Job ID = 6458769 SRX = SRX5436043 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:40 prefetch.2.10.7: 1) Downloading 'SRR8637375'... 2020-06-21T12:53:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:16 prefetch.2.10.7: 1) 'SRR8637375' was downloaded successfully Read 31884106 spots for SRR8637375/SRR8637375.sra Written 31884106 spots for SRR8637375/SRR8637375.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: 00:09:05 31884106 reads; of these: 31884106 (100.00%) were unpaired; of these: 1444244 (4.53%) aligned 0 times 20243340 (63.49%) aligned exactly 1 time 10196522 (31.98%) aligned >1 times 95.47% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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 16 files... [bam_rmdupse_core] 5251613 / 30439862 = 0.1725 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 22:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.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 22:14:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:39: 1000000 INFO @ Sun, 21 Jun 2020 22:14:45: 2000000 INFO @ Sun, 21 Jun 2020 22:14:50: 3000000 INFO @ Sun, 21 Jun 2020 22:14:56: 4000000 INFO @ Sun, 21 Jun 2020 22:15:01: 5000000 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 22:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.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 22:15:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:15:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:15:07: 6000000 INFO @ Sun, 21 Jun 2020 22:15:09: 1000000 INFO @ Sun, 21 Jun 2020 22:15:13: 7000000 INFO @ Sun, 21 Jun 2020 22:15:15: 2000000 INFO @ Sun, 21 Jun 2020 22:15:19: 8000000 INFO @ Sun, 21 Jun 2020 22:15:21: 3000000 INFO @ Sun, 21 Jun 2020 22:15:24: 9000000 INFO @ Sun, 21 Jun 2020 22:15:26: 4000000 INFO @ Sun, 21 Jun 2020 22:15:30: 10000000 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 22:15:32: 5000000 INFO @ Sun, 21 Jun 2020 22:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.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 22:15:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:15:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:15:36: 11000000 INFO @ Sun, 21 Jun 2020 22:15:38: 6000000 INFO @ Sun, 21 Jun 2020 22:15:39: 1000000 INFO @ Sun, 21 Jun 2020 22:15:42: 12000000 INFO @ Sun, 21 Jun 2020 22:15:44: 7000000 INFO @ Sun, 21 Jun 2020 22:15:45: 2000000 INFO @ Sun, 21 Jun 2020 22:15:48: 13000000 INFO @ Sun, 21 Jun 2020 22:15:50: 8000000 INFO @ Sun, 21 Jun 2020 22:15:50: 3000000 INFO @ Sun, 21 Jun 2020 22:15:54: 14000000 INFO @ Sun, 21 Jun 2020 22:15:55: 9000000 INFO @ Sun, 21 Jun 2020 22:15:56: 4000000 INFO @ Sun, 21 Jun 2020 22:15:59: 15000000 INFO @ Sun, 21 Jun 2020 22:16:01: 5000000 INFO @ Sun, 21 Jun 2020 22:16:01: 10000000 INFO @ Sun, 21 Jun 2020 22:16:05: 16000000 INFO @ Sun, 21 Jun 2020 22:16:07: 6000000 INFO @ Sun, 21 Jun 2020 22:16:07: 11000000 INFO @ Sun, 21 Jun 2020 22:16:11: 17000000 INFO @ Sun, 21 Jun 2020 22:16:13: 7000000 INFO @ Sun, 21 Jun 2020 22:16:13: 12000000 INFO @ Sun, 21 Jun 2020 22:16:17: 18000000 INFO @ Sun, 21 Jun 2020 22:16:18: 8000000 INFO @ Sun, 21 Jun 2020 22:16:19: 13000000 INFO @ Sun, 21 Jun 2020 22:16:23: 19000000 INFO @ Sun, 21 Jun 2020 22:16:24: 9000000 INFO @ Sun, 21 Jun 2020 22:16:25: 14000000 INFO @ Sun, 21 Jun 2020 22:16:28: 20000000 INFO @ Sun, 21 Jun 2020 22:16:30: 10000000 INFO @ Sun, 21 Jun 2020 22:16:31: 15000000 INFO @ Sun, 21 Jun 2020 22:16:35: 21000000 INFO @ Sun, 21 Jun 2020 22:16:35: 11000000 INFO @ Sun, 21 Jun 2020 22:16:36: 16000000 INFO @ Sun, 21 Jun 2020 22:16:40: 22000000 INFO @ Sun, 21 Jun 2020 22:16:41: 12000000 INFO @ Sun, 21 Jun 2020 22:16:42: 17000000 INFO @ Sun, 21 Jun 2020 22:16:46: 23000000 INFO @ Sun, 21 Jun 2020 22:16:47: 13000000 INFO @ Sun, 21 Jun 2020 22:16:48: 18000000 INFO @ Sun, 21 Jun 2020 22:16:52: 24000000 INFO @ Sun, 21 Jun 2020 22:16:52: 14000000 INFO @ Sun, 21 Jun 2020 22:16:54: 19000000 INFO @ Sun, 21 Jun 2020 22:16:58: 25000000 INFO @ Sun, 21 Jun 2020 22:16:58: 15000000 INFO @ Sun, 21 Jun 2020 22:16:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:16:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:16:59: #1 total tags in treatment: 25188249 INFO @ Sun, 21 Jun 2020 22:16:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:59: #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 22:17:00: 20000000 INFO @ Sun, 21 Jun 2020 22:17:00: #1 tags after filtering in treatment: 25188206 INFO @ Sun, 21 Jun 2020 22:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:02: #2 number of paired peaks: 1135 INFO @ Sun, 21 Jun 2020 22:17:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:02: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:17:02: #2 alternative fragment length(s) may be 2,42,597 bps INFO @ Sun, 21 Jun 2020 22:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05_model.r WARNING @ Sun, 21 Jun 2020 22:17:02: #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 22:17:02: #2 You may need to consider one of the other alternative d(s): 2,42,597 WARNING @ Sun, 21 Jun 2020 22:17:02: #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 22:17:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:04: 16000000 INFO @ Sun, 21 Jun 2020 22:17:06: 21000000 INFO @ Sun, 21 Jun 2020 22:17:10: 17000000 INFO @ Sun, 21 Jun 2020 22:17:12: 22000000 INFO @ Sun, 21 Jun 2020 22:17:15: 18000000 INFO @ Sun, 21 Jun 2020 22:17:17: 23000000 INFO @ Sun, 21 Jun 2020 22:17:21: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:17:23: 24000000 INFO @ Sun, 21 Jun 2020 22:17:27: 20000000 INFO @ Sun, 21 Jun 2020 22:17:29: 25000000 INFO @ Sun, 21 Jun 2020 22:17:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:17:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:17:30: #1 total tags in treatment: 25188249 INFO @ Sun, 21 Jun 2020 22:17:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:30: #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 22:17:31: #1 tags after filtering in treatment: 25188206 INFO @ Sun, 21 Jun 2020 22:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:33: #2 number of paired peaks: 1135 INFO @ Sun, 21 Jun 2020 22:17:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:33: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:17:33: #2 alternative fragment length(s) may be 2,42,597 bps INFO @ Sun, 21 Jun 2020 22:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10_model.r WARNING @ Sun, 21 Jun 2020 22:17:33: #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 22:17:33: #2 You may need to consider one of the other alternative d(s): 2,42,597 WARNING @ Sun, 21 Jun 2020 22:17:33: #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 22:17:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:33: 21000000 INFO @ Sun, 21 Jun 2020 22:17:39: 22000000 INFO @ Sun, 21 Jun 2020 22:17:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:44: 23000000 INFO @ Sun, 21 Jun 2020 22:17:49: 24000000 INFO @ Sun, 21 Jun 2020 22:17:55: 25000000 INFO @ Sun, 21 Jun 2020 22:17:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:17:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:17:56: #1 total tags in treatment: 25188249 INFO @ Sun, 21 Jun 2020 22:17:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:56: #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 22:17:57: #1 tags after filtering in treatment: 25188206 INFO @ Sun, 21 Jun 2020 22:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:59: #2 number of paired peaks: 1135 INFO @ Sun, 21 Jun 2020 22:17:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:59: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:17:59: #2 alternative fragment length(s) may be 2,42,597 bps INFO @ Sun, 21 Jun 2020 22:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20_model.r WARNING @ Sun, 21 Jun 2020 22:17:59: #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 22:17:59: #2 You may need to consider one of the other alternative d(s): 2,42,597 WARNING @ Sun, 21 Jun 2020 22:17:59: #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 22:17:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.05_summits.bed INFO @ Sun, 21 Jun 2020 22:17:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436043/SRX5436043.20_summits.bed INFO @ Sun, 21 Jun 2020 22:18:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling