Job ID = 6455483 SRX = SRX287822 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:32:21 prefetch.2.10.7: 1) Downloading 'SRR870011'... 2020-06-21T10:32:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:42 prefetch.2.10.7: 1) 'SRR870011' was downloaded successfully Read 21559305 spots for SRR870011/SRR870011.sra Written 21559305 spots for SRR870011/SRR870011.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: 00:05:47 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1516224 (7.03%) aligned 0 times 15525266 (72.01%) aligned exactly 1 time 4517815 (20.96%) aligned >1 times 92.97% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 2294867 / 20043081 = 0.1145 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 19:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.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 19:48:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:46: 1000000 INFO @ Sun, 21 Jun 2020 19:48:50: 2000000 INFO @ Sun, 21 Jun 2020 19:48:55: 3000000 INFO @ Sun, 21 Jun 2020 19:49:00: 4000000 INFO @ Sun, 21 Jun 2020 19:49:04: 5000000 INFO @ Sun, 21 Jun 2020 19:49:09: 6000000 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 19:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.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 19:49:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:14: 7000000 INFO @ Sun, 21 Jun 2020 19:49:16: 1000000 INFO @ Sun, 21 Jun 2020 19:49:19: 8000000 INFO @ Sun, 21 Jun 2020 19:49:21: 2000000 INFO @ Sun, 21 Jun 2020 19:49:23: 9000000 INFO @ Sun, 21 Jun 2020 19:49:25: 3000000 INFO @ Sun, 21 Jun 2020 19:49:28: 10000000 INFO @ Sun, 21 Jun 2020 19:49:30: 4000000 INFO @ Sun, 21 Jun 2020 19:49:33: 11000000 INFO @ Sun, 21 Jun 2020 19:49:35: 5000000 INFO @ Sun, 21 Jun 2020 19:49:38: 12000000 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 19:49:40: 6000000 INFO @ Sun, 21 Jun 2020 19:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.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 19:49:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:42: 13000000 INFO @ Sun, 21 Jun 2020 19:49:45: 7000000 INFO @ Sun, 21 Jun 2020 19:49:46: 1000000 INFO @ Sun, 21 Jun 2020 19:49:47: 14000000 INFO @ Sun, 21 Jun 2020 19:49:49: 8000000 INFO @ Sun, 21 Jun 2020 19:49:51: 2000000 INFO @ Sun, 21 Jun 2020 19:49:52: 15000000 INFO @ Sun, 21 Jun 2020 19:49:54: 9000000 INFO @ Sun, 21 Jun 2020 19:49:56: 3000000 INFO @ Sun, 21 Jun 2020 19:49:57: 16000000 INFO @ Sun, 21 Jun 2020 19:49:59: 10000000 INFO @ Sun, 21 Jun 2020 19:50:00: 4000000 INFO @ Sun, 21 Jun 2020 19:50:02: 17000000 INFO @ Sun, 21 Jun 2020 19:50:04: 11000000 INFO @ Sun, 21 Jun 2020 19:50:05: 5000000 INFO @ Sun, 21 Jun 2020 19:50:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:06: #1 total tags in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:50:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:06: #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 19:50:06: #1 tags after filtering in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:08: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 19:50:08: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:08: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:50:08: #2 alternative fragment length(s) may be 3,38,537 bps INFO @ Sun, 21 Jun 2020 19:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05_model.r WARNING @ Sun, 21 Jun 2020 19:50:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:08: #2 You may need to consider one of the other alternative d(s): 3,38,537 WARNING @ Sun, 21 Jun 2020 19:50:08: #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 19:50:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:08: 12000000 INFO @ Sun, 21 Jun 2020 19:50:10: 6000000 INFO @ Sun, 21 Jun 2020 19:50:13: 13000000 INFO @ Sun, 21 Jun 2020 19:50:14: 7000000 INFO @ Sun, 21 Jun 2020 19:50:18: 14000000 INFO @ Sun, 21 Jun 2020 19:50:19: 8000000 INFO @ Sun, 21 Jun 2020 19:50:23: 15000000 INFO @ Sun, 21 Jun 2020 19:50:24: 9000000 INFO @ Sun, 21 Jun 2020 19:50:28: 16000000 INFO @ Sun, 21 Jun 2020 19:50:28: 10000000 INFO @ Sun, 21 Jun 2020 19:50:33: 17000000 INFO @ Sun, 21 Jun 2020 19:50:33: 11000000 INFO @ Sun, 21 Jun 2020 19:50:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:37: #1 total tags in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:50:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:37: #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 19:50:37: #1 tags after filtering in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:38: 12000000 INFO @ Sun, 21 Jun 2020 19:50:38: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 19:50:38: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:38: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:50:38: #2 alternative fragment length(s) may be 3,38,537 bps INFO @ Sun, 21 Jun 2020 19:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10_model.r WARNING @ Sun, 21 Jun 2020 19:50:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:38: #2 You may need to consider one of the other alternative d(s): 3,38,537 WARNING @ Sun, 21 Jun 2020 19:50:38: #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 19:50:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:43: 13000000 INFO @ Sun, 21 Jun 2020 19:50:47: 14000000 INFO @ Sun, 21 Jun 2020 19:50:52: 15000000 INFO @ Sun, 21 Jun 2020 19:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:56: Done! INFO @ Sun, 21 Jun 2020 19:50:57: 16000000 pass1 - making usageList (512 chroms): 2 millis pass2 - checking and writing primary data (2202 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:02: 17000000 INFO @ Sun, 21 Jun 2020 19:51:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:06: #1 total tags in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:51:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:06: #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 19:51:06: #1 tags after filtering in treatment: 17748214 INFO @ Sun, 21 Jun 2020 19:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:07: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 19:51:07: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:07: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:51:07: #2 alternative fragment length(s) may be 3,38,537 bps INFO @ Sun, 21 Jun 2020 19:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20_model.r WARNING @ Sun, 21 Jun 2020 19:51:07: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:07: #2 You may need to consider one of the other alternative d(s): 3,38,537 WARNING @ Sun, 21 Jun 2020 19:51:07: #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 19:51:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:26: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287822/SRX287822.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:53: Done! pass1 - making usageList (193 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 6 millis CompletedMACS2peakCalling