Job ID = 6453623 SRX = SRX1300692 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:10 prefetch.2.10.7: 1) Downloading 'SRR2548368'... 2020-06-21T08:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:11 prefetch.2.10.7: 1) 'SRR2548368' was downloaded successfully Read 23006347 spots for SRR2548368/SRR2548368.sra Written 23006347 spots for SRR2548368/SRR2548368.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: 00:06:42 23006347 reads; of these: 23006347 (100.00%) were unpaired; of these: 1122042 (4.88%) aligned 0 times 15447772 (67.15%) aligned exactly 1 time 6436533 (27.98%) aligned >1 times 95.12% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 3015821 / 21884305 = 0.1378 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 17:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.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 17:53:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:49: 1000000 INFO @ Sun, 21 Jun 2020 17:53:55: 2000000 INFO @ Sun, 21 Jun 2020 17:54:01: 3000000 INFO @ Sun, 21 Jun 2020 17:54:06: 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 17:54:12: 5000000 INFO @ Sun, 21 Jun 2020 17:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.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 17:54:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:19: 6000000 INFO @ Sun, 21 Jun 2020 17:54:19: 1000000 INFO @ Sun, 21 Jun 2020 17:54:26: 7000000 INFO @ Sun, 21 Jun 2020 17:54:26: 2000000 INFO @ Sun, 21 Jun 2020 17:54:33: 8000000 INFO @ Sun, 21 Jun 2020 17:54:33: 3000000 INFO @ Sun, 21 Jun 2020 17:54:40: 4000000 INFO @ Sun, 21 Jun 2020 17:54:40: 9000000 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 17:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.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 17:54:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:47: 5000000 INFO @ Sun, 21 Jun 2020 17:54:47: 10000000 INFO @ Sun, 21 Jun 2020 17:54:50: 1000000 INFO @ Sun, 21 Jun 2020 17:54:54: 6000000 INFO @ Sun, 21 Jun 2020 17:54:54: 11000000 INFO @ Sun, 21 Jun 2020 17:54:57: 2000000 INFO @ Sun, 21 Jun 2020 17:55:01: 7000000 INFO @ Sun, 21 Jun 2020 17:55:01: 12000000 INFO @ Sun, 21 Jun 2020 17:55:04: 3000000 INFO @ Sun, 21 Jun 2020 17:55:08: 8000000 INFO @ Sun, 21 Jun 2020 17:55:08: 13000000 INFO @ Sun, 21 Jun 2020 17:55:12: 4000000 INFO @ Sun, 21 Jun 2020 17:55:15: 9000000 INFO @ Sun, 21 Jun 2020 17:55:15: 14000000 INFO @ Sun, 21 Jun 2020 17:55:19: 5000000 INFO @ Sun, 21 Jun 2020 17:55:22: 10000000 INFO @ Sun, 21 Jun 2020 17:55:23: 15000000 INFO @ Sun, 21 Jun 2020 17:55:26: 6000000 INFO @ Sun, 21 Jun 2020 17:55:29: 11000000 INFO @ Sun, 21 Jun 2020 17:55:30: 16000000 INFO @ Sun, 21 Jun 2020 17:55:33: 7000000 INFO @ Sun, 21 Jun 2020 17:55:37: 12000000 INFO @ Sun, 21 Jun 2020 17:55:37: 17000000 INFO @ Sun, 21 Jun 2020 17:55:41: 8000000 INFO @ Sun, 21 Jun 2020 17:55:44: 13000000 INFO @ Sun, 21 Jun 2020 17:55:45: 18000000 INFO @ Sun, 21 Jun 2020 17:55:48: 9000000 INFO @ Sun, 21 Jun 2020 17:55:52: 14000000 INFO @ Sun, 21 Jun 2020 17:55:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:55:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:55:52: #1 total tags in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:55:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:52: #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 17:55:53: #1 tags after filtering in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:55:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:54: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 17:55:54: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 17:55:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:54: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:55:54: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 17:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05_model.r WARNING @ Sun, 21 Jun 2020 17:55:54: #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 17:55:54: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 17:55:54: #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 17:55:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:56: 10000000 INFO @ Sun, 21 Jun 2020 17:55:59: 15000000 INFO @ Sun, 21 Jun 2020 17:56:03: 11000000 INFO @ Sun, 21 Jun 2020 17:56:06: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:56:10: 12000000 INFO @ Sun, 21 Jun 2020 17:56:13: 17000000 INFO @ Sun, 21 Jun 2020 17:56:17: 13000000 INFO @ Sun, 21 Jun 2020 17:56:20: 18000000 INFO @ Sun, 21 Jun 2020 17:56:24: 14000000 INFO @ Sun, 21 Jun 2020 17:56:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:26: #1 total tags in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:56:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:26: #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 17:56:27: #1 tags after filtering in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:28: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 17:56:28: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:28: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:56:28: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 17:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10_model.r WARNING @ Sun, 21 Jun 2020 17:56:28: #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 17:56:28: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 17:56:28: #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 17:56:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:30: 15000000 INFO @ Sun, 21 Jun 2020 17:56:37: 16000000 INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:43: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:50: 18000000 INFO @ Sun, 21 Jun 2020 17:56:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:56:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:56:55: #1 total tags in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:56:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:55: #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 17:56:56: #1 tags after filtering in treatment: 18868484 INFO @ Sun, 21 Jun 2020 17:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:57: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 17:56:57: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:57: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:56:57: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 17:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20_model.r WARNING @ Sun, 21 Jun 2020 17:56:57: #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 17:56:57: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 17:56:57: #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 17:56:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.10_summits.bed INFO @ Sun, 21 Jun 2020 17:57:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300692/SRX1300692.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling