 9000000 INFO @ Sun, 21 Jun 2020 18:51:29: 5000000 INFO @ Sun, 21 Jun 2020 18:51:32: 16000000 INFO @ Sun, 21 Jun 2020 18:51:34: 10000000 INFO @ Sun, 21 Jun 2020 18:51:36: 6000000 INFO @ Sun, 21 Jun 2020 18:51:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:37: #1 total tags in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:51:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:37: #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 18:51:37: #1 tags after filtering in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:39: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 18:51:39: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:39: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:51:39: #2 alternative fragment length(s) may be 2,11,16 bps INFO @ Sun, 21 Jun 2020 18:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:39: #2 You may need to consider one of the other alternative d(s): 2,11,16 WARNING @ Sun, 21 Jun 2020 18:51:39: #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 18:51:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:41: 11000000 INFO @ Sun, 21 Jun 2020 18:51:42: 7000000 INFO @ Sun, 21 Jun 2020 18:51:48: 12000000 INFO @ Sun, 21 Jun 2020 18:51:49: 8000000 INFO @ Sun, 21 Jun 2020 18:51:56: 13000000 INFO @ Sun, 21 Jun 2020 18:51:56: 9000000 INFO @ Sun, 21 Jun 2020 18:52:03: 10000000 INFO @ Sun, 21 Jun 2020 18:52:03: 14000000 INFO @ Sun, 21 Jun 2020 18:52:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:10: 11000000 INFO @ Sun, 21 Jun 2020 18:52:11: 15000000 INFO @ Sun, 21 Jun 2020 18:52:17: 12000000 INFO @ Sun, 21 Jun 2020 18:52:18: 16000000 INFO @ Sun, 21 Jun 2020 18:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:23: #1 total tags in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:52:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:23: #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 18:52:24: #1 tags after filtering in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:24: 13000000 INFO @ Sun, 21 Jun 2020 18:52:25: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 18:52:25: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:25: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:52:25: #2 alternative fragment length(s) may be 2,11,16 bps INFO @ Sun, 21 Jun 2020 18:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:25: #2 You may need to consider one of the other alternative d(s): 2,11,16 WARNING @ Sun, 21 Jun 2020 18:52:25: #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 18:52:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:31: 14000000 INFO @ Sun, 21 Jun 2020 18:52:38: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:52:45: 16000000 INFO @ Sun, 21 Jun 2020 18:52:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:50: #1 total tags in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:52:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:50: #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 18:52:51: #1 tags after filtering in treatment: 16749838 INFO @ Sun, 21 Jun 2020 18:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:52: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 18:52:52: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:52: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:52:52: #2 alternative fragment length(s) may be 2,11,16 bps INFO @ Sun, 21 Jun 2020 18:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:52: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:52: #2 You may need to consider one of the other alternative d(s): 2,11,16 WARNING @ Sun, 21 Jun 2020 18:52:52: #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 18:52:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618547/SRX2618547.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling