Job ID = 6457615 SRX = SRX467029 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:24:34 prefetch.2.10.7: 1) Downloading 'SRR1164453'... 2020-06-21T12:24:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:31 prefetch.2.10.7: 1) 'SRR1164453' was downloaded successfully Read 28572025 spots for SRR1164453/SRR1164453.sra Written 28572025 spots for SRR1164453/SRR1164453.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: 00:00:01 Multiseed full-index search: 00:07:05 28572025 reads; of these: 28572025 (100.00%) were unpaired; of these: 10561739 (36.97%) aligned 0 times 12773428 (44.71%) aligned exactly 1 time 5236858 (18.33%) aligned >1 times 63.03% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 5482977 / 18010286 = 0.3044 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 21:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.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 21:44:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:44:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:44:40: 1000000 INFO @ Sun, 21 Jun 2020 21:44:46: 2000000 INFO @ Sun, 21 Jun 2020 21:44:52: 3000000 INFO @ Sun, 21 Jun 2020 21:44:59: 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 21:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.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 21:45:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:06: 5000000 INFO @ Sun, 21 Jun 2020 21:45:10: 1000000 INFO @ Sun, 21 Jun 2020 21:45:13: 6000000 INFO @ Sun, 21 Jun 2020 21:45:17: 2000000 INFO @ Sun, 21 Jun 2020 21:45:19: 7000000 INFO @ Sun, 21 Jun 2020 21:45:24: 3000000 INFO @ Sun, 21 Jun 2020 21:45:26: 8000000 INFO @ Sun, 21 Jun 2020 21:45:31: 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 21:45:33: 9000000 INFO @ Sun, 21 Jun 2020 21:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.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 21:45:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:45:37: 5000000 INFO @ Sun, 21 Jun 2020 21:45:40: 1000000 INFO @ Sun, 21 Jun 2020 21:45:41: 10000000 INFO @ Sun, 21 Jun 2020 21:45:44: 6000000 INFO @ Sun, 21 Jun 2020 21:45:46: 2000000 INFO @ Sun, 21 Jun 2020 21:45:48: 11000000 INFO @ Sun, 21 Jun 2020 21:45:51: 7000000 INFO @ Sun, 21 Jun 2020 21:45:52: 3000000 INFO @ Sun, 21 Jun 2020 21:45:55: 12000000 INFO @ Sun, 21 Jun 2020 21:45:58: 8000000 INFO @ Sun, 21 Jun 2020 21:45:58: 4000000 INFO @ Sun, 21 Jun 2020 21:45:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:45:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:45:59: #1 total tags in treatment: 12527309 INFO @ Sun, 21 Jun 2020 21:45:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:45:59: #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 21:46:00: #1 tags after filtering in treatment: 12527308 INFO @ Sun, 21 Jun 2020 21:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:01: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:46:01: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:46:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:01: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:46:01: #2 alternative fragment length(s) may be 3,593,598 bps INFO @ Sun, 21 Jun 2020 21:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05_model.r WARNING @ Sun, 21 Jun 2020 21:46:01: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:01: #2 You may need to consider one of the other alternative d(s): 3,593,598 WARNING @ Sun, 21 Jun 2020 21:46:01: #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 21:46:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:04: 5000000 INFO @ Sun, 21 Jun 2020 21:46:05: 9000000 INFO @ Sun, 21 Jun 2020 21:46:11: 6000000 INFO @ Sun, 21 Jun 2020 21:46:11: 10000000 INFO @ Sun, 21 Jun 2020 21:46:16: 11000000 INFO @ Sun, 21 Jun 2020 21:46:17: 7000000 INFO @ Sun, 21 Jun 2020 21:46:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:23: 12000000 INFO @ Sun, 21 Jun 2020 21:46:23: 8000000 INFO @ Sun, 21 Jun 2020 21:46:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:28: #1 total tags in treatment: 12527309 INFO @ Sun, 21 Jun 2020 21:46:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:28: #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 21:46:28: #1 tags after filtering in treatment: 12527308 INFO @ Sun, 21 Jun 2020 21:46:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:29: 9000000 INFO @ Sun, 21 Jun 2020 21:46:29: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:46:29: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:46:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:29: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:46:29: #2 alternative fragment length(s) may be 3,593,598 bps INFO @ Sun, 21 Jun 2020 21:46:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10_model.r WARNING @ Sun, 21 Jun 2020 21:46:29: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:29: #2 You may need to consider one of the other alternative d(s): 3,593,598 WARNING @ Sun, 21 Jun 2020 21:46:29: #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 21:46:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.05_summits.bed INFO @ Sun, 21 Jun 2020 21:46:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:46:36: 10000000 INFO @ Sun, 21 Jun 2020 21:46:42: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:46:47: 12000000 INFO @ Sun, 21 Jun 2020 21:46:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:51: #1 total tags in treatment: 12527309 INFO @ Sun, 21 Jun 2020 21:46:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:51: #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 21:46:51: #1 tags after filtering in treatment: 12527308 INFO @ Sun, 21 Jun 2020 21:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:52: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:46:52: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:46:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:52: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:46:52: #2 alternative fragment length(s) may be 3,593,598 bps INFO @ Sun, 21 Jun 2020 21:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20_model.r WARNING @ Sun, 21 Jun 2020 21:46:52: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:52: #2 You may need to consider one of the other alternative d(s): 3,593,598 WARNING @ Sun, 21 Jun 2020 21:46:52: #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 21:46:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:47:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467029/SRX467029.20_summits.bed INFO @ Sun, 21 Jun 2020 21:47:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling