Job ID = 6527934 SRX = SRX330270 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:26:51 prefetch.2.10.7: 1) Downloading 'SRR946216'... 2020-06-29T14:26:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:33:21 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:33:21 prefetch.2.10.7: 1) 'SRR946216' was downloaded successfully Read 33825198 spots for SRR946216/SRR946216.sra Written 33825198 spots for SRR946216/SRR946216.sra 2020-06-29T14:35:17 prefetch.2.10.7: 1) Downloading 'SRR946217'... 2020-06-29T14:35:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:43:09 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:43:09 prefetch.2.10.7: 1) 'SRR946217' was downloaded successfully Read 43780666 spots for SRR946217/SRR946217.sra Written 43780666 spots for SRR946217/SRR946217.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: 00:28:11 77605864 reads; of these: 77605864 (100.00%) were unpaired; of these: 4906805 (6.32%) aligned 0 times 47306554 (60.96%) aligned exactly 1 time 25392505 (32.72%) aligned >1 times 93.68% overall alignment rate Time searching: 00:28:11 Overall time: 00:28:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 36693101 / 72699059 = 0.5047 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 @ Tue, 30 Jun 2020 00:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.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 @ Tue, 30 Jun 2020 00:47:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:47:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:47:14: 1000000 INFO @ Tue, 30 Jun 2020 00:47:20: 2000000 INFO @ Tue, 30 Jun 2020 00:47:25: 3000000 INFO @ Tue, 30 Jun 2020 00:47:31: 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 @ Tue, 30 Jun 2020 00:47:37: 5000000 INFO @ Tue, 30 Jun 2020 00:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.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 @ Tue, 30 Jun 2020 00:47:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:47:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:47:44: 6000000 INFO @ Tue, 30 Jun 2020 00:47:45: 1000000 INFO @ Tue, 30 Jun 2020 00:47:51: 7000000 INFO @ Tue, 30 Jun 2020 00:47:52: 2000000 INFO @ Tue, 30 Jun 2020 00:47:57: 8000000 INFO @ Tue, 30 Jun 2020 00:47:59: 3000000 INFO @ Tue, 30 Jun 2020 00:48:04: 9000000 INFO @ Tue, 30 Jun 2020 00:48:05: 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 @ Tue, 30 Jun 2020 00:48:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.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 @ Tue, 30 Jun 2020 00:48:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:48:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:48:11: 10000000 INFO @ Tue, 30 Jun 2020 00:48:12: 5000000 INFO @ Tue, 30 Jun 2020 00:48:15: 1000000 INFO @ Tue, 30 Jun 2020 00:48:18: 11000000 INFO @ Tue, 30 Jun 2020 00:48:19: 6000000 INFO @ Tue, 30 Jun 2020 00:48:22: 2000000 INFO @ Tue, 30 Jun 2020 00:48:25: 12000000 INFO @ Tue, 30 Jun 2020 00:48:26: 7000000 INFO @ Tue, 30 Jun 2020 00:48:29: 3000000 INFO @ Tue, 30 Jun 2020 00:48:32: 13000000 INFO @ Tue, 30 Jun 2020 00:48:33: 8000000 INFO @ Tue, 30 Jun 2020 00:48:36: 4000000 INFO @ Tue, 30 Jun 2020 00:48:38: 14000000 INFO @ Tue, 30 Jun 2020 00:48:40: 9000000 INFO @ Tue, 30 Jun 2020 00:48:42: 5000000 INFO @ Tue, 30 Jun 2020 00:48:45: 15000000 INFO @ Tue, 30 Jun 2020 00:48:47: 10000000 INFO @ Tue, 30 Jun 2020 00:48:49: 6000000 INFO @ Tue, 30 Jun 2020 00:48:52: 16000000 INFO @ Tue, 30 Jun 2020 00:48:54: 11000000 INFO @ Tue, 30 Jun 2020 00:48:56: 7000000 INFO @ Tue, 30 Jun 2020 00:48:59: 17000000 INFO @ Tue, 30 Jun 2020 00:49:01: 12000000 INFO @ Tue, 30 Jun 2020 00:49:03: 8000000 INFO @ Tue, 30 Jun 2020 00:49:06: 18000000 INFO @ Tue, 30 Jun 2020 00:49:07: 13000000 INFO @ Tue, 30 Jun 2020 00:49:10: 9000000 INFO @ Tue, 30 Jun 2020 00:49:12: 19000000 INFO @ Tue, 30 Jun 2020 00:49:14: 14000000 INFO @ Tue, 30 Jun 2020 00:49:17: 10000000 INFO @ Tue, 30 Jun 2020 00:49:19: 20000000 INFO @ Tue, 30 Jun 2020 00:49:21: 15000000 INFO @ Tue, 30 Jun 2020 00:49:24: 11000000 INFO @ Tue, 30 Jun 2020 00:49:26: 21000000 INFO @ Tue, 30 Jun 2020 00:49:28: 16000000 INFO @ Tue, 30 Jun 2020 00:49:31: 12000000 INFO @ Tue, 30 Jun 2020 00:49:33: 22000000 INFO @ Tue, 30 Jun 2020 00:49:35: 17000000 INFO @ Tue, 30 Jun 2020 00:49:38: 13000000 INFO @ Tue, 30 Jun 2020 00:49:40: 23000000 INFO @ Tue, 30 Jun 2020 00:49:41: 18000000 INFO @ Tue, 30 Jun 2020 00:49:44: 14000000 INFO @ Tue, 30 Jun 2020 00:49:47: 24000000 INFO @ Tue, 30 Jun 2020 00:49:48: 19000000 INFO @ Tue, 30 Jun 2020 00:49:51: 15000000 INFO @ Tue, 30 Jun 2020 00:49:54: 25000000 INFO @ Tue, 30 Jun 2020 00:49:55: 20000000 INFO @ Tue, 30 Jun 2020 00:49:58: 16000000 INFO @ Tue, 30 Jun 2020 00:50:01: 26000000 INFO @ Tue, 30 Jun 2020 00:50:02: 21000000 INFO @ Tue, 30 Jun 2020 00:50:05: 17000000 INFO @ Tue, 30 Jun 2020 00:50:08: 27000000 INFO @ Tue, 30 Jun 2020 00:50:09: 22000000 INFO @ Tue, 30 Jun 2020 00:50:12: 18000000 INFO @ Tue, 30 Jun 2020 00:50:14: 28000000 INFO @ Tue, 30 Jun 2020 00:50:16: 23000000 INFO @ Tue, 30 Jun 2020 00:50:19: 19000000 INFO @ Tue, 30 Jun 2020 00:50:21: 29000000 INFO @ Tue, 30 Jun 2020 00:50:23: 24000000 INFO @ Tue, 30 Jun 2020 00:50:26: 20000000 INFO @ Tue, 30 Jun 2020 00:50:28: 30000000 INFO @ Tue, 30 Jun 2020 00:50:30: 25000000 INFO @ Tue, 30 Jun 2020 00:50:33: 21000000 INFO @ Tue, 30 Jun 2020 00:50:35: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:50:37: 26000000 INFO @ Tue, 30 Jun 2020 00:50:40: 22000000 INFO @ Tue, 30 Jun 2020 00:50:42: 32000000 INFO @ Tue, 30 Jun 2020 00:50:44: 27000000 INFO @ Tue, 30 Jun 2020 00:50:47: 23000000 INFO @ Tue, 30 Jun 2020 00:50:48: 33000000 INFO @ Tue, 30 Jun 2020 00:50:51: 28000000 INFO @ Tue, 30 Jun 2020 00:50:54: 24000000 INFO @ Tue, 30 Jun 2020 00:50:55: 34000000 INFO @ Tue, 30 Jun 2020 00:50:57: 29000000 INFO @ Tue, 30 Jun 2020 00:51:01: 25000000 INFO @ Tue, 30 Jun 2020 00:51:02: 35000000 INFO @ Tue, 30 Jun 2020 00:51:04: 30000000 INFO @ Tue, 30 Jun 2020 00:51:08: 26000000 INFO @ Tue, 30 Jun 2020 00:51:09: 36000000 INFO @ Tue, 30 Jun 2020 00:51:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:51:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:51:09: #1 total tags in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:51:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:51:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:51:10: #1 tags after filtering in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:51:10: #1 finished! INFO @ Tue, 30 Jun 2020 00:51:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:51:11: 31000000 INFO @ Tue, 30 Jun 2020 00:51:12: #2 number of paired peaks: 237 WARNING @ Tue, 30 Jun 2020 00:51:12: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 30 Jun 2020 00:51:12: start model_add_line... INFO @ Tue, 30 Jun 2020 00:51:12: start X-correlation... INFO @ Tue, 30 Jun 2020 00:51:12: end of X-cor INFO @ Tue, 30 Jun 2020 00:51:12: #2 finished! INFO @ Tue, 30 Jun 2020 00:51:12: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:51:12: #2 alternative fragment length(s) may be 1,15,18,47,588 bps INFO @ Tue, 30 Jun 2020 00:51:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05_model.r WARNING @ Tue, 30 Jun 2020 00:51:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:51:12: #2 You may need to consider one of the other alternative d(s): 1,15,18,47,588 WARNING @ Tue, 30 Jun 2020 00:51:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:51:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:51:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:51:15: 27000000 INFO @ Tue, 30 Jun 2020 00:51:18: 32000000 INFO @ Tue, 30 Jun 2020 00:51:22: 28000000 INFO @ Tue, 30 Jun 2020 00:51:25: 33000000 INFO @ Tue, 30 Jun 2020 00:51:29: 29000000 INFO @ Tue, 30 Jun 2020 00:51:31: 34000000 INFO @ Tue, 30 Jun 2020 00:51:36: 30000000 INFO @ Tue, 30 Jun 2020 00:51:38: 35000000 INFO @ Tue, 30 Jun 2020 00:51:42: 31000000 INFO @ Tue, 30 Jun 2020 00:51:45: 36000000 INFO @ Tue, 30 Jun 2020 00:51:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:51:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:51:45: #1 total tags in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:51:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:51:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:51:46: #1 tags after filtering in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:51:46: #1 finished! INFO @ Tue, 30 Jun 2020 00:51:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:51:48: #2 number of paired peaks: 237 WARNING @ Tue, 30 Jun 2020 00:51:48: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 30 Jun 2020 00:51:48: start model_add_line... INFO @ Tue, 30 Jun 2020 00:51:48: start X-correlation... INFO @ Tue, 30 Jun 2020 00:51:48: end of X-cor INFO @ Tue, 30 Jun 2020 00:51:48: #2 finished! INFO @ Tue, 30 Jun 2020 00:51:48: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:51:48: #2 alternative fragment length(s) may be 1,15,18,47,588 bps INFO @ Tue, 30 Jun 2020 00:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10_model.r WARNING @ Tue, 30 Jun 2020 00:51:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:51:48: #2 You may need to consider one of the other alternative d(s): 1,15,18,47,588 WARNING @ Tue, 30 Jun 2020 00:51:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:51:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:51:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:51:49: 32000000 INFO @ Tue, 30 Jun 2020 00:51:55: 33000000 INFO @ Tue, 30 Jun 2020 00:52:01: 34000000 INFO @ Tue, 30 Jun 2020 00:52:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:52:07: 35000000 INFO @ Tue, 30 Jun 2020 00:52:13: 36000000 INFO @ Tue, 30 Jun 2020 00:52:13: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:52:13: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:52:13: #1 total tags in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:52:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:52:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:52:14: #1 tags after filtering in treatment: 36005958 INFO @ Tue, 30 Jun 2020 00:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:52:14: #1 finished! INFO @ Tue, 30 Jun 2020 00:52:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:52:16: #2 number of paired peaks: 237 WARNING @ Tue, 30 Jun 2020 00:52:16: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 30 Jun 2020 00:52:16: start model_add_line... INFO @ Tue, 30 Jun 2020 00:52:16: start X-correlation... INFO @ Tue, 30 Jun 2020 00:52:16: end of X-cor INFO @ Tue, 30 Jun 2020 00:52:16: #2 finished! INFO @ Tue, 30 Jun 2020 00:52:16: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:52:16: #2 alternative fragment length(s) may be 1,15,18,47,588 bps INFO @ Tue, 30 Jun 2020 00:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20_model.r WARNING @ Tue, 30 Jun 2020 00:52:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:52:16: #2 You may need to consider one of the other alternative d(s): 1,15,18,47,588 WARNING @ Tue, 30 Jun 2020 00:52:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:52:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.05_summits.bed INFO @ Tue, 30 Jun 2020 00:52:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:52:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.10_summits.bed INFO @ Tue, 30 Jun 2020 00:53:05: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:53:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX330270/SRX330270.20_summits.bed INFO @ Tue, 30 Jun 2020 00:53:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling