Job ID = 6509147 SRX = SRX685468 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:11:13 prefetch.2.10.7: 1) Downloading 'SRR1556390'... 2020-06-26T15:11:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:16:08 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:16:08 prefetch.2.10.7: 1) 'SRR1556390' was downloaded successfully Read 53620336 spots for SRR1556390/SRR1556390.sra Written 53620336 spots for SRR1556390/SRR1556390.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: 00:15:13 53620336 reads; of these: 53620336 (100.00%) were unpaired; of these: 1727360 (3.22%) aligned 0 times 35434867 (66.08%) aligned exactly 1 time 16458109 (30.69%) aligned >1 times 96.78% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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 24 files... [bam_rmdupse_core] 11918883 / 51892976 = 0.2297 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 @ Sat, 27 Jun 2020 00:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.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 @ Sat, 27 Jun 2020 00:44:34: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:44:34: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:44:40: 1000000 INFO @ Sat, 27 Jun 2020 00:44:47: 2000000 INFO @ Sat, 27 Jun 2020 00:44:53: 3000000 INFO @ Sat, 27 Jun 2020 00:44:59: 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 @ Sat, 27 Jun 2020 00:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.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 @ Sat, 27 Jun 2020 00:45:04: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:45:04: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:45:04: 5000000 INFO @ Sat, 27 Jun 2020 00:45:09: 1000000 INFO @ Sat, 27 Jun 2020 00:45:11: 6000000 INFO @ Sat, 27 Jun 2020 00:45:15: 2000000 INFO @ Sat, 27 Jun 2020 00:45:17: 7000000 INFO @ Sat, 27 Jun 2020 00:45:20: 3000000 INFO @ Sat, 27 Jun 2020 00:45:23: 8000000 INFO @ Sat, 27 Jun 2020 00:45:26: 4000000 INFO @ Sat, 27 Jun 2020 00:45:29: 9000000 INFO @ Sat, 27 Jun 2020 00:45:31: 5000000 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 @ Sat, 27 Jun 2020 00:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.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 @ Sat, 27 Jun 2020 00:45:34: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:45:34: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:45:35: 10000000 INFO @ Sat, 27 Jun 2020 00:45:37: 6000000 INFO @ Sat, 27 Jun 2020 00:45:40: 1000000 INFO @ Sat, 27 Jun 2020 00:45:41: 11000000 INFO @ Sat, 27 Jun 2020 00:45:42: 7000000 INFO @ Sat, 27 Jun 2020 00:45:46: 2000000 INFO @ Sat, 27 Jun 2020 00:45:47: 12000000 INFO @ Sat, 27 Jun 2020 00:45:48: 8000000 INFO @ Sat, 27 Jun 2020 00:45:53: 3000000 INFO @ Sat, 27 Jun 2020 00:45:53: 13000000 INFO @ Sat, 27 Jun 2020 00:45:53: 9000000 INFO @ Sat, 27 Jun 2020 00:45:59: 4000000 INFO @ Sat, 27 Jun 2020 00:45:59: 10000000 INFO @ Sat, 27 Jun 2020 00:45:59: 14000000 INFO @ Sat, 27 Jun 2020 00:46:04: 11000000 INFO @ Sat, 27 Jun 2020 00:46:05: 5000000 INFO @ Sat, 27 Jun 2020 00:46:05: 15000000 INFO @ Sat, 27 Jun 2020 00:46:10: 12000000 INFO @ Sat, 27 Jun 2020 00:46:10: 6000000 INFO @ Sat, 27 Jun 2020 00:46:12: 16000000 INFO @ Sat, 27 Jun 2020 00:46:15: 13000000 INFO @ Sat, 27 Jun 2020 00:46:16: 7000000 INFO @ Sat, 27 Jun 2020 00:46:18: 17000000 INFO @ Sat, 27 Jun 2020 00:46:21: 14000000 INFO @ Sat, 27 Jun 2020 00:46:22: 8000000 INFO @ Sat, 27 Jun 2020 00:46:24: 18000000 INFO @ Sat, 27 Jun 2020 00:46:26: 15000000 INFO @ Sat, 27 Jun 2020 00:46:28: 9000000 INFO @ Sat, 27 Jun 2020 00:46:30: 19000000 INFO @ Sat, 27 Jun 2020 00:46:32: 16000000 INFO @ Sat, 27 Jun 2020 00:46:34: 10000000 INFO @ Sat, 27 Jun 2020 00:46:36: 20000000 INFO @ Sat, 27 Jun 2020 00:46:37: 17000000 INFO @ Sat, 27 Jun 2020 00:46:40: 11000000 INFO @ Sat, 27 Jun 2020 00:46:42: 21000000 INFO @ Sat, 27 Jun 2020 00:46:43: 18000000 INFO @ Sat, 27 Jun 2020 00:46:46: 12000000 INFO @ Sat, 27 Jun 2020 00:46:49: 19000000 INFO @ Sat, 27 Jun 2020 00:46:49: 22000000 INFO @ Sat, 27 Jun 2020 00:46:51: 13000000 INFO @ Sat, 27 Jun 2020 00:46:54: 20000000 INFO @ Sat, 27 Jun 2020 00:46:55: 23000000 INFO @ Sat, 27 Jun 2020 00:46:58: 14000000 INFO @ Sat, 27 Jun 2020 00:46:59: 21000000 INFO @ Sat, 27 Jun 2020 00:47:01: 24000000 INFO @ Sat, 27 Jun 2020 00:47:04: 15000000 INFO @ Sat, 27 Jun 2020 00:47:05: 22000000 INFO @ Sat, 27 Jun 2020 00:47:07: 25000000 INFO @ Sat, 27 Jun 2020 00:47:10: 16000000 INFO @ Sat, 27 Jun 2020 00:47:10: 23000000 INFO @ Sat, 27 Jun 2020 00:47:13: 26000000 INFO @ Sat, 27 Jun 2020 00:47:16: 24000000 INFO @ Sat, 27 Jun 2020 00:47:16: 17000000 INFO @ Sat, 27 Jun 2020 00:47:19: 27000000 INFO @ Sat, 27 Jun 2020 00:47:21: 25000000 INFO @ Sat, 27 Jun 2020 00:47:22: 18000000 INFO @ Sat, 27 Jun 2020 00:47:25: 28000000 INFO @ Sat, 27 Jun 2020 00:47:26: 26000000 INFO @ Sat, 27 Jun 2020 00:47:28: 19000000 INFO @ Sat, 27 Jun 2020 00:47:31: 29000000 INFO @ Sat, 27 Jun 2020 00:47:32: 27000000 INFO @ Sat, 27 Jun 2020 00:47:34: 20000000 INFO @ Sat, 27 Jun 2020 00:47:37: 30000000 INFO @ Sat, 27 Jun 2020 00:47:37: 28000000 INFO @ Sat, 27 Jun 2020 00:47:40: 21000000 INFO @ Sat, 27 Jun 2020 00:47:42: 29000000 INFO @ Sat, 27 Jun 2020 00:47:43: 31000000 INFO @ Sat, 27 Jun 2020 00:47:46: 22000000 INFO @ Sat, 27 Jun 2020 00:47:48: 30000000 INFO @ Sat, 27 Jun 2020 00:47:49: 32000000 INFO @ Sat, 27 Jun 2020 00:47:52: 23000000 INFO @ Sat, 27 Jun 2020 00:47:53: 31000000 INFO @ Sat, 27 Jun 2020 00:47:54: 33000000 INFO @ Sat, 27 Jun 2020 00:47:58: 32000000 INFO @ Sat, 27 Jun 2020 00:47:58: 24000000 INFO @ Sat, 27 Jun 2020 00:48:01: 34000000 INFO @ Sat, 27 Jun 2020 00:48:04: 33000000 INFO @ Sat, 27 Jun 2020 00:48:05: 25000000 INFO @ Sat, 27 Jun 2020 00:48:07: 35000000 INFO @ Sat, 27 Jun 2020 00:48:09: 34000000 INFO @ Sat, 27 Jun 2020 00:48:10: 26000000 INFO @ Sat, 27 Jun 2020 00:48:13: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:48:15: 35000000 INFO @ Sat, 27 Jun 2020 00:48:16: 27000000 INFO @ Sat, 27 Jun 2020 00:48:19: 37000000 INFO @ Sat, 27 Jun 2020 00:48:20: 36000000 INFO @ Sat, 27 Jun 2020 00:48:22: 28000000 INFO @ Sat, 27 Jun 2020 00:48:25: 38000000 INFO @ Sat, 27 Jun 2020 00:48:26: 37000000 INFO @ Sat, 27 Jun 2020 00:48:28: 29000000 INFO @ Sat, 27 Jun 2020 00:48:31: 39000000 INFO @ Sat, 27 Jun 2020 00:48:31: 38000000 INFO @ Sat, 27 Jun 2020 00:48:34: 30000000 INFO @ Sat, 27 Jun 2020 00:48:36: 39000000 INFO @ Sat, 27 Jun 2020 00:48:37: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:48:37: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:48:37: #1 total tags in treatment: 39974093 INFO @ Sat, 27 Jun 2020 00:48:37: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:48:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:48:38: #1 tags after filtering in treatment: 39974051 INFO @ Sat, 27 Jun 2020 00:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:48:38: #1 finished! INFO @ Sat, 27 Jun 2020 00:48:38: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:48:40: 31000000 INFO @ Sat, 27 Jun 2020 00:48:40: #2 number of paired peaks: 119 WARNING @ Sat, 27 Jun 2020 00:48:40: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 27 Jun 2020 00:48:40: start model_add_line... INFO @ Sat, 27 Jun 2020 00:48:40: start X-correlation... INFO @ Sat, 27 Jun 2020 00:48:40: end of X-cor INFO @ Sat, 27 Jun 2020 00:48:40: #2 finished! INFO @ Sat, 27 Jun 2020 00:48:40: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:48:40: #2 alternative fragment length(s) may be 1,33,560,585 bps INFO @ Sat, 27 Jun 2020 00:48:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05_model.r WARNING @ Sat, 27 Jun 2020 00:48:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:48:40: #2 You may need to consider one of the other alternative d(s): 1,33,560,585 WARNING @ Sat, 27 Jun 2020 00:48:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:48:40: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:48:42: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:48:42: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:48:42: #1 total tags in treatment: 39974093 INFO @ Sat, 27 Jun 2020 00:48:42: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:48:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:48:43: #1 tags after filtering in treatment: 39974051 INFO @ Sat, 27 Jun 2020 00:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:48:43: #1 finished! INFO @ Sat, 27 Jun 2020 00:48:43: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:48:45: 32000000 INFO @ Sat, 27 Jun 2020 00:48:46: #2 number of paired peaks: 119 WARNING @ Sat, 27 Jun 2020 00:48:46: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 27 Jun 2020 00:48:46: start model_add_line... INFO @ Sat, 27 Jun 2020 00:48:46: start X-correlation... INFO @ Sat, 27 Jun 2020 00:48:46: end of X-cor INFO @ Sat, 27 Jun 2020 00:48:46: #2 finished! INFO @ Sat, 27 Jun 2020 00:48:46: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:48:46: #2 alternative fragment length(s) may be 1,33,560,585 bps INFO @ Sat, 27 Jun 2020 00:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10_model.r WARNING @ Sat, 27 Jun 2020 00:48:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:48:46: #2 You may need to consider one of the other alternative d(s): 1,33,560,585 WARNING @ Sat, 27 Jun 2020 00:48:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:48:46: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:48:51: 33000000 INFO @ Sat, 27 Jun 2020 00:48:57: 34000000 INFO @ Sat, 27 Jun 2020 00:49:03: 35000000 INFO @ Sat, 27 Jun 2020 00:49:09: 36000000 INFO @ Sat, 27 Jun 2020 00:49:15: 37000000 INFO @ Sat, 27 Jun 2020 00:49:20: 38000000 INFO @ Sat, 27 Jun 2020 00:49:26: 39000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:49:32: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:49:32: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:49:32: #1 total tags in treatment: 39974093 INFO @ Sat, 27 Jun 2020 00:49:32: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:49:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:49:33: #1 tags after filtering in treatment: 39974051 INFO @ Sat, 27 Jun 2020 00:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:49:33: #1 finished! INFO @ Sat, 27 Jun 2020 00:49:33: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:49:35: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:49:36: #2 number of paired peaks: 119 WARNING @ Sat, 27 Jun 2020 00:49:36: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 27 Jun 2020 00:49:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:49:36: start X-correlation... INFO @ Sat, 27 Jun 2020 00:49:36: end of X-cor INFO @ Sat, 27 Jun 2020 00:49:36: #2 finished! INFO @ Sat, 27 Jun 2020 00:49:36: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:49:36: #2 alternative fragment length(s) may be 1,33,560,585 bps INFO @ Sat, 27 Jun 2020 00:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20_model.r WARNING @ Sat, 27 Jun 2020 00:49:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:49:36: #2 You may need to consider one of the other alternative d(s): 1,33,560,585 WARNING @ Sat, 27 Jun 2020 00:49:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:49:36: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:49:41: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:49:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:49:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:49:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.05_summits.bed INFO @ Sat, 27 Jun 2020 00:49:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.10_summits.bed INFO @ Sat, 27 Jun 2020 00:50:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:50:28: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX685468/SRX685468.20_summits.bed INFO @ Sat, 27 Jun 2020 00:50:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling