Job ID = 6458781 SRX = SRX5436054 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:36:41 prefetch.2.10.7: 1) Downloading 'SRR8637386'... 2020-06-21T12:36:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:57 prefetch.2.10.7: 1) 'SRR8637386' was downloaded successfully Read 44412060 spots for SRR8637386/SRR8637386.sra Written 44412060 spots for SRR8637386/SRR8637386.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: 00:11:41 44412060 reads; of these: 44412060 (100.00%) were unpaired; of these: 2364426 (5.32%) aligned 0 times 29610391 (66.67%) aligned exactly 1 time 12437243 (28.00%) aligned >1 times 94.68% overall alignment rate Time searching: 00:11:41 Overall time: 00:11:41 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 20 files... [bam_rmdupse_core] 8786764 / 42047634 = 0.2090 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 22:07:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.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 22:07:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:10: 1000000 INFO @ Sun, 21 Jun 2020 22:07:17: 2000000 INFO @ Sun, 21 Jun 2020 22:07:23: 3000000 INFO @ Sun, 21 Jun 2020 22:07:30: 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 22:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.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 22:07:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:37: 5000000 INFO @ Sun, 21 Jun 2020 22:07:41: 1000000 INFO @ Sun, 21 Jun 2020 22:07:44: 6000000 INFO @ Sun, 21 Jun 2020 22:07:49: 2000000 INFO @ Sun, 21 Jun 2020 22:07:52: 7000000 INFO @ Sun, 21 Jun 2020 22:07:56: 3000000 INFO @ Sun, 21 Jun 2020 22:07:59: 8000000 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 22:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.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 22:08:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:04: 4000000 INFO @ Sun, 21 Jun 2020 22:08:07: 9000000 INFO @ Sun, 21 Jun 2020 22:08:11: 1000000 INFO @ Sun, 21 Jun 2020 22:08:11: 5000000 INFO @ Sun, 21 Jun 2020 22:08:15: 10000000 INFO @ Sun, 21 Jun 2020 22:08:18: 2000000 INFO @ Sun, 21 Jun 2020 22:08:19: 6000000 INFO @ Sun, 21 Jun 2020 22:08:22: 11000000 INFO @ Sun, 21 Jun 2020 22:08:25: 3000000 INFO @ Sun, 21 Jun 2020 22:08:27: 7000000 INFO @ Sun, 21 Jun 2020 22:08:30: 12000000 INFO @ Sun, 21 Jun 2020 22:08:32: 4000000 INFO @ Sun, 21 Jun 2020 22:08:35: 8000000 INFO @ Sun, 21 Jun 2020 22:08:38: 13000000 INFO @ Sun, 21 Jun 2020 22:08:39: 5000000 INFO @ Sun, 21 Jun 2020 22:08:42: 9000000 INFO @ Sun, 21 Jun 2020 22:08:46: 14000000 INFO @ Sun, 21 Jun 2020 22:08:46: 6000000 INFO @ Sun, 21 Jun 2020 22:08:49: 10000000 INFO @ Sun, 21 Jun 2020 22:08:53: 7000000 INFO @ Sun, 21 Jun 2020 22:08:53: 15000000 INFO @ Sun, 21 Jun 2020 22:08:57: 11000000 INFO @ Sun, 21 Jun 2020 22:08:59: 8000000 INFO @ Sun, 21 Jun 2020 22:09:00: 16000000 INFO @ Sun, 21 Jun 2020 22:09:04: 12000000 INFO @ Sun, 21 Jun 2020 22:09:06: 9000000 INFO @ Sun, 21 Jun 2020 22:09:08: 17000000 INFO @ Sun, 21 Jun 2020 22:09:12: 13000000 INFO @ Sun, 21 Jun 2020 22:09:13: 10000000 INFO @ Sun, 21 Jun 2020 22:09:15: 18000000 INFO @ Sun, 21 Jun 2020 22:09:19: 14000000 INFO @ Sun, 21 Jun 2020 22:09:20: 11000000 INFO @ Sun, 21 Jun 2020 22:09:22: 19000000 INFO @ Sun, 21 Jun 2020 22:09:26: 15000000 INFO @ Sun, 21 Jun 2020 22:09:27: 12000000 INFO @ Sun, 21 Jun 2020 22:09:30: 20000000 INFO @ Sun, 21 Jun 2020 22:09:34: 16000000 INFO @ Sun, 21 Jun 2020 22:09:34: 13000000 INFO @ Sun, 21 Jun 2020 22:09:37: 21000000 INFO @ Sun, 21 Jun 2020 22:09:40: 14000000 INFO @ Sun, 21 Jun 2020 22:09:41: 17000000 INFO @ Sun, 21 Jun 2020 22:09:44: 22000000 INFO @ Sun, 21 Jun 2020 22:09:47: 15000000 INFO @ Sun, 21 Jun 2020 22:09:48: 18000000 INFO @ Sun, 21 Jun 2020 22:09:52: 23000000 INFO @ Sun, 21 Jun 2020 22:09:54: 16000000 INFO @ Sun, 21 Jun 2020 22:09:55: 19000000 INFO @ Sun, 21 Jun 2020 22:09:59: 24000000 INFO @ Sun, 21 Jun 2020 22:10:01: 17000000 INFO @ Sun, 21 Jun 2020 22:10:03: 20000000 INFO @ Sun, 21 Jun 2020 22:10:06: 25000000 INFO @ Sun, 21 Jun 2020 22:10:07: 18000000 INFO @ Sun, 21 Jun 2020 22:10:10: 21000000 INFO @ Sun, 21 Jun 2020 22:10:14: 26000000 INFO @ Sun, 21 Jun 2020 22:10:14: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:17: 22000000 INFO @ Sun, 21 Jun 2020 22:10:21: 20000000 INFO @ Sun, 21 Jun 2020 22:10:21: 27000000 INFO @ Sun, 21 Jun 2020 22:10:25: 23000000 INFO @ Sun, 21 Jun 2020 22:10:28: 21000000 INFO @ Sun, 21 Jun 2020 22:10:29: 28000000 INFO @ Sun, 21 Jun 2020 22:10:32: 24000000 INFO @ Sun, 21 Jun 2020 22:10:35: 22000000 INFO @ Sun, 21 Jun 2020 22:10:37: 29000000 INFO @ Sun, 21 Jun 2020 22:10:39: 25000000 INFO @ Sun, 21 Jun 2020 22:10:41: 23000000 INFO @ Sun, 21 Jun 2020 22:10:44: 30000000 INFO @ Sun, 21 Jun 2020 22:10:47: 26000000 INFO @ Sun, 21 Jun 2020 22:10:48: 24000000 INFO @ Sun, 21 Jun 2020 22:10:52: 31000000 INFO @ Sun, 21 Jun 2020 22:10:54: 27000000 INFO @ Sun, 21 Jun 2020 22:10:55: 25000000 INFO @ Sun, 21 Jun 2020 22:11:00: 32000000 INFO @ Sun, 21 Jun 2020 22:11:02: 26000000 INFO @ Sun, 21 Jun 2020 22:11:02: 28000000 INFO @ Sun, 21 Jun 2020 22:11:07: 33000000 INFO @ Sun, 21 Jun 2020 22:11:08: 27000000 INFO @ Sun, 21 Jun 2020 22:11:09: 29000000 INFO @ Sun, 21 Jun 2020 22:11:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:09: #1 total tags in treatment: 33260870 INFO @ Sun, 21 Jun 2020 22:11:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:09: #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 22:11:10: #1 tags after filtering in treatment: 33260825 INFO @ Sun, 21 Jun 2020 22:11:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:10: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:12: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:11:12: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:12: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:11:12: #2 alternative fragment length(s) may be 1,13 bps INFO @ Sun, 21 Jun 2020 22:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05_model.r WARNING @ Sun, 21 Jun 2020 22:11:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:12: #2 You may need to consider one of the other alternative d(s): 1,13 WARNING @ Sun, 21 Jun 2020 22:11:12: #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 22:11:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:16: 28000000 INFO @ Sun, 21 Jun 2020 22:11:16: 30000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:11:22: 29000000 INFO @ Sun, 21 Jun 2020 22:11:24: 31000000 INFO @ Sun, 21 Jun 2020 22:11:29: 30000000 INFO @ Sun, 21 Jun 2020 22:11:31: 32000000 INFO @ Sun, 21 Jun 2020 22:11:36: 31000000 INFO @ Sun, 21 Jun 2020 22:11:38: 33000000 INFO @ Sun, 21 Jun 2020 22:11:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:40: #1 total tags in treatment: 33260870 INFO @ Sun, 21 Jun 2020 22:11:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:40: #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 22:11:41: #1 tags after filtering in treatment: 33260825 INFO @ Sun, 21 Jun 2020 22:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:42: 32000000 INFO @ Sun, 21 Jun 2020 22:11:43: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:11:43: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:43: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:44: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:11:44: #2 alternative fragment length(s) may be 1,13 bps INFO @ Sun, 21 Jun 2020 22:11:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10_model.r WARNING @ Sun, 21 Jun 2020 22:11:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:44: #2 You may need to consider one of the other alternative d(s): 1,13 WARNING @ Sun, 21 Jun 2020 22:11:44: #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 22:11:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:48: 33000000 INFO @ Sun, 21 Jun 2020 22:11:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:50: #1 total tags in treatment: 33260870 INFO @ Sun, 21 Jun 2020 22:11:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:50: #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 22:11:51: #1 tags after filtering in treatment: 33260825 INFO @ Sun, 21 Jun 2020 22:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:53: #2 number of paired peaks: 576 WARNING @ Sun, 21 Jun 2020 22:11:53: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:11:53: #2 alternative fragment length(s) may be 1,13 bps INFO @ Sun, 21 Jun 2020 22:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20_model.r WARNING @ Sun, 21 Jun 2020 22:11:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:53: #2 You may need to consider one of the other alternative d(s): 1,13 WARNING @ Sun, 21 Jun 2020 22:11:53: #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 22:11:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:12:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.05_summits.bed INFO @ Sun, 21 Jun 2020 22:12:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:12:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.10_summits.bed INFO @ Sun, 21 Jun 2020 22:12:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436054/SRX5436054.20_summits.bed INFO @ Sun, 21 Jun 2020 22:13:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling