Job ID = 6453909 SRX = SRX159168 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:02 prefetch.2.10.7: 1) Downloading 'SRR520449'... 2020-06-21T08:45:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:06 prefetch.2.10.7: 1) 'SRR520449' was downloaded successfully Read 64882446 spots for SRR520449/SRR520449.sra Written 64882446 spots for SRR520449/SRR520449.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: 00:17:59 64882446 reads; of these: 64882446 (100.00%) were unpaired; of these: 6487943 (10.00%) aligned 0 times 40678996 (62.70%) aligned exactly 1 time 17715507 (27.30%) aligned >1 times 90.00% overall alignment rate Time searching: 00:17:59 Overall time: 00:17:59 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] 18655075 / 58394503 = 0.3195 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 18:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.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 18:23:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:39: 1000000 INFO @ Sun, 21 Jun 2020 18:23:46: 2000000 INFO @ Sun, 21 Jun 2020 18:23:53: 3000000 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 18:24:00: 4000000 INFO @ Sun, 21 Jun 2020 18:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.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 18:24:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:08: 5000000 INFO @ Sun, 21 Jun 2020 18:24:11: 1000000 INFO @ Sun, 21 Jun 2020 18:24:16: 6000000 INFO @ Sun, 21 Jun 2020 18:24:19: 2000000 INFO @ Sun, 21 Jun 2020 18:24:24: 7000000 INFO @ Sun, 21 Jun 2020 18:24:27: 3000000 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 18:24:32: 8000000 INFO @ Sun, 21 Jun 2020 18:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.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 18:24:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:35: 4000000 INFO @ Sun, 21 Jun 2020 18:24:40: 9000000 INFO @ Sun, 21 Jun 2020 18:24:40: 1000000 INFO @ Sun, 21 Jun 2020 18:24:43: 5000000 INFO @ Sun, 21 Jun 2020 18:24:48: 10000000 INFO @ Sun, 21 Jun 2020 18:24:48: 2000000 INFO @ Sun, 21 Jun 2020 18:24:51: 6000000 INFO @ Sun, 21 Jun 2020 18:24:56: 11000000 INFO @ Sun, 21 Jun 2020 18:24:56: 3000000 INFO @ Sun, 21 Jun 2020 18:24:59: 7000000 INFO @ Sun, 21 Jun 2020 18:25:03: 12000000 INFO @ Sun, 21 Jun 2020 18:25:04: 4000000 INFO @ Sun, 21 Jun 2020 18:25:07: 8000000 INFO @ Sun, 21 Jun 2020 18:25:11: 13000000 INFO @ Sun, 21 Jun 2020 18:25:12: 5000000 INFO @ Sun, 21 Jun 2020 18:25:16: 9000000 INFO @ Sun, 21 Jun 2020 18:25:19: 14000000 INFO @ Sun, 21 Jun 2020 18:25:20: 6000000 INFO @ Sun, 21 Jun 2020 18:25:23: 10000000 INFO @ Sun, 21 Jun 2020 18:25:27: 15000000 INFO @ Sun, 21 Jun 2020 18:25:28: 7000000 INFO @ Sun, 21 Jun 2020 18:25:31: 11000000 INFO @ Sun, 21 Jun 2020 18:25:35: 16000000 INFO @ Sun, 21 Jun 2020 18:25:36: 8000000 INFO @ Sun, 21 Jun 2020 18:25:39: 12000000 INFO @ Sun, 21 Jun 2020 18:25:42: 17000000 INFO @ Sun, 21 Jun 2020 18:25:44: 9000000 INFO @ Sun, 21 Jun 2020 18:25:47: 13000000 INFO @ Sun, 21 Jun 2020 18:25:50: 18000000 INFO @ Sun, 21 Jun 2020 18:25:52: 10000000 INFO @ Sun, 21 Jun 2020 18:25:55: 14000000 INFO @ Sun, 21 Jun 2020 18:25:58: 19000000 INFO @ Sun, 21 Jun 2020 18:26:00: 11000000 INFO @ Sun, 21 Jun 2020 18:26:03: 15000000 INFO @ Sun, 21 Jun 2020 18:26:05: 20000000 INFO @ Sun, 21 Jun 2020 18:26:07: 12000000 INFO @ Sun, 21 Jun 2020 18:26:10: 16000000 INFO @ Sun, 21 Jun 2020 18:26:13: 21000000 INFO @ Sun, 21 Jun 2020 18:26:15: 13000000 INFO @ Sun, 21 Jun 2020 18:26:18: 17000000 INFO @ Sun, 21 Jun 2020 18:26:21: 22000000 INFO @ Sun, 21 Jun 2020 18:26:23: 14000000 INFO @ Sun, 21 Jun 2020 18:26:26: 18000000 INFO @ Sun, 21 Jun 2020 18:26:29: 23000000 INFO @ Sun, 21 Jun 2020 18:26:31: 15000000 INFO @ Sun, 21 Jun 2020 18:26:34: 19000000 INFO @ Sun, 21 Jun 2020 18:26:37: 24000000 INFO @ Sun, 21 Jun 2020 18:26:39: 16000000 INFO @ Sun, 21 Jun 2020 18:26:42: 20000000 INFO @ Sun, 21 Jun 2020 18:26:45: 25000000 INFO @ Sun, 21 Jun 2020 18:26:47: 17000000 INFO @ Sun, 21 Jun 2020 18:26:50: 21000000 INFO @ Sun, 21 Jun 2020 18:26:53: 26000000 INFO @ Sun, 21 Jun 2020 18:26:54: 18000000 INFO @ Sun, 21 Jun 2020 18:26:58: 22000000 INFO @ Sun, 21 Jun 2020 18:27:01: 27000000 INFO @ Sun, 21 Jun 2020 18:27:02: 19000000 INFO @ Sun, 21 Jun 2020 18:27:06: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:10: 28000000 INFO @ Sun, 21 Jun 2020 18:27:10: 20000000 INFO @ Sun, 21 Jun 2020 18:27:14: 24000000 INFO @ Sun, 21 Jun 2020 18:27:18: 29000000 INFO @ Sun, 21 Jun 2020 18:27:19: 21000000 INFO @ Sun, 21 Jun 2020 18:27:22: 25000000 INFO @ Sun, 21 Jun 2020 18:27:26: 30000000 INFO @ Sun, 21 Jun 2020 18:27:27: 22000000 INFO @ Sun, 21 Jun 2020 18:27:31: 26000000 INFO @ Sun, 21 Jun 2020 18:27:34: 31000000 INFO @ Sun, 21 Jun 2020 18:27:35: 23000000 INFO @ Sun, 21 Jun 2020 18:27:38: 27000000 INFO @ Sun, 21 Jun 2020 18:27:42: 32000000 INFO @ Sun, 21 Jun 2020 18:27:43: 24000000 INFO @ Sun, 21 Jun 2020 18:27:47: 28000000 INFO @ Sun, 21 Jun 2020 18:27:50: 33000000 INFO @ Sun, 21 Jun 2020 18:27:51: 25000000 INFO @ Sun, 21 Jun 2020 18:27:55: 29000000 INFO @ Sun, 21 Jun 2020 18:27:59: 34000000 INFO @ Sun, 21 Jun 2020 18:28:00: 26000000 INFO @ Sun, 21 Jun 2020 18:28:03: 30000000 INFO @ Sun, 21 Jun 2020 18:28:07: 35000000 INFO @ Sun, 21 Jun 2020 18:28:08: 27000000 INFO @ Sun, 21 Jun 2020 18:28:11: 31000000 INFO @ Sun, 21 Jun 2020 18:28:15: 36000000 INFO @ Sun, 21 Jun 2020 18:28:16: 28000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:19: 32000000 INFO @ Sun, 21 Jun 2020 18:28:23: 37000000 INFO @ Sun, 21 Jun 2020 18:28:24: 29000000 INFO @ Sun, 21 Jun 2020 18:28:27: 33000000 INFO @ Sun, 21 Jun 2020 18:28:31: 38000000 INFO @ Sun, 21 Jun 2020 18:28:32: 30000000 INFO @ Sun, 21 Jun 2020 18:28:35: 34000000 INFO @ Sun, 21 Jun 2020 18:28:40: 39000000 INFO @ Sun, 21 Jun 2020 18:28:40: 31000000 INFO @ Sun, 21 Jun 2020 18:28:43: 35000000 INFO @ Sun, 21 Jun 2020 18:28:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:28:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:28:45: #1 total tags in treatment: 39739428 INFO @ Sun, 21 Jun 2020 18:28:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:45: #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 18:28:46: #1 tags after filtering in treatment: 39739389 INFO @ Sun, 21 Jun 2020 18:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:48: 32000000 INFO @ Sun, 21 Jun 2020 18:28:49: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 18:28:49: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 18:28:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:49: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:28:49: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05_model.r WARNING @ Sun, 21 Jun 2020 18:28:49: #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 18:28:49: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:28:49: #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 18:28:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:51: 36000000 INFO @ Sun, 21 Jun 2020 18:28:55: 33000000 INFO @ Sun, 21 Jun 2020 18:28:59: 37000000 INFO @ Sun, 21 Jun 2020 18:29:03: 34000000 INFO @ Sun, 21 Jun 2020 18:29:07: 38000000 INFO @ Sun, 21 Jun 2020 18:29:11: 35000000 INFO @ Sun, 21 Jun 2020 18:29:15: 39000000 INFO @ Sun, 21 Jun 2020 18:29:19: 36000000 INFO @ Sun, 21 Jun 2020 18:29:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:29:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:29:21: #1 total tags in treatment: 39739428 INFO @ Sun, 21 Jun 2020 18:29:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:21: #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 18:29:22: #1 tags after filtering in treatment: 39739389 INFO @ Sun, 21 Jun 2020 18:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:24: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 18:29:24: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:24: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:29:24: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10_model.r WARNING @ Sun, 21 Jun 2020 18:29:24: #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 18:29:24: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:29:24: #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 18:29:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:26: 37000000 INFO @ Sun, 21 Jun 2020 18:29:34: 38000000 INFO @ Sun, 21 Jun 2020 18:29:41: 39000000 INFO @ Sun, 21 Jun 2020 18:29:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:29:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:29:46: #1 total tags in treatment: 39739428 INFO @ Sun, 21 Jun 2020 18:29:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:46: #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 18:29:47: #1 tags after filtering in treatment: 39739389 INFO @ Sun, 21 Jun 2020 18:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:50: #2 number of paired peaks: 180 WARNING @ Sun, 21 Jun 2020 18:29:50: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:50: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:29:50: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 18:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20_model.r WARNING @ Sun, 21 Jun 2020 18:29:50: #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 18:29:50: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 18:29:50: #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 18:29:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.05_summits.bed INFO @ Sun, 21 Jun 2020 18:30:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:30:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.10_summits.bed INFO @ Sun, 21 Jun 2020 18:30:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:30:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX159168/SRX159168.20_summits.bed INFO @ Sun, 21 Jun 2020 18:31:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling