Job ID = 6455482 SRX = SRX287821 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:51 prefetch.2.10.7: 1) Downloading 'SRR870010'... 2020-06-21T10:15:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:33 prefetch.2.10.7: 1) 'SRR870010' was downloaded successfully Read 18493128 spots for SRR870010/SRR870010.sra Written 18493128 spots for SRR870010/SRR870010.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: 00:05:09 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1283991 (6.94%) aligned 0 times 13227008 (71.52%) aligned exactly 1 time 3982129 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1868067 / 17209137 = 0.1086 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 19:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.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 19:30:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:23: 1000000 INFO @ Sun, 21 Jun 2020 19:30:29: 2000000 INFO @ Sun, 21 Jun 2020 19:30:34: 3000000 INFO @ Sun, 21 Jun 2020 19:30:39: 4000000 INFO @ Sun, 21 Jun 2020 19:30:45: 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 19:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.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 19:30:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:50: 6000000 INFO @ Sun, 21 Jun 2020 19:30:54: 1000000 INFO @ Sun, 21 Jun 2020 19:30:56: 7000000 INFO @ Sun, 21 Jun 2020 19:30:59: 2000000 INFO @ Sun, 21 Jun 2020 19:31:02: 8000000 INFO @ Sun, 21 Jun 2020 19:31:05: 3000000 INFO @ Sun, 21 Jun 2020 19:31:08: 9000000 INFO @ Sun, 21 Jun 2020 19:31:11: 4000000 INFO @ Sun, 21 Jun 2020 19:31:14: 10000000 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 19:31:17: 5000000 INFO @ Sun, 21 Jun 2020 19:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.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 19:31:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:31:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:31:20: 11000000 INFO @ Sun, 21 Jun 2020 19:31:23: 6000000 INFO @ Sun, 21 Jun 2020 19:31:24: 1000000 INFO @ Sun, 21 Jun 2020 19:31:26: 12000000 INFO @ Sun, 21 Jun 2020 19:31:29: 7000000 INFO @ Sun, 21 Jun 2020 19:31:30: 2000000 INFO @ Sun, 21 Jun 2020 19:31:33: 13000000 INFO @ Sun, 21 Jun 2020 19:31:35: 8000000 INFO @ Sun, 21 Jun 2020 19:31:36: 3000000 INFO @ Sun, 21 Jun 2020 19:31:39: 14000000 INFO @ Sun, 21 Jun 2020 19:31:41: 9000000 INFO @ Sun, 21 Jun 2020 19:31:42: 4000000 INFO @ Sun, 21 Jun 2020 19:31:45: 15000000 INFO @ Sun, 21 Jun 2020 19:31:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:47: #1 total tags in treatment: 15341070 INFO @ Sun, 21 Jun 2020 19:31:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:47: #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 19:31:47: 10000000 INFO @ Sun, 21 Jun 2020 19:31:48: #1 tags after filtering in treatment: 15341069 INFO @ Sun, 21 Jun 2020 19:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:48: 5000000 INFO @ Sun, 21 Jun 2020 19:31:49: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:31:49: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:49: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:31:49: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:31:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05_model.r WARNING @ Sun, 21 Jun 2020 19:31:49: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:49: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:31:49: #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 19:31:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:53: 11000000 INFO @ Sun, 21 Jun 2020 19:31:54: 6000000 INFO @ Sun, 21 Jun 2020 19:31:59: 12000000 INFO @ Sun, 21 Jun 2020 19:32:00: 7000000 INFO @ Sun, 21 Jun 2020 19:32:06: 13000000 INFO @ Sun, 21 Jun 2020 19:32:06: 8000000 INFO @ Sun, 21 Jun 2020 19:32:11: 14000000 INFO @ Sun, 21 Jun 2020 19:32:12: 9000000 INFO @ Sun, 21 Jun 2020 19:32:17: 15000000 INFO @ Sun, 21 Jun 2020 19:32:18: 10000000 INFO @ Sun, 21 Jun 2020 19:32:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:20: #1 total tags in treatment: 15341070 INFO @ Sun, 21 Jun 2020 19:32:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:20: #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 19:32:20: #1 tags after filtering in treatment: 15341069 INFO @ Sun, 21 Jun 2020 19:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:21: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:32:21: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:32:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:21: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:32:21: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10_model.r WARNING @ Sun, 21 Jun 2020 19:32:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:32:21: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:32:21: #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 19:32:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:23: 11000000 INFO @ Sun, 21 Jun 2020 19:32:29: 12000000 INFO @ Sun, 21 Jun 2020 19:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.05_summits.bed INFO @ Sun, 21 Jun 2020 19:32:34: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (2201 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:35: 13000000 INFO @ Sun, 21 Jun 2020 19:32:40: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:32:46: 15000000 INFO @ Sun, 21 Jun 2020 19:32:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:48: #1 total tags in treatment: 15341070 INFO @ Sun, 21 Jun 2020 19:32:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:48: #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 19:32:48: #1 tags after filtering in treatment: 15341069 INFO @ Sun, 21 Jun 2020 19:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:49: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:32:49: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:32:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:50: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:32:50: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20_model.r WARNING @ Sun, 21 Jun 2020 19:32:50: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:32:50: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:32:50: #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 19:32:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.10_summits.bed INFO @ Sun, 21 Jun 2020 19:33:05: Done! pass1 - making usageList (411 chroms): 0 millis pass2 - checking and writing primary data (1186 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:33:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287821/SRX287821.20_summits.bed INFO @ Sun, 21 Jun 2020 19:33:33: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 9 millis CompletedMACS2peakCalling